Done.
-parsing GTF file: /tmp/nxf.W9ht7ITNWX/659_bGc-T1-TRNA-1_A23MVY2LT4_2.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.W9ht7ITNWX/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.W9ht7ITNWX/659_bGc-T1-TRNA-1_A23MVY2LT4_2_1.fastp.fastq.gz /tmp/nxf.W9ht7ITNWX/659_bGc-T1-TRNA-1_A23MVY2LT4_2_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.W9ht7ITNWX/fi_workdir/659_bGc-T1-TRNA-1_A23MVY2LT4_2.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.W9ht7ITNWX/fi_workdir/659_bGc-T1-TRNA-1_A23MVY2LT4_2.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_bGc-T1-TRNA-1_A23MVY2LT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_bGc-T1-TRNA-1_A23MVY2LT4_2.star.sortedByCoord.out.bam
11:16:35 : INFO : Done.
-parsing GTF file: /tmp/nxf.W9ht7ITNWX/fi_workdir/659_bGc-T1-TRNA-1_A23MVY2LT4_2.gtf
-parsing /tmp/nxf.W9ht7ITNWX/fi_workdir/659_bGc-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam
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[720000] -done parsing /tmp/nxf.W9ht7ITNWX/fi_workdir/659_bGc-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 5,
'excessive soft clipping' => 8671,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 35,
'seq-similar region overlap' => 381,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 8,
'exons hit < 2' => 1,
'per_id < 96' => 4849,
'low complexity anchor region' => 9,
'num genes matched < 2' => 10,
' ** passed ** ' => 4256,
'small anchor length' => 188,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 141
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.W9ht7ITNWX/fi_workdir/659_bGc-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[254000] -fusion SPANNING read extraction for scaff: KIF5B--RET
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[36000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
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[36000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1
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[39000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
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[35000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2
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[35000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1
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[37000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13
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[139000] -fusion SPANNING read extraction for scaff: PRSS27--TPSB2
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[62000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[21000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[18000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 1080,
'seq similar region alignment' => 25210
};
EM: Starting log likelihood: -2864.782948
EM: Round [1] log likelihood: -2864.362266
EM: Round [2] log likelihood: -2863.992810
EM: Round [3] log likelihood: -2863.666861
EM: Round [4] log likelihood: -2863.378236
EM: Round [5] log likelihood: -2863.121853
EM: Round [6] log likelihood: -2862.893484
EM: Round [7] log likelihood: -2862.689584
EM: Round [8] log likelihood: -2862.507150
EM: Round [9] log likelihood: -2862.343623
EM: Round [10] log likelihood: -2862.196806
EM: Round [11] log likelihood: -2862.064803
EM: Round [12] log likelihood: -2861.945967
EM: Round [13] log likelihood: -2861.838864
EM: Round [14] log likelihood: -2861.742238
EM: Round [15] log likelihood: -2861.654986
EM: Round [16] log likelihood: -2861.576135
EM: Round [17] log likelihood: -2861.504823
EM: Round [18] log likelihood: -2861.440289
EM: Round [19] log likelihood: -2861.381854
EM: Round [20] log likelihood: -2861.328913
EM: Round [21] log likelihood: -2861.280927
EM: Round [22] log likelihood: -2861.237415
EM: Round [23] log likelihood: -2861.197942
EM: Round [24] log likelihood: -2861.162123
EM: Round [25] log likelihood: -2861.129608
EM: Round [26] log likelihood: -2861.100084
EM: Round [27] log likelihood: -2861.073270
EM: Round [28] log likelihood: -2861.048910
EM: Round [29] log likelihood: -2861.026775
EM: Round [30] log likelihood: -2861.006659
EM: Round [31] log likelihood: -2860.988374
EM: Round [32] log likelihood: -2860.971750
EM: Round [33] log likelihood: -2860.956635
EM: Round [34] log likelihood: -2860.942889
EM: Round [35] log likelihood: -2860.930388
EM: Round [36] log likelihood: -2860.919017
EM: Round [37] log likelihood: -2860.908674
EM: Round [38] log likelihood: -2860.899263
EM: Round [39] log likelihood: -2860.890702
EM: Round [40] log likelihood: -2860.882912
EM: Round [41] log likelihood: -2860.875823
EM: Round [42] log likelihood: -2860.869372
EM: Round [43] log likelihood: -2860.863501
EM: Round [44] log likelihood: -2860.858159
EM: Round [45] log likelihood: -2860.853296
EM: Round [46] log likelihood: -2860.848870
EM: Round [47] log likelihood: -2860.844841
EM: Round [48] log likelihood: -2860.841174
EM: Round [49] log likelihood: -2860.837836
EM: Round [50] log likelihood: -2860.834797
EM: Round [51] log likelihood: -2860.832031
EM: Round [52] log likelihood: -2860.829513
EM: Round [53] log likelihood: -2860.827220
EM: Round [54] log likelihood: -2860.825133
EM: Round [55] log likelihood: -2860.823233
EM: Round [56] log likelihood: -2860.821503
EM: Round [57] log likelihood: -2860.819928
EM: Round [58] log likelihood: -2860.818495
EM: Round [59] log likelihood: -2860.817189
EM: Round [60] log likelihood: -2860.816000
EM: Round [61] log likelihood: -2860.814918
EM: Round [62] log likelihood: -2860.813933
EM: Round [63] log likelihood: -2860.813036
EM: Round [64] log likelihood: -2860.812219
EM: Round [65] log likelihood: -2860.811475
EM: Round [66] log likelihood: -2860.810798
EM: Round [67] log likelihood: -2860.810182
EM: Round [68] log likelihood: -2860.809620
EM: Round [69] log likelihood: -2860.809109
EM: Round [70] log likelihood: -2860.808644
EM: Round [71] log likelihood: -2860.808220
EM: Round [72] log likelihood: -2860.807834
EM: Round [73] log likelihood: -2860.807483
EM: Round [74] log likelihood: -2860.807163
EM: Round [75] log likelihood: -2860.806871
EM: Round [76] log likelihood: -2860.806606
EM: Round [77] log likelihood: -2860.806365
EM: Round [78] log likelihood: -2860.806145
EM: Round [79] log likelihood: -2860.805944
EM: Round [80] log likelihood: -2860.805762
EM: Round [81] log likelihood: -2860.805596
EM: Round [82] log likelihood: -2860.805445
EM: Round [83] log likelihood: -2860.805307
EM: Round [84] log likelihood: -2860.805182
EM: Round [85] log likelihood: -2860.805068
EM: Round [86] log likelihood: -2860.804964
EM: Round [87] log likelihood: -2860.804869
EM: Stopping iterations at round 87 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.W9ht7ITNWX/659_bGc-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam into /tmp/nxf.W9ht7ITNWX/659_bGc-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.read_coords
CMD: touch /tmp/nxf.W9ht7ITNWX/659_bGc-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.W9ht7ITNWX/659_bGc-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.read_coords > /tmp/nxf.W9ht7ITNWX/659_bGc-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.W9ht7ITNWX/659_bGc-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.frag_coords > /tmp/nxf.W9ht7ITNWX/659_bGc-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.W9ht7ITNWX/fi_workdir/659_bGc-T1-TRNA-1_A23MVY2LT4_2.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.W9ht7ITNWX/fi_workdir/659_bGc-T1-TRNA-1_A23MVY2LT4_2.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.W9ht7ITNWX/fi_workdir/659_bGc-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.W9ht7ITNWX/659_bGc-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.W9ht7ITNWX/659_bGc-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2002.098078
EM: Round [1] log likelihood: -2002.097964
EM: Round [2] log likelihood: -2002.097962
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.W9ht7ITNWX/659_bGc-T1-TRNA-1_A23MVY2LT4_2_1.fastp.fastq.gz: 295361732
Warning - not locating file: /tmp/nxf.W9ht7ITNWX/659_bGc-T1-TRNA-1_A23MVY2LT4_2.gmap_trinity_GG.fusions.gff3.bed
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 [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000225393.1]
WARNING, no entry stored in dbm for [ENSG00000225393.1]
ls: cannot access 'IGV_inputs': No such file or directory