Done.
-parsing GTF file: /tmp/nxf.kpybOx6aMA/659_dES-T1-TRNA-1_B23WHTKLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.kpybOx6aMA/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.kpybOx6aMA/659_dES-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.kpybOx6aMA/659_dES-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.kpybOx6aMA/fi_workdir/659_dES-T1-TRNA-1_B23WHTKLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.kpybOx6aMA/fi_workdir/659_dES-T1-TRNA-1_B23WHTKLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_dES-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_dES-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam
11:19:46 : INFO : Done.
-parsing GTF file: /tmp/nxf.kpybOx6aMA/fi_workdir/659_dES-T1-TRNA-1_B23WHTKLT4_1.gtf
-parsing /tmp/nxf.kpybOx6aMA/fi_workdir/659_dES-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
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[5390000] -done parsing /tmp/nxf.kpybOx6aMA/fi_workdir/659_dES-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 6572,
'per_id < 96' => 21677,
'num_hits: 7 != num_counted_on_fusion_contigs 1 ' => 2,
'num_hits: 9 != num_counted_on_fusion_contigs 5 ' => 5,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 870,
'num_hits: 7 != num_counted_on_fusion_contigs 6 ' => 84,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 4,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 2110,
'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 1,
'exons hit < 2' => 5,
'num_hits: 8 != num_counted_on_fusion_contigs 7 ' => 7,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 3243,
'num_hits: 9 != num_counted_on_fusion_contigs 7 ' => 126,
'num genes matched < 2' => 9471,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 4,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 1122,
'excessive soft clipping' => 40169,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 1514,
' ** passed ** ' => 16609,
'low complexity anchor region' => 45,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 1458,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 142,
'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 5,
'small anchor length' => 174,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 4
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.kpybOx6aMA/fi_workdir/659_dES-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[11000] -fusion SPANNING read extraction for scaff: AC211486.4--AC211476.4
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[40000] -fusion SPANNING read extraction for scaff: ADIPOR1--CADPS2
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[13000] -fusion SPANNING read extraction for scaff: AP1M1--OR7A8P
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[12000] -fusion SPANNING read extraction for scaff: AP1M1--OR7A2P
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[157000] -fusion SPANNING read extraction for scaff: BOLA2B--SMG1P5
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[282000] -fusion SPANNING read extraction for scaff: BOP1--CPSF1
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[14000] -fusion SPANNING read extraction for scaff: CCDC75P1--GXYLT2
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[79000] -fusion SPANNING read extraction for scaff: CDC42BPA--WDR64
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[31000] -fusion SPANNING read extraction for scaff: CRK--CCDC92B
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[50000] -fusion SPANNING read extraction for scaff: DMTF1--CROT
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[25000] -fusion SPANNING read extraction for scaff: EFL1--GOLGA6L11P
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[1864000] -fusion SPANNING read extraction for scaff: FGFR3--TACC3
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[217000] -fusion SPANNING read extraction for scaff: INSR--ARHGEF18
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[22000] -fusion SPANNING read extraction for scaff: L3MBTL4--LAMA1
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[41000] -fusion SPANNING read extraction for scaff: MAN1A2--SLC22A15
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[59000] -fusion SPANNING read extraction for scaff: MEGF8--CYP2B7P
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[33000] -fusion SPANNING read extraction for scaff: NRP1--FAM107B
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[50000] -fusion SPANNING read extraction for scaff: PGAM5--XYLT2
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[16000] -fusion SPANNING read extraction for scaff: RB1--AP005901.1
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[53000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A
[1000]
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[10000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[63000] -fusion SPANNING read extraction for scaff: TMCO4--CSE1L
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[15000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[401000] -fusion SPANNING read extraction for scaff: UTRN--PHACTR2
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 55,
'lacks exon overlap' => 98735
};
EM: Starting log likelihood: -22470.843862
EM: Round [1] log likelihood: -22467.312547
EM: Round [2] log likelihood: -22467.309561
EM: Round [3] log likelihood: -22467.309557
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.kpybOx6aMA/659_dES-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.kpybOx6aMA/659_dES-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.kpybOx6aMA/659_dES-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.kpybOx6aMA/659_dES-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.kpybOx6aMA/659_dES-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.kpybOx6aMA/659_dES-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.kpybOx6aMA/659_dES-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.kpybOx6aMA/fi_workdir/659_dES-T1-TRNA-1_B23WHTKLT4_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.kpybOx6aMA/fi_workdir/659_dES-T1-TRNA-1_B23WHTKLT4_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.kpybOx6aMA/fi_workdir/659_dES-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.kpybOx6aMA/659_dES-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.kpybOx6aMA/659_dES-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -22113.468259
EM: Round [1] log likelihood: -22112.275080
EM: Round [2] log likelihood: -22112.274966
EM: Round [3] log likelihood: -22112.274966
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.kpybOx6aMA/659_dES-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz: 296114488
Warning - not locating file: /tmp/nxf.kpybOx6aMA/659_dES-T1-TRNA-1_B23WHTKLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000183604.14]
WARNING, no entry stored in dbm for [ENSG00000183604.14]
WARNING, no entry stored in dbm for [ENSG00000183604.14]
WARNING, no entry stored in dbm for [ENSG00000236438.7]
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 [ENSG00000256612.7]
WARNING, no entry stored in dbm for [ENSG00000256612.7]
WARNING, no entry stored in dbm for [ENSG00000256612.7]
WARNING, no entry stored in dbm for [ENSG00000223698.3]
WARNING, no entry stored in dbm for [ENSG00000275121.1]
WARNING, no entry stored in dbm for [ENSG00000277125.1]
WARNING, no entry stored in dbm for [ENSG00000261442.1]
WARNING, no entry stored in dbm for [ENSG00000261963.3]
ls: cannot access 'IGV_inputs': No such file or directory