File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/ed4c2a4121d0a2db1682f393256ba3/.command.log
Size
199.7 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (FFPE_HD789_01_RNA_0002_B23LG7FLT4_1)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/b018cb46dae724b6f9f02b4ebaae60/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/ed4c2a4121d0a2db1682f393256ba3/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/ed4c2a4121d0a2db1682f393256ba3/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/0c7ae1ce50259967d141acaef2f804/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusionreport.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/b018cb46dae724b6f9f02b4ebaae60/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusionreport.tsv --gtf /tmp/nxf.RYGCkjTtsm/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.RYGCkjTtsm/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1 --shrink_introns --max_intron_length 1000 
Error, strand conflict in gtf info for chr1	ENSEMBL	exon	32087523	32087813	.	-	.	gene_id "Metazoa_SRP^ENSG00000276493.1"; transcript_id "ENST00000613387.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.119-201"; exon_number 1; exon_id "ENSE00003719315.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000276493.1"; orig_coord_info "chr1,32087523,32087813,-";
Error, strand conflict in gtf info for chr1	ENSEMBL	exon	32269338	32269597	.	-	.	gene_id "Metazoa_SRP^ENSG00000277617.1"; transcript_id "ENST00000615681.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.165-201"; exon_number 1; exon_id "ENSE00003743753.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277617.1"; orig_coord_info "chr1,32269338,32269597,-";
Error, strand conflict in gtf info for chr1	ENSEMBL	exon	33029232	33029576	.	-	.	gene_id "Metazoa_SRP^ENSG00000276645.1"; transcript_id "ENST00000610352.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.124-201"; exon_number 1; exon_id "ENSE00003724192.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000276645.1"; orig_coord_info "chr1,33029232,33029576,-";
Error, strand conflict in gtf info for chr1	ENSEMBL	exon	117243212	117243508	.	-	.	gene_id "Metazoa_SRP^ENSG00000277141.1"; transcript_id "ENST00000613165.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.149-201"; exon_number 1; exon_id "ENSE00003734087.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277141.1"; orig_coord_info "chr1,117243212,117243508,-";
Error, strand conflict in gtf info for chr1	ENSEMBL	exon	154950210	154950492	.	-	.	gene_id "Metazoa_SRP^ENSG00000268154.2"; transcript_id "ENST00000600454.2"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.25-201"; exon_number 1; exon_id "ENSE00003038786.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000268154.2"; orig_coord_info "chr1,154950210,154950492,-";
Error, strand conflict in gtf info for chr1	ENSEMBL	exon	164703026	164703309	.	-	.	gene_id "Metazoa_SRP^ENSG00000276359.1"; transcript_id "ENST00000619303.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.115-201"; exon_number 1; exon_id "ENSE00003718765.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000276359.1"; orig_coord_info "chr1,164703026,164703309,-";
Error, strand conflict in gtf info for chr1	ENSEMBL	exon	182576772	182577040	.	-	.	gene_id "Metazoa_SRP^ENSG00000276839.1"; transcript_id "ENST00000616324.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.135-201"; exon_number 1; exon_id "ENSE00003725558.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000276839.1"; orig_coord_info "chr1,182576772,182577040,-";
Error, strand conflict in gtf info for chr1	ENSEMBL	exon	193236794	193237107	.	-	.	gene_id "Metazoa_SRP^ENSG00000276735.1"; transcript_id "ENST00000620543.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.128-201"; exon_number 1; exon_id "ENSE00003723733.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000276735.1"; orig_coord_info "chr1,193236794,193237107,-";
Error, chr discrepancy in gtf info for chr2	ENSEMBL	exon	10691538	10691831	.	+	.	gene_id "Metazoa_SRP^ENSG00000277446.1"; transcript_id "ENST00000487171.3"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.158-201"; exon_number 1; exon_id "ENSE00001896712.3"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277446.1"; orig_coord_info "chr2,10691538,10691831,+";
Error, chr discrepancy in gtf info for chr2	ENSEMBL	exon	14530941	14531223	.	+	.	gene_id "Metazoa_SRP^ENSG00000237261.2"; transcript_id "ENST00000415635.2"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.9-201"; exon_number 1; exon_id "ENSE00001729512.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000237261.2"; orig_coord_info "chr2,14530941,14531223,+";
Error, chr discrepancy in gtf info for chr2	ENSEMBL	exon	42511570	42511851	.	+	.	gene_id "Metazoa_SRP^ENSG00000273913.1"; transcript_id "ENST00000611671.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.40-201"; exon_number 1; exon_id "ENSE00003725055.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000273913.1"; orig_coord_info "chr2,42511570,42511851,+";
Error, chr discrepancy in gtf info for chr2	ENSEMBL	exon	46266690	46266971	.	+	.	gene_id "Metazoa_SRP^ENSG00000278764.1"; transcript_id "ENST00000622034.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.201-201"; exon_number 1; exon_id "ENSE00002581629.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000278764.1"; orig_coord_info "chr2,46266690,46266971,+";
Error, chr discrepancy in gtf info for chr2	ENSEMBL	exon	47383160	47383421	.	+	.	gene_id "Metazoa_SRP^ENSG00000277396.1"; transcript_id "ENST00000622819.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.157-201"; exon_number 1; exon_id "ENSE00003747902.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277396.1"; orig_coord_info "chr2,47383160,47383421,+";
Error, chr discrepancy in gtf info for chr2	ENSEMBL	exon	63168600	63168847	.	+	.	gene_id "Metazoa_SRP^ENSG00000283636.1"; transcript_id "ENST00000636778.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.212-201"; exon_number 1; exon_id "ENSE00003793500.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000283636.1"; orig_coord_info "chr2,63168600,63168847,+";
Error, chr discrepancy in gtf info for chr2	ENSEMBL	exon	96938923	96939203	.	+	.	gene_id "Metazoa_SRP^ENSG00000274206.1"; transcript_id "ENST00000548393.2"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.53-201"; exon_number 1; exon_id "ENSE00003716450.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000274206.1"; orig_coord_info "chr2,96938923,96939203,+";
Error, chr discrepancy in gtf info for chr2	ENSEMBL	exon	109124357	109124609	.	-	.	gene_id "Metazoa_SRP^ENSG00000277628.1"; transcript_id "ENST00000612530.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.166-201"; exon_number 1; exon_id "ENSE00003722078.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277628.1"; orig_coord_info "chr2,109124357,109124609,-";
Error, chr discrepancy in gtf info for chr2	ENSEMBL	exon	127856890	127857147	.	+	.	gene_id "Metazoa_SRP^ENSG00000273950.1"; transcript_id "ENST00000614637.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.41-201"; exon_number 1; exon_id "ENSE00003716389.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000273950.1"; orig_coord_info "chr2,127856890,127857147,+";
Error, chr discrepancy in gtf info for chr2	ENSEMBL	exon	130517049	130517312	.	-	.	gene_id "Metazoa_SRP^ENSG00000274711.1"; transcript_id "ENST00000615602.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.65-201"; exon_number 1; exon_id "ENSE00003733951.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000274711.1"; orig_coord_info "chr2,130517049,130517312,-";
Error, chr discrepancy in gtf info for chr2	ENSEMBL	exon	130603461	130603724	.	+	.	gene_id "Metazoa_SRP^ENSG00000277668.1"; transcript_id "ENST00000621608.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.168-201"; exon_number 1; exon_id "ENSE00003717645.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277668.1"; orig_coord_info "chr2,130603461,130603724,+";
Error, chr discrepancy in gtf info for chr2	ENSEMBL	exon	194658376	194658675	.	-	.	gene_id "Metazoa_SRP^ENSG00000276123.1"; transcript_id "ENST00000621610.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.108-201"; exon_number 1; exon_id "ENSE00003733930.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000276123.1"; orig_coord_info "chr2,194658376,194658675,-";
Error, chr discrepancy in gtf info for chr2	ENSEMBL	exon	201097744	201098091	.	+	.	gene_id "Metazoa_SRP^ENSG00000273975.1"; transcript_id "ENST00000621081.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.42-201"; exon_number 1; exon_id "ENSE00003741993.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000273975.1"; orig_coord_info "chr2,201097744,201098091,+";
Error, chr discrepancy in gtf info for chr3	ENSEMBL	exon	12576961	12577237	.	-	.	gene_id "Metazoa_SRP^ENSG00000274514.1"; transcript_id "ENST00000621376.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.59-201"; exon_number 1; exon_id "ENSE00003712129.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000274514.1"; orig_coord_info "chr3,12576961,12577237,-";
Error, chr discrepancy in gtf info for chr3	ENSEMBL	exon	39161270	39161520	.	+	.	gene_id "Metazoa_SRP^ENSG00000214305.4"; transcript_id "ENST00000398067.2"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.8-201"; exon_number 1; exon_id "ENSE00001531426.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000214305.4"; orig_coord_info "chr3,39161270,39161520,+";
Error, chr discrepancy in gtf info for chr3	ENSEMBL	exon	59584169	59584445	.	+	.	gene_id "Metazoa_SRP^ENSG00000277592.1"; transcript_id "ENST00000611926.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.163-201"; exon_number 1; exon_id "ENSE00003713499.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277592.1"; orig_coord_info "chr3,59584169,59584445,+";
Error, chr discrepancy in gtf info for chr3	ENSEMBL	exon	72926955	72927237	.	-	.	gene_id "Metazoa_SRP^ENSG00000276890.1"; transcript_id "ENST00000614846.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.136-201"; exon_number 1; exon_id "ENSE00003716410.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000276890.1"; orig_coord_info "chr3,72926955,72927237,-";
Error, chr discrepancy in gtf info for chr3	ENSEMBL	exon	73959642	73959927	.	-	.	gene_id "Metazoa_SRP^ENSG00000278554.1"; transcript_id "ENST00000616260.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.192-201"; exon_number 1; exon_id "ENSE00003717511.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000278554.1"; orig_coord_info "chr3,73959642,73959927,-";
Error, chr discrepancy in gtf info for chr3	ENSEMBL	exon	109295239	109295498	.	+	.	gene_id "Metazoa_SRP^ENSG00000277635.1"; transcript_id "ENST00000614947.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.167-201"; exon_number 1; exon_id "ENSE00003715728.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277635.1"; orig_coord_info "chr3,109295239,109295498,+";
Error, chr discrepancy in gtf info for chr3	ENSEMBL	exon	128673681	128674021	.	-	.	gene_id "Metazoa_SRP^ENSG00000277250.1"; transcript_id "ENST00000620153.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.153-201"; exon_number 1; exon_id "ENSE00003750366.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277250.1"; orig_coord_info "chr3,128673681,128674021,-";
Error, chr discrepancy in gtf info for chr3	ENSEMBL	exon	186076306	186076591	.	-	.	gene_id "Metazoa_SRP^ENSG00000277118.1"; transcript_id "ENST00000619409.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.146-201"; exon_number 1; exon_id "ENSE00003725070.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277118.1"; orig_coord_info "chr3,186076306,186076591,-";
Error, chr discrepancy in gtf info for chr3	ENSEMBL	exon	186629936	186630211	.	-	.	gene_id "Metazoa_SRP^ENSG00000275696.1"; transcript_id "ENST00000622525.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.93-201"; exon_number 1; exon_id "ENSE00003724747.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000275696.1"; orig_coord_info "chr3,186629936,186630211,-";
Error, chr discrepancy in gtf info for chr4	ENSEMBL	exon	9711953	9712233	.	-	.	gene_id "Metazoa_SRP^ENSG00000203436.2"; transcript_id "ENST00000356560.3"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.5-201"; exon_number 1; exon_id "ENSE00001425359.3"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000203436.2"; orig_coord_info "chr4,9711953,9712233,-";
Error, chr discrepancy in gtf info for chr4	ENSEMBL	exon	56810422	56810681	.	+	.	gene_id "Metazoa_SRP^ENSG00000278226.1"; transcript_id "ENST00000615776.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.185-201"; exon_number 1; exon_id "ENSE00003752811.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000278226.1"; orig_coord_info "chr4,56810422,56810681,+";
Error, chr discrepancy in gtf info for chr4	ENSEMBL	exon	139155153	139155444	.	+	.	gene_id "Metazoa_SRP^ENSG00000276396.1"; transcript_id "ENST00000615106.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.117-201"; exon_number 1; exon_id "ENSE00003750993.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000276396.1"; orig_coord_info "chr4,139155153,139155444,+";
Error, chr discrepancy in gtf info for chr5	ENSEMBL	exon	7239781	7240018	.	+	.	gene_id "Metazoa_SRP^ENSG00000237611.2"; transcript_id "ENST00000422908.2"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.10-201"; exon_number 1; exon_id "ENSE00001422953.3"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000237611.2"; orig_coord_info "chr5,7239781,7240018,+";
Error, chr discrepancy in gtf info for chr5	ENSEMBL	exon	18958147	18958413	.	-	.	gene_id "Metazoa_SRP^ENSG00000276764.1"; transcript_id "ENST00000622625.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.130-201"; exon_number 1; exon_id "ENSE00003728774.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000276764.1"; orig_coord_info "chr5,18958147,18958413,-";
Error, chr discrepancy in gtf info for chr5	ENSEMBL	exon	24449351	24449615	.	-	.	gene_id "Metazoa_SRP^ENSG00000277455.1"; transcript_id "ENST00000612585.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.159-201"; exon_number 1; exon_id "ENSE00002271476.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277455.1"; orig_coord_info "chr5,24449351,24449615,-";
Error, chr discrepancy in gtf info for chr5	ENSEMBL	exon	91314716	91314997	.	-	.	gene_id "Metazoa_SRP^ENSG00000277001.1"; transcript_id "ENST00000615072.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.141-201"; exon_number 1; exon_id "ENSE00003717635.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277001.1"; orig_coord_info "chr5,91314716,91314997,-";
Error, chr discrepancy in gtf info for chr5	ENSEMBL	exon	148389748	148390029	.	+	.	gene_id "Metazoa_SRP^ENSG00000274799.1"; transcript_id "ENST00000612673.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.68-201"; exon_number 1; exon_id "ENSE00003711918.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000274799.1"; orig_coord_info "chr5,148389748,148390029,+";
Error, chr discrepancy in gtf info for chr5	ENSEMBL	exon	154821943	154822258	.	+	.	gene_id "Metazoa_SRP^ENSG00000277039.1"; transcript_id "ENST00000612810.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.142-201"; exon_number 1; exon_id "ENSE00003731575.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277039.1"; orig_coord_info "chr5,154821943,154822258,+";
Error, chr discrepancy in gtf info for chr5	ENSEMBL	exon	179629151	179629410	.	+	.	gene_id "Metazoa_SRP^ENSG00000273549.1"; transcript_id "ENST00000366402.2"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.28-201"; exon_number 1; exon_id "ENSE00003713858.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000273549.1"; orig_coord_info "chr5,179629151,179629410,+";
Error, chr discrepancy in gtf info for chr6	ENSEMBL	exon	11644067	11644343	.	+	.	gene_id "Metazoa_SRP^ENSG00000277473.1"; transcript_id "ENST00000622203.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.160-201"; exon_number 1; exon_id "ENSE00003747710.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277473.1"; orig_coord_info "chr6,11644067,11644343,+";
Error, chr discrepancy in gtf info for chr6	ENSEMBL	exon	33562880	33563130	.	-	.	gene_id "Metazoa_SRP^ENSG00000276746.1"; transcript_id "ENST00000619776.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.129-201"; exon_number 1; exon_id "ENSE00003719860.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000276746.1"; orig_coord_info "chr6,33562880,33563130,-";
Error, chr discrepancy in gtf info for chr7	ENSEMBL	exon	17205652	17205928	.	+	.	gene_id "Metazoa_SRP^ENSG00000278569.1"; transcript_id "ENST00000622007.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.193-201"; exon_number 1; exon_id "ENSE00003750161.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000278569.1"; orig_coord_info "chr7,17205652,17205928,+";
Error, chr discrepancy in gtf info for chr7	ENSEMBL	exon	55731100	55731403	.	+	.	gene_id "Metazoa_SRP^ENSG00000275853.1"; transcript_id "ENST00000618280.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.97-201"; exon_number 1; exon_id "ENSE00003725909.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000275853.1"; orig_coord_info "chr7,55731100,55731403,+";
Error, chr discrepancy in gtf info for chr7	ENSEMBL	exon	66915063	66915334	.	-	.	gene_id "Metazoa_SRP^ENSG00000274135.1"; transcript_id "ENST00000570437.2"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.51-201"; exon_number 1; exon_id "ENSE00002255875.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000274135.1"; orig_coord_info "chr7,66915063,66915334,-";
Error, chr discrepancy in gtf info for chr7	ENSEMBL	exon	75057877	75058188	.	+	.	gene_id "Metazoa_SRP^ENSG00000277127.1"; transcript_id "ENST00000576563.2"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.147-201"; exon_number 1; exon_id "ENSE00002655363.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277127.1"; orig_coord_info "chr7,75057877,75058188,+";
Error, chr discrepancy in gtf info for chr7	ENSEMBL	exon	116320751	116321031	.	+	.	gene_id "Metazoa_SRP^ENSG00000213167.3"; transcript_id "ENST00000392674.3"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.7-201"; exon_number 1; exon_id "ENSE00002312710.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000213167.3"; orig_coord_info "chr7,116320751,116321031,+";
Error, chr discrepancy in gtf info for chr7	ENSEMBL	exon	128483907	128484158	.	-	.	gene_id "Metazoa_SRP^ENSG00000276988.1"; transcript_id "ENST00000613842.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.140-201"; exon_number 1; exon_id "ENSE00003738567.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000276988.1"; orig_coord_info "chr7,128483907,128484158,-";
Error, chr discrepancy in gtf info for chr7	ENSEMBL	exon	148876018	148876286	.	+	.	gene_id "Metazoa_SRP^ENSG00000275586.1"; transcript_id "ENST00000615890.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.88-201"; exon_number 1; exon_id "ENSE00001720210.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000275586.1"; orig_coord_info "chr7,148876018,148876286,+";
Error, chr discrepancy in gtf info for chr7	ENSEMBL	exon	152025194	152025472	.	-	.	gene_id "Metazoa_SRP^ENSG00000276213.1"; transcript_id "ENST00000613101.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.112-201"; exon_number 1; exon_id "ENSE00003725029.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000276213.1"; orig_coord_info "chr7,152025194,152025472,-";
Error, chr discrepancy in gtf info for chr8	ENSEMBL	exon	9091240	9091508	.	+	.	gene_id "Metazoa_SRP^ENSG00000197334.2"; transcript_id "ENST00000359385.2"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.2-201"; exon_number 1; exon_id "ENSE00003751056.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000197334.2"; orig_coord_info "chr8,9091240,9091508,+";
Error, chr discrepancy in gtf info for chr8	ENSEMBL	exon	28915579	28915864	.	-	.	gene_id "Metazoa_SRP^ENSG00000273710.1"; transcript_id "ENST00000622685.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.32-201"; exon_number 1; exon_id "ENSE00003711847.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000273710.1"; orig_coord_info "chr8,28915579,28915864,-";
Error, chr discrepancy in gtf info for chr8	ENSEMBL	exon	54130582	54130860	.	+	.	gene_id "Metazoa_SRP^ENSG00000276353.1"; transcript_id "ENST00000618435.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.114-201"; exon_number 1; exon_id "ENSE00003731663.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000276353.1"; orig_coord_info "chr8,54130582,54130860,+";
Error, chr discrepancy in gtf info for chr8	ENSEMBL	exon	69851148	69851436	.	-	.	gene_id "Metazoa_SRP^ENSG00000277740.1"; transcript_id "ENST00000614579.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.171-201"; exon_number 1; exon_id "ENSE00003751650.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277740.1"; orig_coord_info "chr8,69851148,69851436,-";
Error, chr discrepancy in gtf info for chr8	ENSEMBL	exon	94655911	94656208	.	+	.	gene_id "Metazoa_SRP^ENSG00000274701.1"; transcript_id "ENST00000617144.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.63-201"; exon_number 1; exon_id "ENSE00003723393.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000274701.1"; orig_coord_info "chr8,94655911,94656208,+";
Error, chr discrepancy in gtf info for chr8	ENSEMBL	exon	100897853	100898136	.	-	.	gene_id "Metazoa_SRP^ENSG00000275041.1"; transcript_id "ENST00000614973.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.74-201"; exon_number 1; exon_id "ENSE00003730963.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000275041.1"; orig_coord_info "chr8,100897853,100898136,-";
Error, chr discrepancy in gtf info for chr8	ENSEMBL	exon	133668420	133668701	.	-	.	gene_id "Metazoa_SRP^ENSG00000276193.1"; transcript_id "ENST00000611670.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.110-201"; exon_number 1; exon_id "ENSE00003753796.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000276193.1"; orig_coord_info "chr8,133668420,133668701,-";
Error, chr discrepancy in gtf info for chr8	ENSEMBL	exon	144683169	144683464	.	+	.	gene_id "Metazoa_SRP^ENSG00000274772.1"; transcript_id "ENST00000617099.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.67-201"; exon_number 1; exon_id "ENSE00003723234.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000274772.1"; orig_coord_info "chr8,144683169,144683464,+";
Error, chr discrepancy in gtf info for chr9	ENSEMBL	exon	98115885	98116135	.	+	.	gene_id "Metazoa_SRP^ENSG00000274011.1"; transcript_id "ENST00000611137.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.46-201"; exon_number 1; exon_id "ENSE00003734244.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000274011.1"; orig_coord_info "chr9,98115885,98116135,+";
Error, chr discrepancy in gtf info for chr9	ENSEMBL	exon	125417305	125417586	.	+	.	gene_id "Metazoa_SRP^ENSG00000274510.1"; transcript_id "ENST00000618720.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.58-201"; exon_number 1; exon_id "ENSE00003738857.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000274510.1"; orig_coord_info "chr9,125417305,125417586,+";
Error, chr discrepancy in gtf info for chr9	ENSEMBL	exon	128745857	128746138	.	-	.	gene_id "Metazoa_SRP^ENSG00000203286.5"; transcript_id "ENST00000366116.3"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.3-201"; exon_number 1; exon_id "ENSE00001440923.3"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000203286.5"; orig_coord_info "chr9,128745857,128746138,-";
Error, chr discrepancy in gtf info for chr9	ENSEMBL	exon	137638128	137638408	.	-	.	gene_id "Metazoa_SRP^ENSG00000274841.1"; transcript_id "ENST00000615730.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.69-201"; exon_number 1; exon_id "ENSE00003724194.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000274841.1"; orig_coord_info "chr9,137638128,137638408,-";
Error, chr discrepancy in gtf info for chr10	ENSEMBL	exon	14391875	14392196	.	+	.	gene_id "Metazoa_SRP^ENSG00000278100.1"; transcript_id "ENST00000612546.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.180-201"; exon_number 1; exon_id "ENSE00003720199.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000278100.1"; orig_coord_info "chr10,14391875,14392196,+";
Error, chr discrepancy in gtf info for chr10	ENSEMBL	exon	21455236	21455515	.	-	.	gene_id "Metazoa_SRP^ENSG00000273566.1"; transcript_id "ENST00000616220.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.29-201"; exon_number 1; exon_id "ENSE00003733108.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000273566.1"; orig_coord_info "chr10,21455236,21455515,-";
Error, chr discrepancy in gtf info for chr10	ENSEMBL	exon	69098496	69098794	.	+	.	gene_id "Metazoa_SRP^ENSG00000274008.1"; transcript_id "ENST00000620896.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.45-201"; exon_number 1; exon_id "ENSE00003732765.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000274008.1"; orig_coord_info "chr10,69098496,69098794,+";
Error, chr discrepancy in gtf info for chr10	ENSEMBL	exon	77966173	77966440	.	+	.	gene_id "Metazoa_SRP^ENSG00000274686.1"; transcript_id "ENST00000619972.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.62-201"; exon_number 1; exon_id "ENSE00002225926.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000274686.1"; orig_coord_info "chr10,77966173,77966440,+";
Error, chr discrepancy in gtf info for chr10	ENSEMBL	exon	97297290	97297557	.	+	.	gene_id "Metazoa_SRP^ENSG00000277308.1"; transcript_id "ENST00000615469.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.154-201"; exon_number 1; exon_id "ENSE00003722420.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277308.1"; orig_coord_info "chr10,97297290,97297557,+";
Error, chr discrepancy in gtf info for chr10	ENSEMBL	exon	100666695	100667009	.	-	.	gene_id "Metazoa_SRP^ENSG00000274660.1"; transcript_id "ENST00000613464.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.61-201"; exon_number 1; exon_id "ENSE00003750929.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000274660.1"; orig_coord_info "chr10,100666695,100667009,-";
Error, chr discrepancy in gtf info for chr10	ENSEMBL	exon	101912998	101913279	.	-	.	gene_id "Metazoa_SRP^ENSG00000274742.1"; transcript_id "ENST00000615609.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.66-201"; exon_number 1; exon_id "ENSE00003736346.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000274742.1"; orig_coord_info "chr10,101912998,101913279,-";
Error, chr discrepancy in gtf info for chr10	ENSEMBL	exon	125869295	125869576	.	+	.	gene_id "Metazoa_SRP^ENSG00000277371.1"; transcript_id "ENST00000616367.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.155-201"; exon_number 1; exon_id "ENSE00001657018.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277371.1"; orig_coord_info "chr10,125869295,125869576,+";
Error, chr discrepancy in gtf info for chr11	ENSEMBL	exon	9279532	9279816	.	-	.	gene_id "Metazoa_SRP^ENSG00000273725.1"; transcript_id "ENST00000613468.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.33-201"; exon_number 1; exon_id "ENSE00003722846.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000273725.1"; orig_coord_info "chr11,9279532,9279816,-";
Error, chr discrepancy in gtf info for chr11	ENSEMBL	exon	18538885	18539189	.	+	.	gene_id "Metazoa_SRP^ENSG00000274589.1"; transcript_id "ENST00000616888.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.60-201"; exon_number 1; exon_id "ENSE00003720786.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000274589.1"; orig_coord_info "chr11,18538885,18539189,+";
Error, chr discrepancy in gtf info for chr11	ENSEMBL	exon	66374138	66374435	.	-	.	gene_id "Metazoa_SRP^ENSG00000276918.1"; transcript_id "ENST00000615369.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.138-201"; exon_number 1; exon_id "ENSE00003733192.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000276918.1"; orig_coord_info "chr11,66374138,66374435,-";
Error, chr discrepancy in gtf info for chr11	ENSEMBL	exon	86216596	86216878	.	+	.	gene_id "Metazoa_SRP^ENSG00000276669.1"; transcript_id "ENST00000618659.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.125-201"; exon_number 1; exon_id "ENSE00003753650.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000276669.1"; orig_coord_info "chr11,86216596,86216878,+";
Error, chr discrepancy in gtf info for chr11	ENSEMBL	exon	105352670	105352956	.	-	.	gene_id "Metazoa_SRP^ENSG00000278640.1"; transcript_id "ENST00000612667.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.195-201"; exon_number 1; exon_id "ENSE00003720340.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000278640.1"; orig_coord_info "chr11,105352670,105352956,-";
Error, chr discrepancy in gtf info for chr11	ENSEMBL	exon	118994334	118994630	.	+	.	gene_id "Metazoa_SRP^ENSG00000280502.1"; transcript_id "ENST00000629083.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.208-201"; exon_number 1; exon_id "ENSE00003762596.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000280502.1"; orig_coord_info "chr11,118994334,118994630,+";
Error, chr discrepancy in gtf info for chr12	ENSEMBL	exon	3124777	3125063	.	+	.	gene_id "Metazoa_SRP^ENSG00000278469.1"; transcript_id "ENST00000620330.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.190-201"; exon_number 1; exon_id "ENSE00003724960.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000278469.1"; orig_coord_info "chr12,3124777,3125063,+";
Error, chr discrepancy in gtf info for chr12	ENSEMBL	exon	7856169	7856471	.	+	.	gene_id "Metazoa_SRP^ENSG00000278459.1"; transcript_id "ENST00000614219.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.189-201"; exon_number 1; exon_id "ENSE00003726612.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000278459.1"; orig_coord_info "chr12,7856169,7856471,+";
Error, chr discrepancy in gtf info for chr12	ENSEMBL	exon	49196784	49197062	.	+	.	gene_id "Metazoa_SRP^ENSG00000274017.1"; transcript_id "ENST00000616942.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.47-201"; exon_number 1; exon_id "ENSE00003725690.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000274017.1"; orig_coord_info "chr12,49196784,49197062,+";
Error, chr discrepancy in gtf info for chr12	ENSEMBL	exon	55731264	55731531	.	-	.	gene_id "Metazoa_SRP^ENSG00000258045.2"; transcript_id "ENST00000553249.2"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.12-201"; exon_number 1; exon_id "ENSE00002389198.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000258045.2"; orig_coord_info "chr12,55731264,55731531,-";
Error, chr discrepancy in gtf info for chr12	ENSEMBL	exon	62393607	62393880	.	-	.	gene_id "Metazoa_SRP^ENSG00000275881.1"; transcript_id "ENST00000610878.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.98-201"; exon_number 1; exon_id "ENSE00003712715.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000275881.1"; orig_coord_info "chr12,62393607,62393880,-";
Error, chr discrepancy in gtf info for chr12	ENSEMBL	exon	68575858	68576136	.	-	.	gene_id "Metazoa_SRP^ENSG00000274459.1"; transcript_id "ENST00000612077.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.56-201"; exon_number 1; exon_id "ENSE00003714552.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000274459.1"; orig_coord_info "chr12,68575858,68576136,-";
Error, chr discrepancy in gtf info for chr12	ENSEMBL	exon	120018900	120019261	.	+	.	gene_id "Metazoa_SRP^ENSG00000278250.1"; transcript_id "ENST00000617234.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.186-201"; exon_number 1; exon_id "ENSE00003726734.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000278250.1"; orig_coord_info "chr12,120018900,120019261,+";
Error, chr discrepancy in gtf info for chr12	ENSEMBL	exon	121897583	121897826	.	-	.	gene_id "Metazoa_SRP^ENSG00000283389.1"; transcript_id "ENST00000637921.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.210-201"; exon_number 1; exon_id "ENSE00003797995.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000283389.1"; orig_coord_info "chr12,121897583,121897826,-";
Error, chr discrepancy in gtf info for chr13	ENSEMBL	exon	29864372	29864629	.	-	.	gene_id "Metazoa_SRP^ENSG00000278172.1"; transcript_id "ENST00000619339.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.184-201"; exon_number 1; exon_id "ENSE00003748703.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000278172.1"; orig_coord_info "chr13,29864372,29864629,-";
Error, chr discrepancy in gtf info for chr13	ENSEMBL	exon	30684029	30684278	.	-	.	gene_id "Metazoa_SRP^ENSG00000275788.1"; transcript_id "ENST00000612609.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.94-201"; exon_number 1; exon_id "ENSE00003716515.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000275788.1"; orig_coord_info "chr13,30684029,30684278,-";
Error, chr discrepancy in gtf info for chr13	ENSEMBL	exon	31975167	31975448	.	+	.	gene_id "Metazoa_SRP^ENSG00000278732.1"; transcript_id "ENST00000622073.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.200-201"; exon_number 1; exon_id "ENSE00003721986.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000278732.1"; orig_coord_info "chr13,31975167,31975448,+";
Error, chr discrepancy in gtf info for chr13	ENSEMBL	exon	34910545	34910815	.	-	.	gene_id "Metazoa_SRP^ENSG00000273886.1"; transcript_id "ENST00000614194.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.39-201"; exon_number 1; exon_id "ENSE00003733017.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000273886.1"; orig_coord_info "chr13,34910545,34910815,-";
Error, chr discrepancy in gtf info for chr13	ENSEMBL	exon	40730981	40731253	.	+	.	gene_id "Metazoa_SRP^ENSG00000277794.1"; transcript_id "ENST00000614020.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.173-201"; exon_number 1; exon_id "ENSE00003737826.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277794.1"; orig_coord_info "chr13,40730981,40731253,+";
Error, chr discrepancy in gtf info for chr13	ENSEMBL	exon	45732082	45732356	.	-	.	gene_id "Metazoa_SRP^ENSG00000274357.1"; transcript_id "ENST00000618452.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.55-201"; exon_number 1; exon_id "ENSE00003715201.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000274357.1"; orig_coord_info "chr13,45732082,45732356,-";
Error, chr discrepancy in gtf info for chr13	ENSEMBL	exon	48429269	48429554	.	+	.	gene_id "Metazoa_SRP^ENSG00000277233.1"; transcript_id "ENST00000614413.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.152-201"; exon_number 1; exon_id "ENSE00003726257.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277233.1"; orig_coord_info "chr13,48429269,48429554,+";
Error, chr discrepancy in gtf info for chr14	ENSEMBL	exon	34659564	34659878	.	-	.	gene_id "Metazoa_SRP^ENSG00000275978.1"; transcript_id "ENST00000613350.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.102-201"; exon_number 1; exon_id "ENSE00002376625.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000275978.1"; orig_coord_info "chr14,34659564,34659878,-";
Error, chr discrepancy in gtf info for chr14	ENSEMBL	exon	49913493	49913760	.	-	.	gene_id "Metazoa_SRP^ENSG00000274704.1"; transcript_id "ENST00000611904.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.64-201"; exon_number 1; exon_id "ENSE00003754707.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000274704.1"; orig_coord_info "chr14,49913493,49913760,-";
Error, chr discrepancy in gtf info for chr14	ENSEMBL	exon	55285227	55285558	.	+	.	gene_id "Metazoa_SRP^ENSG00000278818.1"; transcript_id "ENST00000612004.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.206-201"; exon_number 1; exon_id "ENSE00003721379.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000278818.1"; orig_coord_info "chr14,55285227,55285558,+";
Error, chr discrepancy in gtf info for chr14	ENSEMBL	exon	82429872	82430156	.	+	.	gene_id "Metazoa_SRP^ENSG00000276782.1"; transcript_id "ENST00000619251.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.132-201"; exon_number 1; exon_id "ENSE00003749490.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000276782.1"; orig_coord_info "chr14,82429872,82430156,+";
Error, chr discrepancy in gtf info for chr15	ENSEMBL	exon	28524151	28524440	.	-	.	gene_id "Metazoa_SRP^ENSG00000276955.1"; transcript_id "ENST00000616096.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.139-201"; exon_number 1; exon_id "ENSE00003727301.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000276955.1"; orig_coord_info "chr15,28524151,28524440,-";
Error, chr discrepancy in gtf info for chr15	ENSEMBL	exon	37216617	37216898	.	+	.	gene_id "Metazoa_SRP^ENSG00000274216.1"; transcript_id "ENST00000620533.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.54-201"; exon_number 1; exon_id "ENSE00002595724.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000274216.1"; orig_coord_info "chr15,37216617,37216898,+";
Error, chr discrepancy in gtf info for chr15	ENSEMBL	exon	40585454	40585751	.	-	.	gene_id "Metazoa_SRP^ENSG00000203573.4"; transcript_id "ENST00000366384.4"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.6-201"; exon_number 1; exon_id "ENSE00002278755.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000203573.4"; orig_coord_info "chr15,40585454,40585751,-";
Error, chr discrepancy in gtf info for chr15	ENSEMBL	exon	51858070	51858352	.	-	.	gene_id "Metazoa_SRP^ENSG00000277677.1"; transcript_id "ENST00000613708.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.169-201"; exon_number 1; exon_id "ENSE00002572750.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277677.1"; orig_coord_info "chr15,51858070,51858352,-";
Error, chr discrepancy in gtf info for chr15	ENSEMBL	exon	62244330	62244595	.	-	.	gene_id "Metazoa_SRP^ENSG00000276713.1"; transcript_id "ENST00000618354.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.126-201"; exon_number 1; exon_id "ENSE00003740337.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000276713.1"; orig_coord_info "chr15,62244330,62244595,-";
Error, chr discrepancy in gtf info for chr15	ENSEMBL	exon	74162340	74162620	.	-	.	gene_id "Metazoa_SRP^ENSG00000278348.1"; transcript_id "ENST00000616534.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.187-201"; exon_number 1; exon_id "ENSE00003738276.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000278348.1"; orig_coord_info "chr15,74162340,74162620,-";
Error, chr discrepancy in gtf info for chr15	ENSEMBL	exon	75120265	75120562	.	-	.	gene_id "Metazoa_SRP^ENSG00000203411.3"; transcript_id "ENST00000366232.3"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.4-201"; exon_number 1; exon_id "ENSE00001337967.3"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000203411.3"; orig_coord_info "chr15,75120265,75120562,-";
Error, chr discrepancy in gtf info for chr15	ENSEMBL	exon	76230048	76230390	.	-	.	gene_id "Metazoa_SRP^ENSG00000196274.5"; transcript_id "ENST00000360440.5"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.1-201"; exon_number 1; exon_id "ENSE00001441596.4"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000196274.5"; orig_coord_info "chr15,76230048,76230390,-";
Error, chr discrepancy in gtf info for chr15	ENSEMBL	exon	80057425	80057684	.	-	.	gene_id "Metazoa_SRP^ENSG00000275460.1"; transcript_id "ENST00000610909.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.85-201"; exon_number 1; exon_id "ENSE00003744913.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000275460.1"; orig_coord_info "chr15,80057425,80057684,-";
Error, chr discrepancy in gtf info for chr15	ENSEMBL	exon	84467901	84468147	.	+	.	gene_id "Metazoa_SRP^ENSG00000278785.1"; transcript_id "ENST00000611908.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.204-201"; exon_number 1; exon_id "ENSE00003727116.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000278785.1"; orig_coord_info "chr15,84467901,84468147,+";
Error, chr discrepancy in gtf info for chr15	ENSEMBL	exon	84642487	84642763	.	-	.	gene_id "Metazoa_SRP^ENSG00000277578.1"; transcript_id "ENST00000613066.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.162-201"; exon_number 1; exon_id "ENSE00003733878.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277578.1"; orig_coord_info "chr15,84642487,84642763,-";
Error, chr discrepancy in gtf info for chr15	ENSEMBL	exon	96496180	96496462	.	-	.	gene_id "Metazoa_SRP^ENSG00000274079.1"; transcript_id "ENST00000616811.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.49-201"; exon_number 1; exon_id "ENSE00003733418.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000274079.1"; orig_coord_info "chr15,96496180,96496462,-";
Error, chr discrepancy in gtf info for chr16	ENSEMBL	exon	4658851	4659151	.	+	.	gene_id "Metazoa_SRP^ENSG00000278700.1"; transcript_id "ENST00000613380.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.196-201"; exon_number 1; exon_id "ENSE00003725171.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000278700.1"; orig_coord_info "chr16,4658851,4659151,+";
Error, chr discrepancy in gtf info for chr16	ENSEMBL	exon	4756338	4756633	.	+	.	gene_id "Metazoa_SRP^ENSG00000276096.1"; transcript_id "ENST00000622471.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.106-201"; exon_number 1; exon_id "ENSE00003729360.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000276096.1"; orig_coord_info "chr16,4756338,4756633,+";
Error, chr discrepancy in gtf info for chr16	ENSEMBL	exon	11753666	11753948	.	-	.	gene_id "Metazoa_SRP^ENSG00000274505.1"; transcript_id "ENST00000597717.2"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.57-201"; exon_number 1; exon_id "ENSE00003175399.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000274505.1"; orig_coord_info "chr16,11753666,11753948,-";
Error, chr discrepancy in gtf info for chr16	ENSEMBL	exon	30816030	30816302	.	+	.	gene_id "Metazoa_SRP^ENSG00000274848.1"; transcript_id "ENST00000612622.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.70-201"; exon_number 1; exon_id "ENSE00003722713.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000274848.1"; orig_coord_info "chr16,30816030,30816302,+";
Error, chr discrepancy in gtf info for chr16	ENSEMBL	exon	48432927	48433208	.	-	.	gene_id "Metazoa_SRP^ENSG00000275909.1"; transcript_id "ENST00000447610.2"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.100-201"; exon_number 1; exon_id "ENSE00001531433.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000275909.1"; orig_coord_info "chr16,48432927,48433208,-";
Error, chr discrepancy in gtf info for chr16	ENSEMBL	exon	50054143	50054430	.	+	.	gene_id "Metazoa_SRP^ENSG00000273829.1"; transcript_id "ENST00000611402.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.35-201"; exon_number 1; exon_id "ENSE00003721726.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000273829.1"; orig_coord_info "chr16,50054143,50054430,+";
Error, chr discrepancy in gtf info for chr16	ENSEMBL	exon	59004213	59004494	.	+	.	gene_id "Metazoa_SRP^ENSG00000275808.1"; transcript_id "ENST00000619648.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.95-201"; exon_number 1; exon_id "ENSE00003719229.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000275808.1"; orig_coord_info "chr16,59004213,59004494,+";
Error, chr discrepancy in gtf info for chr17	ENSEMBL	exon	1101007	1101273	.	-	.	gene_id "Metazoa_SRP^ENSG00000278794.1"; transcript_id "ENST00000620071.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.205-201"; exon_number 1; exon_id "ENSE00003738918.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000278794.1"; orig_coord_info "chr17,1101007,1101273,-";
Error, chr discrepancy in gtf info for chr17	ENSEMBL	exon	6521131	6521412	.	+	.	gene_id "Metazoa_SRP^ENSG00000274860.1"; transcript_id "ENST00000612122.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.71-201"; exon_number 1; exon_id "ENSE00003733716.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000274860.1"; orig_coord_info "chr17,6521131,6521412,+";
Error, chr discrepancy in gtf info for chr17	ENSEMBL	exon	18605054	18605356	.	-	.	gene_id "Metazoa_SRP^ENSG00000276532.1"; transcript_id "ENST00000578843.2"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.121-201"; exon_number 1; exon_id "ENSE00002690398.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000276532.1"; orig_coord_info "chr17,18605054,18605356,-";
Error, chr discrepancy in gtf info for chr17	ENSEMBL	exon	20340743	20341045	.	+	.	gene_id "Metazoa_SRP^ENSG00000278701.1"; transcript_id "ENST00000618956.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.197-201"; exon_number 1; exon_id "ENSE00002713637.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000278701.1"; orig_coord_info "chr17,20340743,20341045,+";
Error, chr discrepancy in gtf info for chr17	ENSEMBL	exon	43607436	43607723	.	-	.	gene_id "Metazoa_SRP^ENSG00000278109.1"; transcript_id "ENST00000616636.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.181-201"; exon_number 1; exon_id "ENSE00003731893.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000278109.1"; orig_coord_info "chr17,43607436,43607723,-";
Error, chr discrepancy in gtf info for chr17	ENSEMBL	exon	45526466	45526746	.	-	.	gene_id "Metazoa_SRP^ENSG00000278770.1"; transcript_id "ENST00000585071.2"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.202-201"; exon_number 1; exon_id "ENSE00002694270.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000278770.1"; orig_coord_info "chr17,45526466,45526746,-";
Error, chr discrepancy in gtf info for chr17	ENSEMBL	exon	45931806	45932083	.	+	.	gene_id "Metazoa_SRP^ENSG00000274883.1"; transcript_id "ENST00000617458.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.72-201"; exon_number 1; exon_id "ENSE00003716654.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000274883.1"; orig_coord_info "chr17,45931806,45932083,+";
Error, chr discrepancy in gtf info for chr17	ENSEMBL	exon	49017793	49018061	.	-	.	gene_id "Metazoa_SRP^ENSG00000255851.2"; transcript_id "ENST00000537819.2"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.11-201"; exon_number 1; exon_id "ENSE00003689828.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000255851.2"; orig_coord_info "chr17,49017793,49018061,-";
Error, chr discrepancy in gtf info for chr17	ENSEMBL	exon	58785323	58785608	.	-	.	gene_id "Metazoa_SRP^ENSG00000276601.1"; transcript_id "ENST00000616695.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.123-201"; exon_number 1; exon_id "ENSE00003739856.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000276601.1"; orig_coord_info "chr17,58785323,58785608,-";
Error, chr discrepancy in gtf info for chr17	ENSEMBL	exon	58951185	58951513	.	+	.	gene_id "Metazoa_SRP^ENSG00000275680.1"; transcript_id "ENST00000613789.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.92-201"; exon_number 1; exon_id "ENSE00003720022.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000275680.1"; orig_coord_info "chr17,58951185,58951513,+";
Error, chr discrepancy in gtf info for chr17	ENSEMBL	exon	77014880	77015138	.	+	.	gene_id "Metazoa_SRP^ENSG00000276202.1"; transcript_id "ENST00000614073.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.111-201"; exon_number 1; exon_id "ENSE00003736300.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000276202.1"; orig_coord_info "chr17,77014880,77015138,+";
Error, chr discrepancy in gtf info for chr18	ENSEMBL	exon	24179038	24179295	.	-	.	gene_id "Metazoa_SRP^ENSG00000273524.1"; transcript_id "ENST00000617573.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.27-201"; exon_number 1; exon_id "ENSE00003742793.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000273524.1"; orig_coord_info "chr18,24179038,24179295,-";
Error, chr discrepancy in gtf info for chr18	ENSEMBL	exon	76840838	76841102	.	-	.	gene_id "Metazoa_SRP^ENSG00000275355.1"; transcript_id "ENST00000611637.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.82-201"; exon_number 1; exon_id "ENSE00003714134.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000275355.1"; orig_coord_info "chr18,76840838,76841102,-";
Error, chr discrepancy in gtf info for chr19	ENSEMBL	exon	1724115	1724395	.	+	.	gene_id "Metazoa_SRP^ENSG00000275642.1"; transcript_id "ENST00000622745.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.91-201"; exon_number 1; exon_id "ENSE00003742142.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000275642.1"; orig_coord_info "chr19,1724115,1724395,+";
Error, chr discrepancy in gtf info for chr19	ENSEMBL	exon	4127492	4127732	.	+	.	gene_id "Metazoa_SRP^ENSG00000278007.1"; transcript_id "ENST00000619020.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.179-201"; exon_number 1; exon_id "ENSE00003754295.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000278007.1"; orig_coord_info "chr19,4127492,4127732,+";
Error, chr discrepancy in gtf info for chr19	ENSEMBL	exon	6928345	6928629	.	+	.	gene_id "Metazoa_SRP^ENSG00000276568.1"; transcript_id "ENST00000610476.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.122-201"; exon_number 1; exon_id "ENSE00003749181.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000276568.1"; orig_coord_info "chr19,6928345,6928629,+";
Error, chr discrepancy in gtf info for chr19	ENSEMBL	exon	16187313	16187566	.	+	.	gene_id "Metazoa_SRP^ENSG00000275901.1"; transcript_id "ENST00000621370.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.99-201"; exon_number 1; exon_id "ENSE00003752377.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000275901.1"; orig_coord_info "chr19,16187313,16187566,+";
Error, chr discrepancy in gtf info for chr19	ENSEMBL	exon	40450225	40450480	.	+	.	gene_id "Metazoa_SRP^ENSG00000277510.1"; transcript_id "ENST00000617435.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.161-201"; exon_number 1; exon_id "ENSE00003739021.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277510.1"; orig_coord_info "chr19,40450225,40450480,+";
Error, chr discrepancy in gtf info for chr19	ENSEMBL	exon	41442102	41442392	.	-	.	gene_id "Metazoa_SRP^ENSG00000277136.1"; transcript_id "ENST00000614489.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.148-201"; exon_number 1; exon_id "ENSE00001600426.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277136.1"; orig_coord_info "chr19,41442102,41442392,-";
Error, chr discrepancy in gtf info for chr19	ENSEMBL	exon	50019019	50019320	.	+	.	gene_id "Metazoa_SRP^ENSG00000276729.1"; transcript_id "ENST00000614914.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.127-201"; exon_number 1; exon_id "ENSE00003744398.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000276729.1"; orig_coord_info "chr19,50019019,50019320,+";
Error, chr discrepancy in gtf info for chr19	ENSEMBL	exon	50258443	50258722	.	+	.	gene_id "Metazoa_SRP^ENSG00000276002.1"; transcript_id "ENST00000622099.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.104-201"; exon_number 1; exon_id "ENSE00001425316.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000276002.1"; orig_coord_info "chr19,50258443,50258722,+";
Error, chr discrepancy in gtf info for chr20	ENSEMBL	exon	8998849	8999100	.	+	.	gene_id "Metazoa_SRP^ENSG00000275222.1"; transcript_id "ENST00000616915.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.77-201"; exon_number 1; exon_id "ENSE00003735074.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000275222.1"; orig_coord_info "chr20,8998849,8999100,+";
Error, chr discrepancy in gtf info for chr20	ENSEMBL	exon	10025917	10026168	.	+	.	gene_id "Metazoa_SRP^ENSG00000276525.1"; transcript_id "ENST00000614195.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.120-201"; exon_number 1; exon_id "ENSE00003742433.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000276525.1"; orig_coord_info "chr20,10025917,10026168,+";
Error, chr discrepancy in gtf info for chr20	ENSEMBL	exon	36561237	36561530	.	-	.	gene_id "Metazoa_SRP^ENSG00000273986.1"; transcript_id "ENST00000615037.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.44-201"; exon_number 1; exon_id "ENSE00003740121.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000273986.1"; orig_coord_info "chr20,36561237,36561530,-";
Error, chr discrepancy in gtf info for chr20	ENSEMBL	exon	38711821	38712103	.	-	.	gene_id "Metazoa_SRP^ENSG00000277965.1"; transcript_id "ENST00000621099.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.177-201"; exon_number 1; exon_id "ENSE00003751450.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277965.1"; orig_coord_info "chr20,38711821,38712103,-";
Error, chr discrepancy in gtf info for chr20	ENSEMBL	exon	45847630	45847940	.	-	.	gene_id "Metazoa_SRP^ENSG00000277051.1"; transcript_id "ENST00000617007.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.144-201"; exon_number 1; exon_id "ENSE00003751117.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277051.1"; orig_coord_info "chr20,45847630,45847940,-";
Error, chr discrepancy in gtf info for chr20	ENSEMBL	exon	49932795	49933078	.	+	.	gene_id "Metazoa_SRP^ENSG00000269103.2"; transcript_id "ENST00000547793.3"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.26-201"; exon_number 1; exon_id "ENSE00001260772.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000269103.2"; orig_coord_info "chr20,49932795,49933078,+";
Error, chr discrepancy in gtf info for chr22	ENSEMBL	exon	18524620	18524935	.	+	.	gene_id "Metazoa_SRP^ENSG00000275319.1"; transcript_id "ENST00000618466.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.81-201"; exon_number 1; exon_id "ENSE00003733958.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000275319.1"; orig_coord_info "chr22,18524620,18524935,+";
Error, chr discrepancy in gtf info for chr22	ENSEMBL	exon	18615581	18615900	.	+	.	gene_id "Metazoa_SRP^ENSG00000275362.1"; transcript_id "ENST00000611762.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.83-201"; exon_number 1; exon_id "ENSE00003725800.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000275362.1"; orig_coord_info "chr22,18615581,18615900,+";
Error, chr discrepancy in gtf info for chr22	ENSEMBL	exon	20070716	20070965	.	+	.	gene_id "Metazoa_SRP^ENSG00000277950.1"; transcript_id "ENST00000619837.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.175-201"; exon_number 1; exon_id "ENSE00003735665.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277950.1"; orig_coord_info "chr22,20070716,20070965,+";
Error, chr discrepancy in gtf info for chr22	ENSEMBL	exon	21379382	21379701	.	-	.	gene_id "Metazoa_SRP^ENSG00000273846.1"; transcript_id "ENST00000617743.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.37-201"; exon_number 1; exon_id "ENSE00003717206.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000273846.1"; orig_coord_info "chr22,21379382,21379701,-";
Error, chr discrepancy in gtf info for chr22	ENSEMBL	exon	21396273	21396590	.	-	.	gene_id "Metazoa_SRP^ENSG00000275840.1"; transcript_id "ENST00000621315.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.96-201"; exon_number 1; exon_id "ENSE00003715289.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000275840.1"; orig_coord_info "chr22,21396273,21396590,-";
Error, chr discrepancy in gtf info for chr22	ENSEMBL	exon	21463963	21464279	.	+	.	gene_id "Metazoa_SRP^ENSG00000276800.1"; transcript_id "ENST00000612964.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.133-201"; exon_number 1; exon_id "ENSE00003712104.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000276800.1"; orig_coord_info "chr22,21463963,21464279,+";
Error, chr discrepancy in gtf info for chr22	ENSEMBL	exon	21555138	21555457	.	+	.	gene_id "Metazoa_SRP^ENSG00000275293.1"; transcript_id "ENST00000619894.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.80-201"; exon_number 1; exon_id "ENSE00003747676.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000275293.1"; orig_coord_info "chr22,21555138,21555457,+";
Error, chr discrepancy in gtf info for chr22	ENSEMBL	exon	23132730	23133005	.	-	.	gene_id "Metazoa_SRP^ENSG00000283438.1"; transcript_id "ENST00000635920.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.211-201"; exon_number 1; exon_id "ENSE00003798476.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000283438.1"; orig_coord_info "chr22,23132730,23133005,-";
Error, chr discrepancy in gtf info for chr22	ENSEMBL	exon	37578669	37578922	.	+	.	gene_id "Metazoa_SRP^ENSG00000273866.1"; transcript_id "ENST00000615981.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.38-201"; exon_number 1; exon_id "ENSE00003750743.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000273866.1"; orig_coord_info "chr22,37578669,37578922,+";
Error, chr discrepancy in gtf info for chr22	ENSEMBL	exon	38281028	38281289	.	-	.	gene_id "Metazoa_SRP^ENSG00000277385.1"; transcript_id "ENST00000622344.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.156-201"; exon_number 1; exon_id "ENSE00003737036.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277385.1"; orig_coord_info "chr22,38281028,38281289,-";
Error, chr discrepancy in gtf info for chr22	ENSEMBL	exon	40917111	40917381	.	+	.	gene_id "Metazoa_SRP^ENSG00000273979.1"; transcript_id "ENST00000616394.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.43-201"; exon_number 1; exon_id "ENSE00003744603.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000273979.1"; orig_coord_info "chr22,40917111,40917381,+";
Error, chr discrepancy in gtf info for chr22	ENSEMBL	exon	49846456	49846720	.	+	.	gene_id "Metazoa_SRP^ENSG00000277771.1"; transcript_id "ENST00000621807.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.172-201"; exon_number 1; exon_id "ENSE00003719937.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277771.1"; orig_coord_info "chr22,49846456,49846720,+";
Error, chr discrepancy in gtf info for chrX	ENSEMBL	exon	388100	388389	.	-	.	gene_id "Metazoa_SRP^ENSG00000275287.5"; transcript_id "ENST00000610676.5"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.79-201"; exon_number 1; exon_id "ENSE00003740571.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000275287.5"; orig_coord_info "chrX,388100,388389,-";
Error, chr discrepancy in gtf info for chrX	ENSEMBL	exon	46073651	46073935	.	-	.	gene_id "Metazoa_SRP^ENSG00000278838.1"; transcript_id "ENST00000612254.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.207-201"; exon_number 1; exon_id "ENSE00003730310.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000278838.1"; orig_coord_info "chrX,46073651,46073935,-";
Error, chr discrepancy in gtf info for chrX	ENSEMBL	exon	46553522	46553775	.	-	.	gene_id "Metazoa_SRP^ENSG00000277721.1"; transcript_id "ENST00000616060.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.170-201"; exon_number 1; exon_id "ENSE00001463378.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277721.1"; orig_coord_info "chrX,46553522,46553775,-";
Error, chr discrepancy in gtf info for chrX	ENSEMBL	exon	47476822	47477152	.	-	.	gene_id "Metazoa_SRP^ENSG00000277605.1"; transcript_id "ENST00000620748.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.164-201"; exon_number 1; exon_id "ENSE00003752596.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277605.1"; orig_coord_info "chrX,47476822,47477152,-";
Error, chr discrepancy in gtf info for chrX	ENSEMBL	exon	48524480	48524806	.	+	.	gene_id "Metazoa_SRP^ENSG00000276823.1"; transcript_id "ENST00000610965.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.134-201"; exon_number 1; exon_id "ENSE00003751716.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000276823.1"; orig_coord_info "chrX,48524480,48524806,+";
Error, chr discrepancy in gtf info for chrX	ENSEMBL	exon	71368666	71368968	.	+	.	gene_id "Metazoa_SRP^ENSG00000275975.1"; transcript_id "ENST00000611704.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.101-201"; exon_number 1; exon_id "ENSE00003727318.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000275975.1"; orig_coord_info "chrX,71368666,71368968,+";
Error, chr discrepancy in gtf info for chrX	ENSEMBL	exon	97081674	97081956	.	+	.	gene_id "Metazoa_SRP^ENSG00000277900.1"; transcript_id "ENST00000619127.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.174-201"; exon_number 1; exon_id "ENSE00003737860.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000277900.1"; orig_coord_info "chrX,97081674,97081956,+";
Error, chr discrepancy in gtf info for chrX	ENSEMBL	exon	129796491	129796783	.	-	.	gene_id "Metazoa_SRP^ENSG00000275070.1"; transcript_id "ENST00000614439.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.75-201"; exon_number 1; exon_id "ENSE00003718708.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000275070.1"; orig_coord_info "chrX,129796491,129796783,-";
Error, chr discrepancy in gtf info for chrX	ENSEMBL	exon	151275509	151275789	.	+	.	gene_id "Metazoa_SRP^ENSG00000278724.1"; transcript_id "ENST00000615501.1"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.199-201"; exon_number 1; exon_id "ENSE00002258300.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "Metazoa_SRP^ENSG00000278724.1"; orig_coord_info "chrX,151275509,151275789,+";
Error, chr discrepancy in gtf info for chrY	ENSEMBL	exon	388100	388389	.	-	.	gene_id "Metazoa_SRP^ENSG00000275287.5_PAR_Y"; transcript_id "ENST00000610676.5_PAR_Y"; gene_type "misc_RNA"; gene_name "Metazoa_SRP"; transcript_type "misc_RNA"; transcript_name "Metazoa_SRP.79-201"; exon_number 1; exon_id "ENSE00003740571.1"; level 3; transcript_support_level "NA"; tag "basic"; tag "PAR"; FI_gene_label "Metazoa_SRP^ENSG00000275287.5_PAR_Y"; orig_coord_info "chrY,388100,388389,-";
Error - no gene spans 100M bases in length.... likely problem at /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl line 589.
	main::get_gene_span_info("chr1\x{9}ENSEMBL\x{9}exon\x{9}29041199\x{9}29041480\x{9}.\x{9}+\x{9}.\x{9}gene_id \"Metazoa_SR"...) called at /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl line 417
	main::get_gene_contig_gtf("chr1\x{9}ENSEMBL\x{9}exon\x{9}29041199\x{9}29041480\x{9}.\x{9}+\x{9}.\x{9}gene_id \"Metazoa_SR"..., "/tmp/nxf.RYGCkjTtsm/ctat_genome_lib_build_dir/ref_genome.fa") called at /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl line 214
	eval {...} called at /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl line 210

Error, chr discrepancy in gtf info for chr2	ENSEMBL	exon	86347062	86347195	.	-	.	gene_id "U8^ENSG00000202537.1"; transcript_id "ENST00000365667.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.9-201"; exon_number 1; exon_id "ENSE00001440430.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000202537.1"; orig_coord_info "chr2,86347062,86347195,-";
Error, chr discrepancy in gtf info for chr2	ENSEMBL	exon	185661774	185661906	.	+	.	gene_id "U8^ENSG00000212581.1"; transcript_id "ENST00000391279.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.16-201"; exon_number 1; exon_id "ENSE00001509063.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000212581.1"; orig_coord_info "chr2,185661774,185661906,+";
Error, chr discrepancy in gtf info for chr3	ENSEMBL	exon	41899111	41899253	.	-	.	gene_id "U8^ENSG00000212145.2"; transcript_id "ENST00000390843.2"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.14-201"; exon_number 1; exon_id "ENSE00001508627.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000212145.2"; orig_coord_info "chr3,41899111,41899253,-";
Error, chr discrepancy in gtf info for chr3	ENSEMBL	exon	154007367	154007502	.	-	.	gene_id "U8^ENSG00000201398.1"; transcript_id "ENST00000364528.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.5-201"; exon_number 1; exon_id "ENSE00001439291.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000201398.1"; orig_coord_info "chr3,154007367,154007502,-";
Error, chr discrepancy in gtf info for chr3	ENSEMBL	exon	180542701	180542836	.	+	.	gene_id "U8^ENSG00000201810.1"; transcript_id "ENST00000364940.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.7-201"; exon_number 1; exon_id "ENSE00001439703.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000201810.1"; orig_coord_info "chr3,180542701,180542836,+";
Error, chr discrepancy in gtf info for chr5	ENSEMBL	exon	15110786	15110920	.	-	.	gene_id "U8^ENSG00000202269.1"; transcript_id "ENST00000365399.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.8-201"; exon_number 1; exon_id "ENSE00001440162.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000202269.1"; orig_coord_info "chr5,15110786,15110920,-";
Error, chr discrepancy in gtf info for chr5	ENSEMBL	exon	68873954	68874087	.	+	.	gene_id "U8^ENSG00000212249.2"; transcript_id "ENST00000390947.2"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.15-201"; exon_number 1; exon_id "ENSE00001508731.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000212249.2"; orig_coord_info "chr5,68873954,68874087,+";
Error, chr discrepancy in gtf info for chr6	ENSEMBL	exon	154905076	154905206	.	-	.	gene_id "U8^ENSG00000238963.2"; transcript_id "ENST00000459445.2"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.20-201"; exon_number 1; exon_id "ENSE00001807926.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000238963.2"; orig_coord_info "chr6,154905076,154905206,-";
Error, chr discrepancy in gtf info for chr8	ENSEMBL	exon	71815494	71815625	.	-	.	gene_id "U8^ENSG00000200191.1"; transcript_id "ENST00000363321.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.3-201"; exon_number 1; exon_id "ENSE00001438084.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000200191.1"; orig_coord_info "chr8,71815494,71815625,-";
Error, chr discrepancy in gtf info for chr9	ENSEMBL	exon	38147428	38147561	.	+	.	gene_id "U8^ENSG00000200026.1"; transcript_id "ENST00000363156.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.2-201"; exon_number 1; exon_id "ENSE00001437919.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000200026.1"; orig_coord_info "chr9,38147428,38147561,+";
Error, chr discrepancy in gtf info for chr10	ENSEMBL	exon	4962436	4962568	.	-	.	gene_id "U8^ENSG00000238840.1"; transcript_id "ENST00000459095.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.19-201"; exon_number 1; exon_id "ENSE00001808956.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000238840.1"; orig_coord_info "chr10,4962436,4962568,-";
Error, chr discrepancy in gtf info for chr10	ENSEMBL	exon	5004710	5004842	.	+	.	gene_id "U8^ENSG00000239148.1"; transcript_id "ENST00000459141.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.22-201"; exon_number 1; exon_id "ENSE00001809269.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000239148.1"; orig_coord_info "chr10,5004710,5004842,+";
Error, chr discrepancy in gtf info for chr10	ENSEMBL	exon	5093408	5093543	.	-	.	gene_id "U8^ENSG00000239142.1"; transcript_id "ENST00000459536.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.21-201"; exon_number 1; exon_id "ENSE00001809201.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000239142.1"; orig_coord_info "chr10,5093408,5093543,-";
Error, chr discrepancy in gtf info for chr11	ENSEMBL	exon	123301390	123301523	.	+	.	gene_id "U8^ENSG00000200496.1"; transcript_id "ENST00000363626.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.4-201"; exon_number 1; exon_id "ENSE00001438389.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000200496.1"; orig_coord_info "chr11,123301390,123301523,+";
Error, chr discrepancy in gtf info for chr12	ENSEMBL	exon	73764279	73764413	.	-	.	gene_id "U8^ENSG00000201809.1"; transcript_id "ENST00000364939.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.6-201"; exon_number 1; exon_id "ENSE00001439702.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000201809.1"; orig_coord_info "chr12,73764279,73764413,-";
Error, chr discrepancy in gtf info for chr12	ENSEMBL	exon	103592112	103592243	.	+	.	gene_id "U8^ENSG00000212594.1"; transcript_id "ENST00000391292.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.17-201"; exon_number 1; exon_id "ENSE00001509076.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000212594.1"; orig_coord_info "chr12,103592112,103592243,+";
Error, chr discrepancy in gtf info for chr15	ENSEMBL	exon	30112198	30112330	.	+	.	gene_id "U8^ENSG00000207432.1"; transcript_id "ENST00000384701.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.12-201"; exon_number 1; exon_id "ENSE00001807133.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000207432.1"; orig_coord_info "chr15,30112198,30112330,+";
Error, chr discrepancy in gtf info for chr15	ENSEMBL	exon	30384959	30385091	.	-	.	gene_id "U8^ENSG00000238519.1"; transcript_id "ENST00000459285.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.18-201"; exon_number 1; exon_id "ENSE00001807694.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000238519.1"; orig_coord_info "chr15,30384959,30385091,-";
Error, chr discrepancy in gtf info for chr15	ENSEMBL	exon	30581184	30581316	.	+	.	gene_id "U8^ENSG00000207430.1"; transcript_id "ENST00000384699.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.11-201"; exon_number 1; exon_id "ENSE00001808585.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000207430.1"; orig_coord_info "chr15,30581184,30581316,+";
Error, chr discrepancy in gtf info for chr15	ENSEMBL	exon	32426288	32426420	.	-	.	gene_id "U8^ENSG00000206987.1"; transcript_id "ENST00000384260.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.10-201"; exon_number 1; exon_id "ENSE00001808229.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000206987.1"; orig_coord_info "chr15,32426288,32426420,-";
Error, chr discrepancy in gtf info for chr18	ENSEMBL	exon	58818883	58819016	.	-	.	gene_id "U8^ENSG00000199713.1"; transcript_id "ENST00000362843.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.1-201"; exon_number 1; exon_id "ENSE00001437606.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000199713.1"; orig_coord_info "chr18,58818883,58819016,-";
Done.
Execution Time = 0.14 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusionreport.tsv --gtf /tmp/nxf.RYGCkjTtsm/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.RYGCkjTtsm/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fa /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fa /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fa
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.gtf /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.gtf /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.gtf
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fa /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.gtf > /tmp/nxf.RYGCkjTtsm/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fa /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.gtf > /tmp/nxf.RYGCkjTtsm/cytoBand.txt
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.gtf > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.bed
-parsing GTF file: /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.gtf
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.gtf > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.bed
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.bed > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.bed > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fa
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.RYGCkjTtsm/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.gtf --CPU 8 --out_prefix FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star --out_dir /tmp/nxf.RYGCkjTtsm/fi_workdir --reads "/tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.RYGCkjTtsm/ctat_genome_lib_build_dir/ref_genome.fa.star.idx  --outSAMtype BAM SortedByCoordinate  --twopassMode None  --alignSJDBoverhangMin 10  --genomeSuffixLengthMax 10000 --limitBAMsortRAM 47271261705  --alignInsertionFlush Right   --alignMatesGapMax 100000  --alignIntronMax 100000  --outSAMattributes All  --readFilesIn /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 10:23:11 ..... started STAR run
Jun 08 10:23:11 ..... loading genome
Jun 08 10:24:57 ... generating Suffix Array index
Jun 08 10:28:47 ... completed Suffix Array index
Jun 08 10:28:47 ..... processing annotations GTF
Jun 08 10:28:48 ..... inserting junctions into the genome indices
Jun 08 10:29:49 ..... started mapping
Jun 08 11:37:21 ..... finished mapping
Jun 08 11:37:23 ..... started sorting BAM
Jun 08 11:37:26 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.sortedByCoord.out.bam
Execution Time = 74.35 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.RYGCkjTtsm/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.gtf --CPU 8 --out_prefix FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star --out_dir /tmp/nxf.RYGCkjTtsm/fi_workdir --reads "/tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
11:38:06 : INFO : Done.
Execution Time = 0.56 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.07 minutes. CMD: samtools index /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/mark_dups_reads.index.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.gtf
-parsing /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.cSorted.dupsMarked.bam

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[5830000]   -done parsing /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num genes matched < 2' => 70,
          'excessive soft clipping' => 41177,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 124,
          'seq-similar region overlap' => 38,
          'small anchor length' => 31,
          ' ** passed ** ' => 17378,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 88,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 50,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 589,
          'per_id < 96' => 27789,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 51,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 15,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 8,
          'exons hit < 2' => 22,
          'low complexity anchor region' => 41
        };
-writing fusion junction support info.
Execution Time = 4.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[48000]   -fusion SPANNING read extraction for scaff: AC004980.3--UPK3BL1

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[91000]   -fusion SPANNING read extraction for scaff: ANTXR1--AC011897.1

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[90000]   -fusion SPANNING read extraction for scaff: ANTXR1--RN7SKP168

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[90000]   -fusion SPANNING read extraction for scaff: ANTXR1--ZFYVE9P2

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[32000]   -fusion SPANNING read extraction for scaff: ANTXR2--TNFSF10

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[60000]   -fusion SPANNING read extraction for scaff: ATG16L2--C11orf80

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[37000]   -fusion SPANNING read extraction for scaff: B9D1--CD82

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[133000]   -fusion SPANNING read extraction for scaff: BCL2L13--EP300

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[43000]   -fusion SPANNING read extraction for scaff: C18orf25--GREB1L

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[33000]   
[34000]   -fusion SPANNING read extraction for scaff: CASP8--STRADB

[1000]   -fusion SPANNING read extraction for scaff: CCDC169--SOHLH2

[1000]   
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[175000]   -fusion SPANNING read extraction for scaff: CCDC6--RET

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[17000]   -fusion SPANNING read extraction for scaff: CCNJL--FABP6

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[70000]   -fusion SPANNING read extraction for scaff: CENPM--PACSIN2

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[180000]   -fusion SPANNING read extraction for scaff: CHMP1A--FANCA

[1000]   
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[81000]   -fusion SPANNING read extraction for scaff: CMIP--AP001970.1

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[80000]   
[81000]   -fusion SPANNING read extraction for scaff: CMIP--U8

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[43000]   -fusion SPANNING read extraction for scaff: CUL4B--TMEM255A

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[245000]   -fusion SPANNING read extraction for scaff: DDX1--AC068286.1

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[60000]   -fusion SPANNING read extraction for scaff: EFNA5--IKBKB

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[28000]   -fusion SPANNING read extraction for scaff: ELF2--EGFLAM

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[169000]   
[170000]   -fusion SPANNING read extraction for scaff: FANCA--CDK10

[1000]   
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[257000]   
[258000]   -fusion SPANNING read extraction for scaff: HERC2--SNAP23

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[245000]   -fusion SPANNING read extraction for scaff: HERC2--AC018362.1

[1000]   
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[89000]   -fusion SPANNING read extraction for scaff: IARS2--MTRNR2L12

[1000]   
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[46000]   
[47000]   -fusion SPANNING read extraction for scaff: IKBKB--CHRNA6

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[50000]   
[51000]   -fusion SPANNING read extraction for scaff: IKBKB--THAP1

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[66000]   -fusion SPANNING read extraction for scaff: KDM4B--CYP4F22

[1000]   -fusion SPANNING read extraction for scaff: KLRC4--KLRK1

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[109000]   
[110000]   -fusion SPANNING read extraction for scaff: MDK--CREB3L1

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[247000]   -fusion SPANNING read extraction for scaff: MGA--GABRB3

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[9000]   
[10000]   -fusion SPANNING read extraction for scaff: MIPOL1--TTC6

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[11000]   
[12000]   -fusion SPANNING read extraction for scaff: MRPS14--TNR

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[112000]   -fusion SPANNING read extraction for scaff: MYO5C--SHC4

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[1007000]   
[1008000]   -fusion SPANNING read extraction for scaff: NPM1--MT-RNR2

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[109000]   
[110000]   
[111000]   
[112000]   -fusion SPANNING read extraction for scaff: PANK2--MAVS

[1000]   
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[4000]   
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[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1

[1000]   
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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13

[1000]   
[2000]   
[3000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

[1000]   
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[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
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[6000]   
[7000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

[1000]   
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[4000]   
[5000]   
[6000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

[1000]   
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[5000]   
[6000]   
[7000]   
[8000]   
[9000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

[1000]   
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[4000]   
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[6000]   
[7000]   
[8000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

[1000]   
[2000]   
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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

[1000]   
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[5000]   
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[29000]   
[30000]   -fusion SPANNING read extraction for scaff: PEX3--AIG1

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[63000]   
[64000]   -fusion SPANNING read extraction for scaff: PPIP5K1--OTUD7A

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[152000]   
[153000]   -fusion SPANNING read extraction for scaff: PPL--SEC14L5

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[194000]   
[195000]   -fusion SPANNING read extraction for scaff: RBM14--RBM4

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[453000]   -fusion SPANNING read extraction for scaff: SLC34A2--ROS1

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[5000]   -fusion SPANNING read extraction for scaff: SLCO1B3--SLCO1B7

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[52000]   -fusion SPANNING read extraction for scaff: SNU13--LLPH

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[37000]   -fusion SPANNING read extraction for scaff: SOGA3--KIAA0408

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[113000]   
[114000]   -fusion SPANNING read extraction for scaff: SPAG9--MBTD1

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[53000]   
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[57000]   
[58000]   -fusion SPANNING read extraction for scaff: TCF7L2--AL158212.1

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[65000]   
[66000]   -fusion SPANNING read extraction for scaff: THAP12--ACO1

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[83000]   
[84000]   
[85000]   
[86000]   
[87000]   
[88000]   
[89000]   
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[91000]   
[92000]   
[93000]   
[94000]   
[95000]   
[96000]   
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[99000]   
[100000]   
[101000]   
[102000]   
[103000]   
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[111000]   
[112000]   
[113000]   
[114000]   
[115000]   
[116000]   
[117000]   
[118000]   
[119000]   -fusion SPANNING read extraction for scaff: TRIP10--KDM4B

[1000]   
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[7000]   
[8000]   
[9000]   
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[13000]   
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[15000]   
[16000]   
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[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

[1000]   
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[8000]   
[9000]   
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[71000]   
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[73000]   
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[75000]   
[76000]   
[77000]   
[78000]   
[79000]   -fusion SPANNING read extraction for scaff: WAC--SFMBT2

[1000]   
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[8000]   
[9000]   
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[20000]   
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[23000]   
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[25000]   
[26000]   
[27000]   
[28000]   -fusion SPANNING read extraction for scaff: ZDHHC9--AL034405.1

[1000]   
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[8000]   
[9000]   
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[12000]   
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[16000]   
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[21000]   
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[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   -fusion SPANNING read extraction for scaff: ZNF227--GAB2

[1000]   
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[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: ZNF419--ZNF772
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 122518,
          'seq similar region alignment' => 23764
        };
Execution Time = 10.11 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -26682.212455
EM: Round [1] log likelihood: -26661.019018
EM: Round [2] log likelihood: -26660.965895
EM: Round [3] log likelihood: -26660.965840
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/init_EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/prep_igv_extract_junc_reads.ok
Running: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.junction_reads.bam
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.junction_reads.bam > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.junction_reads.bam.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.junction_reads.bam > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.junction_reads.bam.bed > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.junction_reads.bam.bed > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.spanning_reads.bam || : 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.spanning_reads.bam || : 
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.spanning_reads.bam > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.spanning_reads.bam > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.spanning_reads.bam.bed > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.spanning_reads.bam.bed > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.consolidated.bam
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.consolidated.bam
Execution Time = 0.06 minutes. CMD: samtools index /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.consolidated.bam
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.consolidated.bam into /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.consolidated.bam.read_coords > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.consolidated.bam.frag_coords > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 1.52 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/prep_igv_sam_frag_coordss.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.consolidated.bam.frag_coords > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.igv.FusionJuncSpan
Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.consolidated.bam.frag_coords > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.igv.Pfam.gff3 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.igv.Pfam.gff3 
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.igv.Pfam.gff3 > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.igv.Pfam.gff3 > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/prep_igv_pfam_bed.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.igv.seqsimilar.gff3 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/prep_igv_seqsim_bed.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fa > /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fa > /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter  --genome_lib_dir ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 50 
CMD: cp /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.post_blast_and_promiscuity_filter
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.RYGCkjTtsm/fi_workdir/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.RYGCkjTtsm/ctat_genome_lib_build_dir
-done, see /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.RYGCkjTtsm/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -25260.377652
EM: Round [1] log likelihood: -25255.401152
EM: Round [2] log likelihood: -25255.397780
EM: Round [3] log likelihood: -25255.397775
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1_1.fastp.fastq.gz: 294435155
Execution Time = 6.08 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fa --gtf /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.gtf  > /tmp/nxf.RYGCkjTtsm/fi_workdir/microH.dat
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fa --gtf /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.gtf  > /tmp/nxf.RYGCkjTtsm/fi_workdir/microH.dat
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.RYGCkjTtsm/fi_workdir/microH.dat /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.RYGCkjTtsm/fi_workdir/microH.dat /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.RYGCkjTtsm --json_outfile /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_inspector_web.json --file_prefix FFPE_HD789_01_RNA_0002_B23LG7FLT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.RYGCkjTtsm --json_outfile /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_inspector_web.json --file_prefix FFPE_HD789_01_RNA_0002_B23LG7FLT4_1
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/create_fi_igvjs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_inspector_web.json --input_file_prefix FFPE_HD789_01_RNA_0002_B23LG7FLT4_1 --html_output /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_inspector_web.json --input_file_prefix FFPE_HD789_01_RNA_0002_B23LG7FLT4_1 --html_output /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.RYGCkjTtsm/ctat_genome_lib_build_dir > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.RYGCkjTtsm/ctat_genome_lib_build_dir > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.RYGCkjTtsm/ctat_genome_lib_build_dir > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000228505.5]
WARNING, no entry stored in dbm for [ENSG00000228505.5]
WARNING, no entry stored in dbm for [ENSG00000228505.5]
WARNING, no entry stored in dbm for [ENSG00000230305.2]
WARNING, no entry stored in dbm for [ENSG00000230305.2]
WARNING, no entry stored in dbm for [ENSG00000225292.2]
WARNING, no entry stored in dbm for [ENSG00000225292.2]
WARNING, no entry stored in dbm for [ENSG00000225292.2]
WARNING, no entry stored in dbm for [ENSG00000225292.2]
WARNING, no entry stored in dbm for [ENSG00000225292.2]
WARNING, no entry stored in dbm for [ENSG00000225292.2]
WARNING, no entry stored in dbm for [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000235189.2]
WARNING, no entry stored in dbm for [ENSG00000235127.1]
WARNING, no entry stored in dbm for [ENSG00000235127.1]
WARNING, no entry stored in dbm for [ENSG00000235127.1]
WARNING, no entry stored in dbm for [ENSG00000235127.1]
WARNING, no entry stored in dbm for [ENSG00000261684.2]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.RYGCkjTtsm/ctat_genome_lib_build_dir > /tmp/nxf.RYGCkjTtsm/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.RYGCkjTtsm/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory