Done.
-parsing GTF file: /tmp/nxf.3Kz68mZ8J3/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.3Kz68mZ8J3/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.3Kz68mZ8J3/aih-tih-sc-fe8311-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.3Kz68mZ8J3/aih-tih-sc-fe8311-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.3Kz68mZ8J3/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.3Kz68mZ8J3/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
22:25:55 : INFO : Done.
-parsing GTF file: /tmp/nxf.3Kz68mZ8J3/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.3Kz68mZ8J3/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
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[720000] -done parsing /tmp/nxf.3Kz68mZ8J3/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'seq-similar region overlap' => 110,
' ** passed ** ' => 8761,
'per_id < 96' => 2384,
'low complexity anchor region' => 10,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 2,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 1,
'num_hits: 10 != num_counted_on_fusion_contigs 9 ' => 18,
'num genes matched < 2' => 15,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 18,
'excessive soft clipping' => 3477,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 8,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 8,
'small anchor length' => 46,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 21
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.3Kz68mZ8J3/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[75000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[27000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 33639,
'lacks exon overlap' => 2645
};
EM: Starting log likelihood: -3555.675454
EM: Round [1] log likelihood: -3554.541146
EM: Round [2] log likelihood: -3553.766733
EM: Round [3] log likelihood: -3553.098799
EM: Round [4] log likelihood: -3552.516180
EM: Round [5] log likelihood: -3552.002671
EM: Round [6] log likelihood: -3551.545651
EM: Round [7] log likelihood: -3551.135175
EM: Round [8] log likelihood: -3550.763340
EM: Round [9] log likelihood: -3550.423811
EM: Round [10] log likelihood: -3550.111487
EM: Round [11] log likelihood: -3549.822232
EM: Round [12] log likelihood: -3549.552682
EM: Round [13] log likelihood: -3549.300090
EM: Round [14] log likelihood: -3549.062203
EM: Round [15] log likelihood: -3548.837168
EM: Round [16] log likelihood: -3548.623457
EM: Round [17] log likelihood: -3548.419806
EM: Round [18] log likelihood: -3548.225164
EM: Round [19] log likelihood: -3548.038658
EM: Round [20] log likelihood: -3547.859557
EM: Round [21] log likelihood: -3547.687248
EM: Round [22] log likelihood: -3547.521215
EM: Round [23] log likelihood: -3547.361018
EM: Round [24] log likelihood: -3547.206286
EM: Round [25] log likelihood: -3547.056699
EM: Round [26] log likelihood: -3546.911979
EM: Round [27] log likelihood: -3546.771887
EM: Round [28] log likelihood: -3546.636211
EM: Round [29] log likelihood: -3546.504765
EM: Round [30] log likelihood: -3546.377382
EM: Round [31] log likelihood: -3546.253910
EM: Round [32] log likelihood: -3546.134213
EM: Round [33] log likelihood: -3546.018164
EM: Round [34] log likelihood: -3545.905647
EM: Round [35] log likelihood: -3545.796552
EM: Round [36] log likelihood: -3545.690775
EM: Round [37] log likelihood: -3545.588219
EM: Round [38] log likelihood: -3545.488791
EM: Round [39] log likelihood: -3545.392401
EM: Round [40] log likelihood: -3545.298963
EM: Round [41] log likelihood: -3545.208394
EM: Round [42] log likelihood: -3545.120612
EM: Round [43] log likelihood: -3545.035539
EM: Round [44] log likelihood: -3544.953099
EM: Round [45] log likelihood: -3544.873216
EM: Round [46] log likelihood: -3544.795818
EM: Round [47] log likelihood: -3544.720834
EM: Round [48] log likelihood: -3544.648194
EM: Round [49] log likelihood: -3544.577829
EM: Round [50] log likelihood: -3544.509674
EM: Round [51] log likelihood: -3544.443663
EM: Round [52] log likelihood: -3544.379732
EM: Round [53] log likelihood: -3544.317819
EM: Round [54] log likelihood: -3544.257863
EM: Round [55] log likelihood: -3544.199804
EM: Round [56] log likelihood: -3544.143586
EM: Round [57] log likelihood: -3544.089150
EM: Round [58] log likelihood: -3544.036442
EM: Round [59] log likelihood: -3543.985407
EM: Round [60] log likelihood: -3543.935994
EM: Round [61] log likelihood: -3543.888151
EM: Round [62] log likelihood: -3543.841828
EM: Round [63] log likelihood: -3543.796976
EM: Round [64] log likelihood: -3543.753549
EM: Round [65] log likelihood: -3543.711500
EM: Round [66] log likelihood: -3543.670785
EM: Round [67] log likelihood: -3543.631360
EM: Round [68] log likelihood: -3543.593184
EM: Round [69] log likelihood: -3543.556215
EM: Round [70] log likelihood: -3543.520414
EM: Round [71] log likelihood: -3543.485742
EM: Round [72] log likelihood: -3543.452162
EM: Round [73] log likelihood: -3543.419637
EM: Round [74] log likelihood: -3543.388133
EM: Round [75] log likelihood: -3543.357616
EM: Round [76] log likelihood: -3543.328052
EM: Round [77] log likelihood: -3543.299409
EM: Round [78] log likelihood: -3543.271658
EM: Round [79] log likelihood: -3543.244767
EM: Round [80] log likelihood: -3543.218707
EM: Round [81] log likelihood: -3543.193452
EM: Round [82] log likelihood: -3543.168973
EM: Round [83] log likelihood: -3543.145245
EM: Round [84] log likelihood: -3543.122241
EM: Round [85] log likelihood: -3543.099939
EM: Round [86] log likelihood: -3543.078313
EM: Round [87] log likelihood: -3543.057341
EM: Round [88] log likelihood: -3543.037001
EM: Round [89] log likelihood: -3543.017271
EM: Round [90] log likelihood: -3542.998131
EM: Round [91] log likelihood: -3542.979561
EM: Round [92] log likelihood: -3542.961541
EM: Round [93] log likelihood: -3542.944054
EM: Round [94] log likelihood: -3542.927080
EM: Round [95] log likelihood: -3542.910603
EM: Round [96] log likelihood: -3542.894605
EM: Round [97] log likelihood: -3542.879071
EM: Round [98] log likelihood: -3542.863985
EM: Round [99] log likelihood: -3542.849332
EM: Round [100] log likelihood: -3542.835097
EM: Round [101] log likelihood: -3542.821266
EM: Round [102] log likelihood: -3542.807826
EM: Round [103] log likelihood: -3542.794764
EM: Round [104] log likelihood: -3542.782067
EM: Round [105] log likelihood: -3542.769722
EM: Round [106] log likelihood: -3542.757718
EM: Round [107] log likelihood: -3542.746044
EM: Round [108] log likelihood: -3542.734688
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EM: Round [111] log likelihood: -3542.702430
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EM: Round [120] log likelihood: -3542.619775
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EM: Round [128] log likelihood: -3542.560619
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EM: Round [141] log likelihood: -3542.485387
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EM: Round [154] log likelihood: -3542.428474
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EM: Round [206] log likelihood: -3542.294997
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EM: Round [209] log likelihood: -3542.289926
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EM: Round [211] log likelihood: -3542.286649
EM: Round [212] log likelihood: -3542.285040
EM: Round [213] log likelihood: -3542.283451
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EM: Round [216] log likelihood: -3542.278795
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EM: Round [468] log likelihood: -3542.137738
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EM: Round [471] log likelihood: -3542.137297
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EM: Round [480] log likelihood: -3542.136039
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EM: Round [482] log likelihood: -3542.135773
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EM: Round [488] log likelihood: -3542.134999
EM: Round [489] log likelihood: -3542.134874
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EM: Round [491] log likelihood: -3542.134627
EM: Round [492] log likelihood: -3542.134505
EM: Round [493] log likelihood: -3542.134384
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EM: Round [495] log likelihood: -3542.134146
EM: Round [496] log likelihood: -3542.134028
EM: Round [497] log likelihood: -3542.133911
EM: Round [498] log likelihood: -3542.133795
EM: Round [499] log likelihood: -3542.133680
EM: Round [500] log likelihood: -3542.133566
EM: Round [501] log likelihood: -3542.133453
EM: Round [502] log likelihood: -3542.133341
EM: Round [503] log likelihood: -3542.133230
EM: Round [504] log likelihood: -3542.133120
EM: Round [505] log likelihood: -3542.133011
EM: Round [506] log likelihood: -3542.132902
EM: Round [507] log likelihood: -3542.132795
EM: Round [508] log likelihood: -3542.132688
EM: Round [509] log likelihood: -3542.132583
EM: Round [510] log likelihood: -3542.132478
EM: Round [511] log likelihood: -3542.132374
EM: Round [512] log likelihood: -3542.132271
EM: Round [513] log likelihood: -3542.132169
EM: Round [514] log likelihood: -3542.132068
EM: Round [515] log likelihood: -3542.131968
EM: Round [516] log likelihood: -3542.131868
EM: Stopping iterations at round 516 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.3Kz68mZ8J3/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.3Kz68mZ8J3/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.3Kz68mZ8J3/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.3Kz68mZ8J3/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.3Kz68mZ8J3/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.3Kz68mZ8J3/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.3Kz68mZ8J3/aih-tih-sc-fe8311-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.3Kz68mZ8J3/fi_workdir/aih-tih-sc-fe8311-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.3Kz68mZ8J3/fi_workdir/aih-tih-sc-fe8311-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.3Kz68mZ8J3/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.3Kz68mZ8J3/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.3Kz68mZ8J3/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2340.175499
EM: Round [1] log likelihood: -2339.953691
EM: Round [2] log likelihood: -2339.953628
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.3Kz68mZ8J3/aih-tih-sc-fe8311-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296655419
Warning - not locating file: /tmp/nxf.3Kz68mZ8J3/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000280136.2]
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 [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
ls: cannot access 'IGV_inputs': No such file or directory