.command.err - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (tih_rna_sample_00116_23H5VFLT4_s36)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/fb5b1029ed8d8b10397bc926bb7639/.command.err
Size: 13.7 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (tih_rna_sample_00116_23H5VFLT4_s36)
Attempt
Content

Done.
-parsing GTF file: /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.R3SmTO1c36/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.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36_1.fastp.fastq.gz /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00116_23H5VFLT4_s36.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00116_23H5VFLT4_s36.star.sortedByCoord.out.bam
10:37:05 : INFO : Done.
-parsing GTF file: /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.gtf
-parsing /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam

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[270000]   -done parsing /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 14,
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 8,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 24,
          'per_id < 96' => 1905,
          'seq-similar region overlap' => 193,
          ' ** passed ** ' => 2310,
          'num genes matched < 2' => 2,
          'small anchor length' => 8,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 18,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 6,
          'excessive soft clipping' => 3470
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[41000]   -fusion SPANNING read extraction for scaff: AC013268.1--MALL

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[11000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[3000]   -fusion SPANNING read extraction for scaff: LINC00937--AC083906.5

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[3000]   -fusion SPANNING read extraction for scaff: LINC00937--AC083906.2

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[37000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2

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[38000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1

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[29000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13

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[15000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[98000]   -fusion SPANNING read extraction for scaff: ZNF587--CLASRP
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 18934,
          'lacks exon overlap' => 5272
        };
EM: Starting log likelihood: -1656.805582
EM: Round [1] log likelihood: -1656.287130
EM: Round [2] log likelihood: -1655.821445
EM: Round [3] log likelihood: -1655.401864
EM: Round [4] log likelihood: -1655.022796
EM: Round [5] log likelihood: -1654.679514
EM: Round [6] log likelihood: -1654.367983
EM: Round [7] log likelihood: -1654.084735
EM: Round [8] log likelihood: -1653.826771
EM: Round [9] log likelihood: -1653.591481
EM: Round [10] log likelihood: -1653.376585
EM: Round [11] log likelihood: -1653.180076
EM: Round [12] log likelihood: -1653.000184
EM: Round [13] log likelihood: -1652.835342
EM: Round [14] log likelihood: -1652.684154
EM: Round [15] log likelihood: -1652.545377
EM: Round [16] log likelihood: -1652.417897
EM: Round [17] log likelihood: -1652.300716
EM: Round [18] log likelihood: -1652.192936
EM: Round [19] log likelihood: -1652.093746
EM: Round [20] log likelihood: -1652.002415
EM: Round [21] log likelihood: -1651.918280
EM: Round [22] log likelihood: -1651.840742
EM: Round [23] log likelihood: -1651.769255
EM: Round [24] log likelihood: -1651.703322
EM: Round [25] log likelihood: -1651.642492
EM: Round [26] log likelihood: -1651.586353
EM: Round [27] log likelihood: -1651.534528
EM: Round [28] log likelihood: -1651.486674
EM: Round [29] log likelihood: -1651.442475
EM: Round [30] log likelihood: -1651.401644
EM: Round [31] log likelihood: -1651.363917
EM: Round [32] log likelihood: -1651.329050
EM: Round [33] log likelihood: -1651.296822
EM: Round [34] log likelihood: -1651.267028
EM: Round [35] log likelihood: -1651.239480
EM: Round [36] log likelihood: -1651.214005
EM: Round [37] log likelihood: -1651.190445
EM: Round [38] log likelihood: -1651.168653
EM: Round [39] log likelihood: -1651.148494
EM: Round [40] log likelihood: -1651.129844
EM: Round [41] log likelihood: -1651.112589
EM: Round [42] log likelihood: -1651.096622
EM: Round [43] log likelihood: -1651.081847
EM: Round [44] log likelihood: -1651.068174
EM: Round [45] log likelihood: -1651.055519
EM: Round [46] log likelihood: -1651.043806
EM: Round [47] log likelihood: -1651.032965
EM: Round [48] log likelihood: -1651.022929
EM: Round [49] log likelihood: -1651.013639
EM: Round [50] log likelihood: -1651.005039
EM: Round [51] log likelihood: -1650.997077
EM: Round [52] log likelihood: -1650.989705
EM: Round [53] log likelihood: -1650.982880
EM: Round [54] log likelihood: -1650.976561
EM: Round [55] log likelihood: -1650.970710
EM: Round [56] log likelihood: -1650.965292
EM: Round [57] log likelihood: -1650.960276
EM: Round [58] log likelihood: -1650.955631
EM: Round [59] log likelihood: -1650.951329
EM: Round [60] log likelihood: -1650.947346
EM: Round [61] log likelihood: -1650.943657
EM: Round [62] log likelihood: -1650.940241
EM: Round [63] log likelihood: -1650.937078
EM: Round [64] log likelihood: -1650.934148
EM: Round [65] log likelihood: -1650.931435
EM: Round [66] log likelihood: -1650.928922
EM: Round [67] log likelihood: -1650.926595
EM: Round [68] log likelihood: -1650.924440
EM: Round [69] log likelihood: -1650.922444
EM: Round [70] log likelihood: -1650.920595
EM: Round [71] log likelihood: -1650.918883
EM: Round [72] log likelihood: -1650.917297
EM: Round [73] log likelihood: -1650.915828
EM: Round [74] log likelihood: -1650.914468
EM: Round [75] log likelihood: -1650.913208
EM: Round [76] log likelihood: -1650.912041
EM: Round [77] log likelihood: -1650.910960
EM: Round [78] log likelihood: -1650.909959
EM: Round [79] log likelihood: -1650.909032
EM: Round [80] log likelihood: -1650.908173
EM: Round [81] log likelihood: -1650.907378
EM: Round [82] log likelihood: -1650.906641
EM: Round [83] log likelihood: -1650.905959
EM: Round [84] log likelihood: -1650.905327
EM: Round [85] log likelihood: -1650.904742
EM: Round [86] log likelihood: -1650.904199
EM: Round [87] log likelihood: -1650.903697
EM: Round [88] log likelihood: -1650.903232
EM: Round [89] log likelihood: -1650.902801
EM: Round [90] log likelihood: -1650.902402
EM: Round [91] log likelihood: -1650.902032
EM: Round [92] log likelihood: -1650.901690
EM: Round [93] log likelihood: -1650.901373
EM: Round [94] log likelihood: -1650.901079
EM: Round [95] log likelihood: -1650.900807
EM: Round [96] log likelihood: -1650.900555
EM: Round [97] log likelihood: -1650.900322
EM: Round [98] log likelihood: -1650.900105
EM: Round [99] log likelihood: -1650.899905
EM: Round [100] log likelihood: -1650.899720
EM: Round [101] log likelihood: -1650.899548
EM: Round [102] log likelihood: -1650.899389
EM: Round [103] log likelihood: -1650.899241
EM: Round [104] log likelihood: -1650.899105
EM: Round [105] log likelihood: -1650.898978
EM: Round [106] log likelihood: -1650.898861
EM: Round [107] log likelihood: -1650.898752
EM: Round [108] log likelihood: -1650.898652
EM: Round [109] log likelihood: -1650.898559
EM: Stopping iterations at round 109 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.consolidated.bam into /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.consolidated.bam.read_coords

CMD: touch /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.consolidated.bam.read_coords > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.consolidated.bam.frag_coords > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.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.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.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.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -1577.000478
EM: Round [1] log likelihood: -1577.000478
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36_1.fastp.fastq.gz: 296460757
Warning - not locating file: /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000186148.13]
WARNING, no entry stored in dbm for [ENSG00000186148.13]
WARNING, no entry stored in dbm for [ENSG00000186148.13]
WARNING, no entry stored in dbm for [ENSG00000186148.13]
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 [ENSG00000282057.1]
ls: cannot access 'IGV_inputs': No such file or directory