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.
-parsing GTF file: /tmp/nxf.4rVImRf8iV/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.4rVImRf8iV/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.4rVImRf8iV/aih-tih-sc-b8457f-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.4rVImRf8iV/aih-tih-sc-b8457f-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.4rVImRf8iV/fi_workdir/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.4rVImRf8iV/fi_workdir/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-b8457f-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-b8457f-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
11:31:59 : INFO : Done.
-parsing GTF file: /tmp/nxf.4rVImRf8iV/fi_workdir/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.4rVImRf8iV/fi_workdir/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
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[4450000] -done parsing /tmp/nxf.4rVImRf8iV/fi_workdir/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'exons hit < 2' => 5,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 4,
'low complexity anchor region' => 9,
'num genes matched < 2' => 94,
'excessive soft clipping' => 26133,
' ** passed ** ' => 6531,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 228,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 2,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 75,
'per_id < 96' => 15228,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 85,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 587,
'small anchor length' => 102,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 87,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 12,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 24,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 76
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.4rVImRf8iV/fi_workdir/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
[1000]
[2000] -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L
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[30000] -fusion SPANNING read extraction for scaff: COX7A2L--SPRED2
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[58000] -fusion SPANNING read extraction for scaff: CRYZL2P--SEC16B
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[35000] -fusion SPANNING read extraction for scaff: EXOC6B--SPRED2
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[12000] -fusion SPANNING read extraction for scaff: LDAH--AC013460.1
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[12000] -fusion SPANNING read extraction for scaff: LDAH--RNU6ATAC37P
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[26000] -fusion SPANNING read extraction for scaff: MBOAT2--AC093702.1
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[26000] -fusion SPANNING read extraction for scaff: MBOAT2--LINC01121
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[103000] -fusion SPANNING read extraction for scaff: NOL10--ASAP2
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[451000] -fusion SPANNING read extraction for scaff: NOTCH1--AL590226.1
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[54000] -fusion SPANNING read extraction for scaff: NOTCH2NLA--CD160
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[6000] -fusion SPANNING read extraction for scaff: PRKCE--AC092155.1
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[105000] -fusion SPANNING read extraction for scaff: PUM2--MBOAT2
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[111000] -fusion SPANNING read extraction for scaff: RCN3--FCGRT
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[55000] -fusion SPANNING read extraction for scaff: RN7SL341P--NBAS
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[65000] -fusion SPANNING read extraction for scaff: SERTAD2--NBAS
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[18000] -fusion SPANNING read extraction for scaff: SPRED2--LINC01115
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[18000] -fusion SPANNING read extraction for scaff: SPRED2--LINC01939
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[447000] -fusion SPANNING read extraction for scaff: SPTBN1--AC092155.1
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[66000] -fusion SPANNING read extraction for scaff: STAMBP--SPRED2
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[63000] -fusion SPANNING read extraction for scaff: TCF7L2--AC010998.3
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[63000] -fusion SPANNING read extraction for scaff: TCF7L2--RPL19P16
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[63000] -fusion SPANNING read extraction for scaff: TCF7L2--AC010998.1
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[31000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[131000] -fusion SPANNING read extraction for scaff: TP53--ARHGAP44
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[21000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
[1000]
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[3000]
[4000]
[5000]
[6000] -fusion SPANNING read extraction for scaff: U8--AKR1C2
[1000]
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[5000]
[6000]
[7000]
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[158000] -fusion SPANNING read extraction for scaff: USP34--NOTO
[1000]
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[10000] -fusion SPANNING read extraction for scaff: VSNL1--RN7SKP27
[1000]
[2000]
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[10000] -fusion SPANNING read extraction for scaff: VSNL1--AC018467.1
[1000]
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[58000] -fusion SPANNING read extraction for scaff: WDR43--EML4-AS1
[1000]
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[3000] -fusion SPANNING read extraction for scaff: ZNF519--ANKRD20A11P
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 32487
};
EM: Starting log likelihood: -11598.367324
EM: Round [1] log likelihood: -11595.607728
EM: Round [2] log likelihood: -11595.599049
EM: Round [3] log likelihood: -11595.599007
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.4rVImRf8iV/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.4rVImRf8iV/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.4rVImRf8iV/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.4rVImRf8iV/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.4rVImRf8iV/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.4rVImRf8iV/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.4rVImRf8iV/aih-tih-sc-b8457f-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.4rVImRf8iV/fi_workdir/aih-tih-sc-b8457f-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.4rVImRf8iV/fi_workdir/aih-tih-sc-b8457f-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.4rVImRf8iV/fi_workdir/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.4rVImRf8iV/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.4rVImRf8iV/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -11277.881566
EM: Round [1] log likelihood: -11276.558765
EM: Round [2] log likelihood: -11276.554573
EM: Round [3] log likelihood: -11276.554555
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.4rVImRf8iV/aih-tih-sc-b8457f-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296889510
Warning - not locating file: /tmp/nxf.4rVImRf8iV/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000224184.6]
WARNING, no entry stored in dbm for [ENSG00000224184.6]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000260126.2]
WARNING, no entry stored in dbm for [ENSG00000254681.6]
WARNING, no entry stored in dbm for [ENSG00000260126.2]
WARNING, no entry stored in dbm for [ENSG00000254681.6]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
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 [ENSG00000224875.2]
WARNING, no entry stored in dbm for [ENSG00000224875.2]
WARNING, no entry stored in dbm for [ENSG00000224875.2]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286065.2]
WARNING, no entry stored in dbm for [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000226622.6]
WARNING, no entry stored in dbm for [ENSG00000226622.6]
WARNING, no entry stored in dbm for [ENSG00000279141.3]
ls: cannot access 'IGV_inputs': No such file or directory