Done.
-parsing GTF file: /tmp/nxf.6WdINnBGtE/659_cRa-T1-TRNA-1_B23WHTKLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.6WdINnBGtE/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.6WdINnBGtE/659_cRa-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.6WdINnBGtE/659_cRa-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.6WdINnBGtE/fi_workdir/659_cRa-T1-TRNA-1_B23WHTKLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.6WdINnBGtE/fi_workdir/659_cRa-T1-TRNA-1_B23WHTKLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_cRa-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_cRa-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam
11:27:54 : INFO : Done.
-parsing GTF file: /tmp/nxf.6WdINnBGtE/fi_workdir/659_cRa-T1-TRNA-1_B23WHTKLT4_1.gtf
-parsing /tmp/nxf.6WdINnBGtE/fi_workdir/659_cRa-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
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[850000] -done parsing /tmp/nxf.6WdINnBGtE/fi_workdir/659_cRa-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'small anchor length' => 1,
'num genes matched < 2' => 21,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 100,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 40,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 275,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 18,
'low complexity anchor region' => 1,
' ** passed ** ' => 1267,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 51,
'per_id < 96' => 3651,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 54,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 10,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 108,
'excessive soft clipping' => 5376,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 6
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.6WdINnBGtE/fi_workdir/659_cRa-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[77000] -fusion SPANNING read extraction for scaff: AFF1--C4orf36
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[20000] -fusion SPANNING read extraction for scaff: C2CD5--PTPRD
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[185000] -fusion SPANNING read extraction for scaff: GLI1--SCNN1A
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[285000] -fusion SPANNING read extraction for scaff: GOLGA4--FLNB
[1000]
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[14000] -fusion SPANNING read extraction for scaff: NLRP2--ADAMTS13
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[39000] -fusion SPANNING read extraction for scaff: NPHP3--ACAD11
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[21000] -fusion SPANNING read extraction for scaff: PARN--AC104042.1
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[6000] -fusion SPANNING read extraction for scaff: SH3BGRL2--BX890604.1
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[23000] -fusion SPANNING read extraction for scaff: TLK2--LINC01347
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[15000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[13000] -fusion SPANNING read extraction for scaff: UBE2N--MRPL42
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 5348
};
EM: Starting log likelihood: -1512.304344
EM: Round [1] log likelihood: -1507.697787
EM: Round [2] log likelihood: -1504.841191
EM: Round [3] log likelihood: -1502.914871
EM: Round [4] log likelihood: -1501.555698
EM: Round [5] log likelihood: -1500.570487
EM: Round [6] log likelihood: -1499.844185
EM: Round [7] log likelihood: -1499.302737
EM: Round [8] log likelihood: -1498.895942
EM: Round [9] log likelihood: -1498.588573
EM: Round [10] log likelihood: -1498.355335
EM: Round [11] log likelihood: -1498.177762
EM: Round [12] log likelihood: -1498.042218
EM: Round [13] log likelihood: -1497.938541
EM: Round [14] log likelihood: -1497.859107
EM: Round [15] log likelihood: -1497.798167
EM: Round [16] log likelihood: -1497.751363
EM: Round [17] log likelihood: -1497.715385
EM: Round [18] log likelihood: -1497.687709
EM: Round [19] log likelihood: -1497.666406
EM: Round [20] log likelihood: -1497.650000
EM: Round [21] log likelihood: -1497.637361
EM: Round [22] log likelihood: -1497.627621
EM: Round [23] log likelihood: -1497.620113
EM: Round [24] log likelihood: -1497.614323
EM: Round [25] log likelihood: -1497.609858
EM: Round [26] log likelihood: -1497.606415
EM: Round [27] log likelihood: -1497.603758
EM: Round [28] log likelihood: -1497.601708
EM: Round [29] log likelihood: -1497.600127
EM: Round [30] log likelihood: -1497.598906
EM: Round [31] log likelihood: -1497.597964
EM: Round [32] log likelihood: -1497.597237
EM: Round [33] log likelihood: -1497.596676
EM: Round [34] log likelihood: -1497.596244
EM: Round [35] log likelihood: -1497.595909
EM: Round [36] log likelihood: -1497.595651
EM: Round [37] log likelihood: -1497.595452
EM: Round [38] log likelihood: -1497.595299
EM: Round [39] log likelihood: -1497.595180
EM: Round [40] log likelihood: -1497.595088
EM: Stopping iterations at round 40 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.6WdINnBGtE/659_cRa-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.6WdINnBGtE/659_cRa-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.6WdINnBGtE/659_cRa-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.6WdINnBGtE/659_cRa-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.6WdINnBGtE/659_cRa-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.6WdINnBGtE/659_cRa-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.6WdINnBGtE/659_cRa-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.6WdINnBGtE/fi_workdir/659_cRa-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.6WdINnBGtE/fi_workdir/659_cRa-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.6WdINnBGtE/fi_workdir/659_cRa-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.6WdINnBGtE/659_cRa-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.6WdINnBGtE/659_cRa-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -1476.811062
EM: Round [1] log likelihood: -1476.797879
EM: Round [2] log likelihood: -1476.797797
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.6WdINnBGtE/659_cRa-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz: 295675936
Warning - not locating file: /tmp/nxf.6WdINnBGtE/659_cRa-T1-TRNA-1_B23WHTKLT4_1.gmap_trinity_GG.fusions.gff3.bed
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 [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000285756.2]
ls: cannot access 'IGV_inputs': No such file or directory