.command.err - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (aih-tih-sc-835699-R1_A23WJ53LT4_1)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/d10d7a7699fcb90a9da076ba265dd2/.command.err
Size: 15.0 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (aih-tih-sc-835699-R1_A23WJ53LT4_1)
Attempt
Content

Done.
-parsing GTF file: /tmp/nxf.YdUKGijqd9/aih-tih-sc-835699-R1_A23WJ53LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.YdUKGijqd9/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.YdUKGijqd9/aih-tih-sc-835699-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.YdUKGijqd9/aih-tih-sc-835699-R1_A23WJ53LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.YdUKGijqd9/fi_workdir/aih-tih-sc-835699-R1_A23WJ53LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.YdUKGijqd9/fi_workdir/aih-tih-sc-835699-R1_A23WJ53LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-835699-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-835699-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
11:27:49 : INFO : Done.
-parsing GTF file: /tmp/nxf.YdUKGijqd9/fi_workdir/aih-tih-sc-835699-R1_A23WJ53LT4_1.gtf
-parsing /tmp/nxf.YdUKGijqd9/fi_workdir/aih-tih-sc-835699-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam

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[260000]   -done parsing /tmp/nxf.YdUKGijqd9/fi_workdir/aih-tih-sc-835699-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'excessive soft clipping' => 2121,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 8,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 30,
          'exons hit < 2' => 2,
          'per_id < 96' => 1085,
          'small anchor length' => 1,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 9,
          ' ** passed ** ' => 1412,
          'seq-similar region overlap' => 90,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 4
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.YdUKGijqd9/fi_workdir/aih-tih-sc-835699-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[65000]   -fusion SPANNING read extraction for scaff: AD000091.1--TBC1D1

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[79000]   -fusion SPANNING read extraction for scaff: LINC02067--TBC1D1

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[9000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

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[9000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

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[6000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC1

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[6000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1

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[18000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 6927,
          'lacks exon overlap' => 9554
        };
EM: Starting log likelihood: -1396.411106
EM: Round [1] log likelihood: -1395.242346
EM: Round [2] log likelihood: -1395.106999
EM: Round [3] log likelihood: -1394.998615
EM: Round [4] log likelihood: -1394.899285
EM: Round [5] log likelihood: -1394.807872
EM: Round [6] log likelihood: -1394.723603
EM: Round [7] log likelihood: -1394.645805
EM: Round [8] log likelihood: -1394.573882
EM: Round [9] log likelihood: -1394.507306
EM: Round [10] log likelihood: -1394.445610
EM: Round [11] log likelihood: -1394.388375
EM: Round [12] log likelihood: -1394.335225
EM: Round [13] log likelihood: -1394.285824
EM: Round [14] log likelihood: -1394.239867
EM: Round [15] log likelihood: -1394.197080
EM: Round [16] log likelihood: -1394.157214
EM: Round [17] log likelihood: -1394.120044
EM: Round [18] log likelihood: -1394.085363
EM: Round [19] log likelihood: -1394.052985
EM: Round [20] log likelihood: -1394.022738
EM: Round [21] log likelihood: -1393.994465
EM: Round [22] log likelihood: -1393.968024
EM: Round [23] log likelihood: -1393.943283
EM: Round [24] log likelihood: -1393.920120
EM: Round [25] log likelihood: -1393.898424
EM: Round [26] log likelihood: -1393.878094
EM: Round [27] log likelihood: -1393.859033
EM: Round [28] log likelihood: -1393.841156
EM: Round [29] log likelihood: -1393.824381
EM: Round [30] log likelihood: -1393.808634
EM: Round [31] log likelihood: -1393.793846
EM: Round [32] log likelihood: -1393.779953
EM: Round [33] log likelihood: -1393.766896
EM: Round [34] log likelihood: -1393.754619
EM: Round [35] log likelihood: -1393.743073
EM: Round [36] log likelihood: -1393.732208
EM: Round [37] log likelihood: -1393.721982
EM: Round [38] log likelihood: -1393.712353
EM: Round [39] log likelihood: -1393.703283
EM: Round [40] log likelihood: -1393.694736
EM: Round [41] log likelihood: -1393.686681
EM: Round [42] log likelihood: -1393.679085
EM: Round [43] log likelihood: -1393.671920
EM: Round [44] log likelihood: -1393.665159
EM: Round [45] log likelihood: -1393.658778
EM: Round [46] log likelihood: -1393.652753
EM: Round [47] log likelihood: -1393.647062
EM: Round [48] log likelihood: -1393.641685
EM: Round [49] log likelihood: -1393.636602
EM: Round [50] log likelihood: -1393.631797
EM: Round [51] log likelihood: -1393.627252
EM: Round [52] log likelihood: -1393.622952
EM: Round [53] log likelihood: -1393.618883
EM: Round [54] log likelihood: -1393.615030
EM: Round [55] log likelihood: -1393.611382
EM: Round [56] log likelihood: -1393.607925
EM: Round [57] log likelihood: -1393.604649
EM: Round [58] log likelihood: -1393.601544
EM: Round [59] log likelihood: -1393.598599
EM: Round [60] log likelihood: -1393.595806
EM: Round [61] log likelihood: -1393.593156
EM: Round [62] log likelihood: -1393.590640
EM: Round [63] log likelihood: -1393.588251
EM: Round [64] log likelihood: -1393.585983
EM: Round [65] log likelihood: -1393.583827
EM: Round [66] log likelihood: -1393.581778
EM: Round [67] log likelihood: -1393.579831
EM: Round [68] log likelihood: -1393.577979
EM: Round [69] log likelihood: -1393.576217
EM: Round [70] log likelihood: -1393.574541
EM: Round [71] log likelihood: -1393.572945
EM: Round [72] log likelihood: -1393.571426
EM: Round [73] log likelihood: -1393.569979
EM: Round [74] log likelihood: -1393.568600
EM: Round [75] log likelihood: -1393.567286
EM: Round [76] log likelihood: -1393.566034
EM: Round [77] log likelihood: -1393.564840
EM: Round [78] log likelihood: -1393.563701
EM: Round [79] log likelihood: -1393.562615
EM: Round [80] log likelihood: -1393.561578
EM: Round [81] log likelihood: -1393.560588
EM: Round [82] log likelihood: -1393.559643
EM: Round [83] log likelihood: -1393.558741
EM: Round [84] log likelihood: -1393.557878
EM: Round [85] log likelihood: -1393.557054
EM: Round [86] log likelihood: -1393.556267
EM: Round [87] log likelihood: -1393.555514
EM: Round [88] log likelihood: -1393.554794
EM: Round [89] log likelihood: -1393.554105
EM: Round [90] log likelihood: -1393.553446
EM: Round [91] log likelihood: -1393.552816
EM: Round [92] log likelihood: -1393.552212
EM: Round [93] log likelihood: -1393.551634
EM: Round [94] log likelihood: -1393.551081
EM: Round [95] log likelihood: -1393.550551
EM: Round [96] log likelihood: -1393.550043
EM: Round [97] log likelihood: -1393.549557
EM: Round [98] log likelihood: -1393.549090
EM: Round [99] log likelihood: -1393.548643
EM: Round [100] log likelihood: -1393.548215
EM: Round [101] log likelihood: -1393.547804
EM: Round [102] log likelihood: -1393.547409
EM: Round [103] log likelihood: -1393.547031
EM: Round [104] log likelihood: -1393.546668
EM: Round [105] log likelihood: -1393.546320
EM: Round [106] log likelihood: -1393.545986
EM: Round [107] log likelihood: -1393.545665
EM: Round [108] log likelihood: -1393.545357
EM: Round [109] log likelihood: -1393.545061
EM: Round [110] log likelihood: -1393.544777
EM: Round [111] log likelihood: -1393.544503
EM: Round [112] log likelihood: -1393.544241
EM: Round [113] log likelihood: -1393.543989
EM: Round [114] log likelihood: -1393.543747
EM: Round [115] log likelihood: -1393.543514
EM: Round [116] log likelihood: -1393.543290
EM: Round [117] log likelihood: -1393.543075
EM: Round [118] log likelihood: -1393.542868
EM: Round [119] log likelihood: -1393.542669
EM: Round [120] log likelihood: -1393.542478
EM: Round [121] log likelihood: -1393.542293
EM: Round [122] log likelihood: -1393.542116
EM: Round [123] log likelihood: -1393.541946
EM: Round [124] log likelihood: -1393.541782
EM: Round [125] log likelihood: -1393.541624
EM: Round [126] log likelihood: -1393.541472
EM: Round [127] log likelihood: -1393.541326
EM: Round [128] log likelihood: -1393.541185
EM: Round [129] log likelihood: -1393.541050
EM: Round [130] log likelihood: -1393.540920
EM: Round [131] log likelihood: -1393.540794
EM: Round [132] log likelihood: -1393.540673
EM: Round [133] log likelihood: -1393.540557
EM: Round [134] log likelihood: -1393.540444
EM: Round [135] log likelihood: -1393.540336
EM: Round [136] log likelihood: -1393.540232
EM: Round [137] log likelihood: -1393.540132
EM: Round [138] log likelihood: -1393.540035
EM: Stopping iterations at round 138 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.YdUKGijqd9/aih-tih-sc-835699-R1_A23WJ53LT4_1.consolidated.bam into /tmp/nxf.YdUKGijqd9/aih-tih-sc-835699-R1_A23WJ53LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.YdUKGijqd9/aih-tih-sc-835699-R1_A23WJ53LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.YdUKGijqd9/aih-tih-sc-835699-R1_A23WJ53LT4_1.consolidated.bam.read_coords > /tmp/nxf.YdUKGijqd9/aih-tih-sc-835699-R1_A23WJ53LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.YdUKGijqd9/aih-tih-sc-835699-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.YdUKGijqd9/aih-tih-sc-835699-R1_A23WJ53LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.YdUKGijqd9/fi_workdir/aih-tih-sc-835699-R1_A23WJ53LT4_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.YdUKGijqd9/fi_workdir/aih-tih-sc-835699-R1_A23WJ53LT4_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.YdUKGijqd9/fi_workdir/aih-tih-sc-835699-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.YdUKGijqd9/aih-tih-sc-835699-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.YdUKGijqd9/aih-tih-sc-835699-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -973.823010
EM: Round [1] log likelihood: -973.787943
EM: Round [2] log likelihood: -973.787745
EM: Round [3] log likelihood: -973.787743
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.YdUKGijqd9/aih-tih-sc-835699-R1_A23WJ53LT4_1_1.fastp.fastq.gz: 296759568
Warning - not locating file: /tmp/nxf.YdUKGijqd9/aih-tih-sc-835699-R1_A23WJ53LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000267135.2]
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 [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286065.2]
ls: cannot access 'IGV_inputs': No such file or directory