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.wyygLYFfIj/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.wyygLYFfIj/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.wyygLYFfIj/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.wyygLYFfIj/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.wyygLYFfIj/fi_workdir/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.wyygLYFfIj/fi_workdir/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam
11:55:21 : INFO : Done.
-parsing GTF file: /tmp/nxf.wyygLYFfIj/fi_workdir/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_1.gtf
-parsing /tmp/nxf.wyygLYFfIj/fi_workdir/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam
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[4800000] -done parsing /tmp/nxf.wyygLYFfIj/fi_workdir/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'exons hit < 2' => 1,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 16,
'num genes matched < 2' => 45,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 4,
'low complexity anchor region' => 35,
'per_id < 96' => 17703,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 2,
'excessive soft clipping' => 39577,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 6,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 426,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 63,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 473,
'small anchor length' => 6,
' ** passed ** ' => 4354,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 64,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 2
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.wyygLYFfIj/fi_workdir/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[84000] -fusion SPANNING read extraction for scaff: AC135050.3--SMG1P4
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[44000] -fusion SPANNING read extraction for scaff: ADCY9--AC007610.5
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[45000] -fusion SPANNING read extraction for scaff: ADCY9--AC007610.2
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[107000] -fusion SPANNING read extraction for scaff: AP1B1--GPAT4
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[131000] -fusion SPANNING read extraction for scaff: ARHGAP21--TBC1D22A
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[767000] -fusion SPANNING read extraction for scaff: NKD1--AC138904.1
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[847000] -fusion SPANNING read extraction for scaff: NKD1--CARHSP1
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[766000] -fusion SPANNING read extraction for scaff: NKD1--LITAFD
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[2000] -fusion SPANNING read extraction for scaff: PANX2--AC087698.1
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[51000] -fusion SPANNING read extraction for scaff: SLC7A5P1--N4BP1
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[178000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[85000] -fusion SPANNING read extraction for scaff: SUPV3L1--SPIDR
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[51000] -fusion SPANNING read extraction for scaff: TBC1D22A--AC022535.3
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[51000] -fusion SPANNING read extraction for scaff: TBC1D22A--AC022535.2
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[77000] -fusion SPANNING read extraction for scaff: ZNF668--BCL7C
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 703,
'lacks exon overlap' => 42169
};
EM: Starting log likelihood: -5271.829118
EM: Round [1] log likelihood: -5271.776032
EM: Round [2] log likelihood: -5271.776032
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.wyygLYFfIj/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam into /tmp/nxf.wyygLYFfIj/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.wyygLYFfIj/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.wyygLYFfIj/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords > /tmp/nxf.wyygLYFfIj/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.wyygLYFfIj/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.wyygLYFfIj/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.wyygLYFfIj/fi_workdir/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_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.wyygLYFfIj/fi_workdir/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_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.wyygLYFfIj/fi_workdir/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.wyygLYFfIj/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.wyygLYFfIj/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -5137.369954
EM: Round [1] log likelihood: -5137.369954
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.wyygLYFfIj/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz: 294835613
Warning - not locating file: /tmp/nxf.wyygLYFfIj/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000246465.1]
WARNING, no entry stored in dbm for [ENSG00000246465.1]
WARNING, no entry stored in dbm for [ENSG00000260413.1]
WARNING, no entry stored in dbm for [ENSG00000260413.1]
WARNING, no entry stored in dbm for [ENSG00000123201.14]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000260727.2]
WARNING, no entry stored in dbm for [ENSG00000241621.1]
WARNING, no entry stored in dbm for [ENSG00000287444.1]
WARNING, no entry stored in dbm for [ENSG00000260911.2]
WARNING, no entry stored in dbm for [ENSG00000185710.9]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
ls: cannot access 'IGV_inputs': No such file or directory