.command.err - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (aih-tih-sc-a97ce1-R1_A23YTGFLT4_1)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/99d0b92f6047b9fa925cf00bf907af/.command.err
Size: 18.4 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (aih-tih-sc-a97ce1-R1_A23YTGFLT4_1)
Attempt
Content

Done.
-parsing GTF file: /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.dIpS1I9D8d/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.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
21:37:50 : INFO : Done.
-parsing GTF file: /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

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[90000]   -done parsing /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 11,
          'per_id < 96' => 364,
          ' ** passed ** ' => 1042,
          'excessive soft clipping' => 913,
          'seq-similar region overlap' => 37,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 30,
          'low complexity anchor region' => 1
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[12000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1

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[11000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2

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[12000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13

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[9000]   -fusion SPANNING read extraction for scaff: PRCP--RAB30

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[35000]   -fusion SPANNING read extraction for scaff: TLK2--AL669831.1

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[14000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 10336,
          'lacks exon overlap' => 644
        };
EM: Starting log likelihood: -506.204039
EM: Round [1] log likelihood: -506.188481
EM: Round [2] log likelihood: -506.173288
EM: Round [3] log likelihood: -506.158451
EM: Round [4] log likelihood: -506.143958
EM: Round [5] log likelihood: -506.129798
EM: Round [6] log likelihood: -506.115962
EM: Round [7] log likelihood: -506.102441
EM: Round [8] log likelihood: -506.089224
EM: Round [9] log likelihood: -506.076303
EM: Round [10] log likelihood: -506.063671
EM: Round [11] log likelihood: -506.051317
EM: Round [12] log likelihood: -506.039236
EM: Round [13] log likelihood: -506.027418
EM: Round [14] log likelihood: -506.015858
EM: Round [15] log likelihood: -506.004547
EM: Round [16] log likelihood: -505.993479
EM: Round [17] log likelihood: -505.982648
EM: Round [18] log likelihood: -505.972047
EM: Round [19] log likelihood: -505.961670
EM: Round [20] log likelihood: -505.951512
EM: Round [21] log likelihood: -505.941566
EM: Round [22] log likelihood: -505.931827
EM: Round [23] log likelihood: -505.922290
EM: Round [24] log likelihood: -505.912950
EM: Round [25] log likelihood: -505.903802
EM: Round [26] log likelihood: -505.894841
EM: Round [27] log likelihood: -505.886062
EM: Round [28] log likelihood: -505.877461
EM: Round [29] log likelihood: -505.869034
EM: Round [30] log likelihood: -505.860776
EM: Round [31] log likelihood: -505.852684
EM: Round [32] log likelihood: -505.844752
EM: Round [33] log likelihood: -505.836979
EM: Round [34] log likelihood: -505.829358
EM: Round [35] log likelihood: -505.821889
EM: Round [36] log likelihood: -505.814565
EM: Round [37] log likelihood: -505.807385
EM: Round [38] log likelihood: -505.800345
EM: Round [39] log likelihood: -505.793442
EM: Round [40] log likelihood: -505.786672
EM: Round [41] log likelihood: -505.780033
EM: Round [42] log likelihood: -505.773522
EM: Round [43] log likelihood: -505.767135
EM: Round [44] log likelihood: -505.760871
EM: Round [45] log likelihood: -505.754725
EM: Round [46] log likelihood: -505.748697
EM: Round [47] log likelihood: -505.742782
EM: Round [48] log likelihood: -505.736980
EM: Round [49] log likelihood: -505.731286
EM: Round [50] log likelihood: -505.725699
EM: Round [51] log likelihood: -505.720217
EM: Round [52] log likelihood: -505.714838
EM: Round [53] log likelihood: -505.709558
EM: Round [54] log likelihood: -505.704377
EM: Round [55] log likelihood: -505.699291
EM: Round [56] log likelihood: -505.694300
EM: Round [57] log likelihood: -505.689400
EM: Round [58] log likelihood: -505.684590
EM: Round [59] log likelihood: -505.679869
EM: Round [60] log likelihood: -505.675234
EM: Round [61] log likelihood: -505.670684
EM: Round [62] log likelihood: -505.666217
EM: Round [63] log likelihood: -505.661830
EM: Round [64] log likelihood: -505.657524
EM: Round [65] log likelihood: -505.653295
EM: Round [66] log likelihood: -505.649143
EM: Round [67] log likelihood: -505.645065
EM: Round [68] log likelihood: -505.641061
EM: Round [69] log likelihood: -505.637129
EM: Round [70] log likelihood: -505.633267
EM: Round [71] log likelihood: -505.629474
EM: Round [72] log likelihood: -505.625749
EM: Round [73] log likelihood: -505.622090
EM: Round [74] log likelihood: -505.618497
EM: Round [75] log likelihood: -505.614967
EM: Round [76] log likelihood: -505.611499
EM: Round [77] log likelihood: -505.608093
EM: Round [78] log likelihood: -505.604748
EM: Round [79] log likelihood: -505.601461
EM: Round [80] log likelihood: -505.598232
EM: Round [81] log likelihood: -505.595059
EM: Round [82] log likelihood: -505.591943
EM: Round [83] log likelihood: -505.588881
EM: Round [84] log likelihood: -505.585872
EM: Round [85] log likelihood: -505.582917
EM: Round [86] log likelihood: -505.580012
EM: Round [87] log likelihood: -505.577158
EM: Round [88] log likelihood: -505.574354
EM: Round [89] log likelihood: -505.571599
EM: Round [90] log likelihood: -505.568891
EM: Round [91] log likelihood: -505.566230
EM: Round [92] log likelihood: -505.563616
EM: Round [93] log likelihood: -505.561046
EM: Round [94] log likelihood: -505.558521
EM: Round [95] log likelihood: -505.556039
EM: Round [96] log likelihood: -505.553600
EM: Round [97] log likelihood: -505.551203
EM: Round [98] log likelihood: -505.548847
EM: Round [99] log likelihood: -505.546532
EM: Round [100] log likelihood: -505.544256
EM: Round [101] log likelihood: -505.542019
EM: Round [102] log likelihood: -505.539820
EM: Round [103] log likelihood: -505.537659
EM: Round [104] log likelihood: -505.535535
EM: Round [105] log likelihood: -505.533447
EM: Round [106] log likelihood: -505.531394
EM: Round [107] log likelihood: -505.529376
EM: Round [108] log likelihood: -505.527393
EM: Round [109] log likelihood: -505.525443
EM: Round [110] log likelihood: -505.523526
EM: Round [111] log likelihood: -505.521642
EM: Round [112] log likelihood: -505.519790
EM: Round [113] log likelihood: -505.517969
EM: Round [114] log likelihood: -505.516178
EM: Round [115] log likelihood: -505.514418
EM: Round [116] log likelihood: -505.512688
EM: Round [117] log likelihood: -505.510987
EM: Round [118] log likelihood: -505.509314
EM: Round [119] log likelihood: -505.507670
EM: Round [120] log likelihood: -505.506053
EM: Round [121] log likelihood: -505.504463
EM: Round [122] log likelihood: -505.502900
EM: Round [123] log likelihood: -505.501363
EM: Round [124] log likelihood: -505.499852
EM: Round [125] log likelihood: -505.498366
EM: Round [126] log likelihood: -505.496905
EM: Round [127] log likelihood: -505.495468
EM: Round [128] log likelihood: -505.494056
EM: Round [129] log likelihood: -505.492667
EM: Round [130] log likelihood: -505.491301
EM: Round [131] log likelihood: -505.489958
EM: Round [132] log likelihood: -505.488637
EM: Round [133] log likelihood: -505.487338
EM: Round [134] log likelihood: -505.486061
EM: Round [135] log likelihood: -505.484805
EM: Round [136] log likelihood: -505.483570
EM: Round [137] log likelihood: -505.482356
EM: Round [138] log likelihood: -505.481161
EM: Round [139] log likelihood: -505.479987
EM: Round [140] log likelihood: -505.478832
EM: Round [141] log likelihood: -505.477696
EM: Round [142] log likelihood: -505.476579
EM: Round [143] log likelihood: -505.475480
EM: Round [144] log likelihood: -505.474399
EM: Round [145] log likelihood: -505.473337
EM: Round [146] log likelihood: -505.472292
EM: Round [147] log likelihood: -505.471264
EM: Round [148] log likelihood: -505.470253
EM: Round [149] log likelihood: -505.469259
EM: Round [150] log likelihood: -505.468281
EM: Round [151] log likelihood: -505.467319
EM: Round [152] log likelihood: -505.466373
EM: Round [153] log likelihood: -505.465443
EM: Round [154] log likelihood: -505.464528
EM: Round [155] log likelihood: -505.463628
EM: Round [156] log likelihood: -505.462743
EM: Round [157] log likelihood: -505.461872
EM: Round [158] log likelihood: -505.461016
EM: Round [159] log likelihood: -505.460174
EM: Round [160] log likelihood: -505.459345
EM: Round [161] log likelihood: -505.458530
EM: Round [162] log likelihood: -505.457729
EM: Round [163] log likelihood: -505.456941
EM: Round [164] log likelihood: -505.456165
EM: Round [165] log likelihood: -505.455402
EM: Round [166] log likelihood: -505.454652
EM: Round [167] log likelihood: -505.453914
EM: Round [168] log likelihood: -505.453188
EM: Round [169] log likelihood: -505.452474
EM: Round [170] log likelihood: -505.451772
EM: Round [171] log likelihood: -505.451081
EM: Round [172] log likelihood: -505.450402
EM: Round [173] log likelihood: -505.449733
EM: Round [174] log likelihood: -505.449075
EM: Round [175] log likelihood: -505.448429
EM: Round [176] log likelihood: -505.447792
EM: Round [177] log likelihood: -505.447166
EM: Round [178] log likelihood: -505.446551
EM: Round [179] log likelihood: -505.445945
EM: Round [180] log likelihood: -505.445349
EM: Round [181] log likelihood: -505.444763
EM: Round [182] log likelihood: -505.444187
EM: Round [183] log likelihood: -505.443620
EM: Round [184] log likelihood: -505.443062
EM: Round [185] log likelihood: -505.442513
EM: Round [186] log likelihood: -505.441973
EM: Round [187] log likelihood: -505.441442
EM: Round [188] log likelihood: -505.440919
EM: Round [189] log likelihood: -505.440405
EM: Round [190] log likelihood: -505.439900
EM: Round [191] log likelihood: -505.439402
EM: Round [192] log likelihood: -505.438913
EM: Round [193] log likelihood: -505.438431
EM: Round [194] log likelihood: -505.437958
EM: Round [195] log likelihood: -505.437492
EM: Round [196] log likelihood: -505.437033
EM: Round [197] log likelihood: -505.436583
EM: Round [198] log likelihood: -505.436139
EM: Round [199] log likelihood: -505.435703
EM: Round [200] log likelihood: -505.435273
EM: Round [201] log likelihood: -505.434851
EM: Round [202] log likelihood: -505.434435
EM: Round [203] log likelihood: -505.434027
EM: Round [204] log likelihood: -505.433624
EM: Round [205] log likelihood: -505.433229
EM: Round [206] log likelihood: -505.432839
EM: Round [207] log likelihood: -505.432457
EM: Round [208] log likelihood: -505.432080
EM: Round [209] log likelihood: -505.431709
EM: Round [210] log likelihood: -505.431344
EM: Round [211] log likelihood: -505.430986
EM: Round [212] log likelihood: -505.430633
EM: Round [213] log likelihood: -505.430286
EM: Round [214] log likelihood: -505.429944
EM: Round [215] log likelihood: -505.429608
EM: Round [216] log likelihood: -505.429277
EM: Round [217] log likelihood: -505.428952
EM: Round [218] log likelihood: -505.428632
EM: Round [219] log likelihood: -505.428317
EM: Round [220] log likelihood: -505.428007
EM: Round [221] log likelihood: -505.427702
EM: Round [222] log likelihood: -505.427402
EM: Round [223] log likelihood: -505.427107
EM: Round [224] log likelihood: -505.426817
EM: Round [225] log likelihood: -505.426531
EM: Round [226] log likelihood: -505.426250
EM: Round [227] log likelihood: -505.425974
EM: Round [228] log likelihood: -505.425702
EM: Round [229] log likelihood: -505.425434
EM: Round [230] log likelihood: -505.425171
EM: Round [231] log likelihood: -505.424912
EM: Round [232] log likelihood: -505.424657
EM: Round [233] log likelihood: -505.424406
EM: Round [234] log likelihood: -505.424160
EM: Round [235] log likelihood: -505.423917
EM: Round [236] log likelihood: -505.423678
EM: Round [237] log likelihood: -505.423443
EM: Round [238] log likelihood: -505.423212
EM: Round [239] log likelihood: -505.422984
EM: Round [240] log likelihood: -505.422761
EM: Round [241] log likelihood: -505.422541
EM: Round [242] log likelihood: -505.422324
EM: Round [243] log likelihood: -505.422111
EM: Round [244] log likelihood: -505.421901
EM: Round [245] log likelihood: -505.421695
EM: Round [246] log likelihood: -505.421492
EM: Round [247] log likelihood: -505.421292
EM: Round [248] log likelihood: -505.421095
EM: Round [249] log likelihood: -505.420902
EM: Round [250] log likelihood: -505.420712
EM: Round [251] log likelihood: -505.420524
EM: Round [252] log likelihood: -505.420340
EM: Round [253] log likelihood: -505.420159
EM: Round [254] log likelihood: -505.419981
EM: Round [255] log likelihood: -505.419805
EM: Round [256] log likelihood: -505.419633
EM: Round [257] log likelihood: -505.419463
EM: Round [258] log likelihood: -505.419296
EM: Round [259] log likelihood: -505.419131
EM: Round [260] log likelihood: -505.418970
EM: Round [261] log likelihood: -505.418810
EM: Round [262] log likelihood: -505.418654
EM: Round [263] log likelihood: -505.418500
EM: Round [264] log likelihood: -505.418348
EM: Round [265] log likelihood: -505.418199
EM: Round [266] log likelihood: -505.418052
EM: Round [267] log likelihood: -505.417908
EM: Round [268] log likelihood: -505.417765
EM: Round [269] log likelihood: -505.417626
EM: Round [270] log likelihood: -505.417488
EM: Round [271] log likelihood: -505.417353
EM: Round [272] log likelihood: -505.417220
EM: Round [273] log likelihood: -505.417088
EM: Round [274] log likelihood: -505.416960
EM: Round [275] log likelihood: -505.416833
EM: Round [276] log likelihood: -505.416708
EM: Round [277] log likelihood: -505.416585
EM: Round [278] log likelihood: -505.416464
EM: Round [279] log likelihood: -505.416345
EM: Round [280] log likelihood: -505.416228
EM: Round [281] log likelihood: -505.416113
EM: Round [282] log likelihood: -505.416000
EM: Round [283] log likelihood: -505.415888
EM: Round [284] log likelihood: -505.415779
EM: Round [285] log likelihood: -505.415671
EM: Round [286] log likelihood: -505.415564
EM: Round [287] log likelihood: -505.415460
EM: Round [288] log likelihood: -505.415357
EM: Round [289] log likelihood: -505.415256
EM: Round [290] log likelihood: -505.415157
EM: Stopping iterations at round 290 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-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.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-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.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-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.dIpS1I9D8d/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -505.409045
EM: Round [1] log likelihood: -505.409045
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 216439276
Warning - not locating file: /tmp/nxf.dIpS1I9D8d/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000228327.3]
WARNING, no entry stored in dbm for [ENSG00000228327.3]
ls: cannot access 'IGV_inputs': No such file or directory