.command.err - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (tih_rna_sample_00467_B23WHTKLT4_1)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/851b38565decfc82f615d4f9d67f3b/.command.err
Size: 16.3 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (tih_rna_sample_00467_B23WHTKLT4_1)
Attempt
Content

Done.
-parsing GTF file: /tmp/nxf.5AmcRU16E2/tih_rna_sample_00467_B23WHTKLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.5AmcRU16E2/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.5AmcRU16E2/tih_rna_sample_00467_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.5AmcRU16E2/tih_rna_sample_00467_B23WHTKLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.5AmcRU16E2/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.5AmcRU16E2/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00467_B23WHTKLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00467_B23WHTKLT4_1.star.sortedByCoord.out.bam
11:14:57 : INFO : Done.
-parsing GTF file: /tmp/nxf.5AmcRU16E2/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_1.gtf
-parsing /tmp/nxf.5AmcRU16E2/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_1.star.cSorted.dupsMarked.bam

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[410000]   -done parsing /tmp/nxf.5AmcRU16E2/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'excessive soft clipping' => 1902,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
          ' ** passed ** ' => 2974,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 18,
          'per_id < 96' => 1658,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 4,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 28,
          'small anchor length' => 18,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 34,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 5,
          'seq-similar region overlap' => 74,
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
          'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 66
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.5AmcRU16E2/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[122000]   -fusion SPANNING read extraction for scaff: DIP2B--RPRD2

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[46000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2

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[52000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1

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[54000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13

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[38000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2

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[44000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1

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[46000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13

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[16000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 45340,
          'lacks exon overlap' => 412
        };
EM: Starting log likelihood: -1226.667418
EM: Round [1] log likelihood: -1226.227245
EM: Round [2] log likelihood: -1225.822451
EM: Round [3] log likelihood: -1225.449457
EM: Round [4] log likelihood: -1225.105152
EM: Round [5] log likelihood: -1224.786819
EM: Round [6] log likelihood: -1224.492070
EM: Round [7] log likelihood: -1224.218796
EM: Round [8] log likelihood: -1223.965125
EM: Round [9] log likelihood: -1223.729391
EM: Round [10] log likelihood: -1223.510105
EM: Round [11] log likelihood: -1223.305929
EM: Round [12] log likelihood: -1223.115660
EM: Round [13] log likelihood: -1222.938211
EM: Round [14] log likelihood: -1222.772599
EM: Round [15] log likelihood: -1222.617930
EM: Round [16] log likelihood: -1222.473392
EM: Round [17] log likelihood: -1222.338243
EM: Round [18] log likelihood: -1222.211806
EM: Round [19] log likelihood: -1222.093462
EM: Round [20] log likelihood: -1221.982641
EM: Round [21] log likelihood: -1221.878820
EM: Round [22] log likelihood: -1221.781520
EM: Round [23] log likelihood: -1221.690296
EM: Round [24] log likelihood: -1221.604740
EM: Round [25] log likelihood: -1221.524473
EM: Round [26] log likelihood: -1221.449146
EM: Round [27] log likelihood: -1221.378435
EM: Round [28] log likelihood: -1221.312040
EM: Round [29] log likelihood: -1221.249682
EM: Round [30] log likelihood: -1221.191102
EM: Round [31] log likelihood: -1221.136059
EM: Round [32] log likelihood: -1221.084330
EM: Round [33] log likelihood: -1221.035705
EM: Round [34] log likelihood: -1220.989990
EM: Round [35] log likelihood: -1220.947005
EM: Round [36] log likelihood: -1220.906579
EM: Round [37] log likelihood: -1220.868555
EM: Round [38] log likelihood: -1220.832785
EM: Round [39] log likelihood: -1220.799131
EM: Round [40] log likelihood: -1220.767465
EM: Round [41] log likelihood: -1220.737665
EM: Round [42] log likelihood: -1220.709618
EM: Round [43] log likelihood: -1220.683219
EM: Round [44] log likelihood: -1220.658369
EM: Round [45] log likelihood: -1220.634974
EM: Round [46] log likelihood: -1220.612948
EM: Round [47] log likelihood: -1220.592209
EM: Round [48] log likelihood: -1220.572680
EM: Round [49] log likelihood: -1220.554289
EM: Round [50] log likelihood: -1220.536969
EM: Round [51] log likelihood: -1220.520657
EM: Round [52] log likelihood: -1220.505293
EM: Round [53] log likelihood: -1220.490820
EM: Round [54] log likelihood: -1220.477188
EM: Round [55] log likelihood: -1220.464346
EM: Round [56] log likelihood: -1220.452247
EM: Round [57] log likelihood: -1220.440850
EM: Round [58] log likelihood: -1220.430111
EM: Round [59] log likelihood: -1220.419993
EM: Round [60] log likelihood: -1220.410460
EM: Round [61] log likelihood: -1220.401478
EM: Round [62] log likelihood: -1220.393014
EM: Round [63] log likelihood: -1220.385039
EM: Round [64] log likelihood: -1220.377523
EM: Round [65] log likelihood: -1220.370440
EM: Round [66] log likelihood: -1220.363766
EM: Round [67] log likelihood: -1220.357476
EM: Round [68] log likelihood: -1220.351548
EM: Round [69] log likelihood: -1220.345962
EM: Round [70] log likelihood: -1220.340697
EM: Round [71] log likelihood: -1220.335734
EM: Round [72] log likelihood: -1220.331058
EM: Round [73] log likelihood: -1220.326650
EM: Round [74] log likelihood: -1220.322495
EM: Round [75] log likelihood: -1220.318579
EM: Round [76] log likelihood: -1220.314888
EM: Round [77] log likelihood: -1220.311409
EM: Round [78] log likelihood: -1220.308130
EM: Round [79] log likelihood: -1220.305039
EM: Round [80] log likelihood: -1220.302126
EM: Round [81] log likelihood: -1220.299379
EM: Round [82] log likelihood: -1220.296791
EM: Round [83] log likelihood: -1220.294351
EM: Round [84] log likelihood: -1220.292051
EM: Round [85] log likelihood: -1220.289882
EM: Round [86] log likelihood: -1220.287839
EM: Round [87] log likelihood: -1220.285912
EM: Round [88] log likelihood: -1220.284096
EM: Round [89] log likelihood: -1220.282384
EM: Round [90] log likelihood: -1220.280770
EM: Round [91] log likelihood: -1220.279249
EM: Round [92] log likelihood: -1220.277815
EM: Round [93] log likelihood: -1220.276463
EM: Round [94] log likelihood: -1220.275188
EM: Round [95] log likelihood: -1220.273987
EM: Round [96] log likelihood: -1220.272854
EM: Round [97] log likelihood: -1220.271787
EM: Round [98] log likelihood: -1220.270780
EM: Round [99] log likelihood: -1220.269831
EM: Round [100] log likelihood: -1220.268937
EM: Round [101] log likelihood: -1220.268093
EM: Round [102] log likelihood: -1220.267299
EM: Round [103] log likelihood: -1220.266549
EM: Round [104] log likelihood: -1220.265843
EM: Round [105] log likelihood: -1220.265177
EM: Round [106] log likelihood: -1220.264549
EM: Round [107] log likelihood: -1220.263957
EM: Round [108] log likelihood: -1220.263399
EM: Round [109] log likelihood: -1220.262873
EM: Round [110] log likelihood: -1220.262377
EM: Round [111] log likelihood: -1220.261909
EM: Round [112] log likelihood: -1220.261469
EM: Round [113] log likelihood: -1220.261053
EM: Round [114] log likelihood: -1220.260662
EM: Round [115] log likelihood: -1220.260292
EM: Round [116] log likelihood: -1220.259944
EM: Round [117] log likelihood: -1220.259616
EM: Round [118] log likelihood: -1220.259306
EM: Round [119] log likelihood: -1220.259015
EM: Round [120] log likelihood: -1220.258740
EM: Round [121] log likelihood: -1220.258481
EM: Round [122] log likelihood: -1220.258236
EM: Round [123] log likelihood: -1220.258006
EM: Round [124] log likelihood: -1220.257788
EM: Round [125] log likelihood: -1220.257584
EM: Round [126] log likelihood: -1220.257391
EM: Round [127] log likelihood: -1220.257209
EM: Round [128] log likelihood: -1220.257037
EM: Round [129] log likelihood: -1220.256875
EM: Round [130] log likelihood: -1220.256723
EM: Round [131] log likelihood: -1220.256579
EM: Round [132] log likelihood: -1220.256443
EM: Round [133] log likelihood: -1220.256316
EM: Round [134] log likelihood: -1220.256195
EM: Round [135] log likelihood: -1220.256082
EM: Round [136] log likelihood: -1220.255975
EM: Round [137] log likelihood: -1220.255874
EM: Round [138] log likelihood: -1220.255778
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.5AmcRU16E2/tih_rna_sample_00467_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.5AmcRU16E2/tih_rna_sample_00467_B23WHTKLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.5AmcRU16E2/tih_rna_sample_00467_B23WHTKLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.5AmcRU16E2/tih_rna_sample_00467_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.5AmcRU16E2/tih_rna_sample_00467_B23WHTKLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.5AmcRU16E2/tih_rna_sample_00467_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.5AmcRU16E2/tih_rna_sample_00467_B23WHTKLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.5AmcRU16E2/fi_workdir/tih_rna_sample_00467_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.5AmcRU16E2/fi_workdir/tih_rna_sample_00467_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.5AmcRU16E2/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.5AmcRU16E2/tih_rna_sample_00467_B23WHTKLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.5AmcRU16E2/tih_rna_sample_00467_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -588.636482
EM: Round [1] log likelihood: -588.636482
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.5AmcRU16E2/tih_rna_sample_00467_B23WHTKLT4_1_1.fastp.fastq.gz: 289417500
Warning - not locating file: /tmp/nxf.5AmcRU16E2/tih_rna_sample_00467_B23WHTKLT4_1.gmap_trinity_GG.fusions.gff3.bed
ls: cannot access 'IGV_inputs': No such file or directory