Error, chr discrepancy in gtf info for chr20	ENSEMBL	exon	29297095	29297246	.	-	.	gene_id "5_8S_rRNA^ENSG00000283568.1"; transcript_id "ENST00000637374.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.9-201"; exon_number 1; exon_id "ENSE00003799614.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000283568.1"; orig_coord_info "chr20,29297095,29297246,-";
Error, chr discrepancy in gtf info for chr20	ENSEMBL	exon	29741510	29741661	.	-	.	gene_id "5_8S_rRNA^ENSG00000283291.1"; transcript_id "ENST00000638132.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.8-201"; exon_number 1; exon_id "ENSE00003794628.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000283291.1"; orig_coord_info "chr20,29741510,29741661,-";
Error, chr discrepancy in gtf info for chr20	ENSEMBL	exon	30484925	30485076	.	-	.	gene_id "5_8S_rRNA^ENSG00000275877.1"; transcript_id "ENST00000614365.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.3-201"; exon_number 1; exon_id "ENSE00003742842.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000275877.1"; orig_coord_info "chr20,30484925,30485076,-";
Error, chr discrepancy in gtf info for chr21	ENSEMBL	exon	8256781	8256933	.	+	.	gene_id "5_8S_rRNA^ENSG00000277739.1"; transcript_id "ENST00000610460.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.5-201"; exon_number 1; exon_id "ENSE00003746458.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000277739.1"; orig_coord_info "chr21,8256781,8256933,+";
Error, chr discrepancy in gtf info for chr22	ENSEMBL	exon	11249809	11249959	.	-	.	gene_id "5_8S_rRNA^ENSG00000276871.1"; transcript_id "ENST00000612732.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.4-201"; exon_number 1; exon_id "ENSE00003735240.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000276871.1"; orig_coord_info "chr22,11249809,11249959,-";
Done.
-parsing GTF file: /tmp/nxf.DfCxQrsuHr/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.DfCxQrsuHr/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.DfCxQrsuHr/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.DfCxQrsuHr/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.DfCxQrsuHr/fi_workdir/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.DfCxQrsuHr/fi_workdir/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
11:26:11 : INFO : Done.
-parsing GTF file: /tmp/nxf.DfCxQrsuHr/fi_workdir/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.DfCxQrsuHr/fi_workdir/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

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[520000]   -done parsing /tmp/nxf.DfCxQrsuHr/fi_workdir/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          ' ** passed ** ' => 1060,
          'small anchor length' => 7,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 14,
          'per_id < 96' => 1891,
          'num genes matched < 2' => 13,
          'excessive soft clipping' => 3959,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 59,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 4
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.DfCxQrsuHr/fi_workdir/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[102000]   
[103000]   
[104000]   -fusion SPANNING read extraction for scaff: DTX2--PTPN12
-fusion SPANNING read extraction for scaff: FRG1DP--MLLT10P1
-fusion SPANNING read extraction for scaff: FRG1DP--5_8S_rRNA

[1000]   
[2000]   -fusion SPANNING read extraction for scaff: KLRC4--KLRK1

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[62000]   
[63000]   -fusion SPANNING read extraction for scaff: PTPN12--MAGI2

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[101000]   -fusion SPANNING read extraction for scaff: SRRM1--CLIC4

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[62000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[29000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[6000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[17000]   -fusion SPANNING read extraction for scaff: TOPORS--LINGO2

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[43000]   -fusion SPANNING read extraction for scaff: TOPORS--BNC2

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[17000]   -fusion SPANNING read extraction for scaff: TOPORS--AL162725.2

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[51000]   -fusion SPANNING read extraction for scaff: TSBP1--NOTCH4

[1000]   
[2000]   -fusion SPANNING read extraction for scaff: TSBP1--TSBP1-AS1

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[23000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 4133,
          'seq similar region alignment' => 162
        };
EM: Starting log likelihood: -1232.850211
EM: Round [1] log likelihood: -1232.802635
EM: Round [2] log likelihood: -1232.801970
EM: Round [3] log likelihood: -1232.801958
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.DfCxQrsuHr/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.DfCxQrsuHr/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.DfCxQrsuHr/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.DfCxQrsuHr/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.DfCxQrsuHr/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.DfCxQrsuHr/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.DfCxQrsuHr/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.DfCxQrsuHr/fi_workdir/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_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.DfCxQrsuHr/fi_workdir/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_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.DfCxQrsuHr/fi_workdir/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.DfCxQrsuHr/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.DfCxQrsuHr/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -1189.905162
EM: Round [1] log likelihood: -1189.857587
EM: Round [2] log likelihood: -1189.856922
EM: Round [3] log likelihood: -1189.856909
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.DfCxQrsuHr/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296760770
Warning - not locating file: /tmp/nxf.DfCxQrsuHr/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
ls: cannot access 'IGV_inputs': No such file or directory