.command.err - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (aih-tih-sc-96d0f6-R1_A23YTGFLT4_1)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/ce56b31213c67529e2739cfa0170c9/.command.err
Size: 11.3 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (aih-tih-sc-96d0f6-R1_A23YTGFLT4_1)
Attempt
Content

Done.
-parsing GTF file: /tmp/nxf.Oz0e6MmjbU/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.Oz0e6MmjbU/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.Oz0e6MmjbU/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.Oz0e6MmjbU/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.Oz0e6MmjbU/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.Oz0e6MmjbU/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
11:15:59 : INFO : Done.
-parsing GTF file: /tmp/nxf.Oz0e6MmjbU/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.Oz0e6MmjbU/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

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[90000]   -done parsing /tmp/nxf.Oz0e6MmjbU/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'exons hit < 2' => 2,
          ' ** passed ** ' => 848,
          'seq-similar region overlap' => 19,
          'num genes matched < 2' => 2,
          'per_id < 96' => 417,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 20,
          'excessive soft clipping' => 828
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.Oz0e6MmjbU/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[7000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[5000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

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[6000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

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[6000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
-fusion SPANNING read extraction for scaff: PMS2P12--AC004980.4

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[30000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[6000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[28000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 752,
          'seq similar region alignment' => 3815
        };
EM: Starting log likelihood: -961.246992
EM: Round [1] log likelihood: -961.175633
EM: Round [2] log likelihood: -961.156723
EM: Round [3] log likelihood: -961.138975
EM: Round [4] log likelihood: -961.122287
EM: Round [5] log likelihood: -961.106582
EM: Round [6] log likelihood: -961.091787
EM: Round [7] log likelihood: -961.077837
EM: Round [8] log likelihood: -961.064673
EM: Round [9] log likelihood: -961.052241
EM: Round [10] log likelihood: -961.040493
EM: Round [11] log likelihood: -961.029384
EM: Round [12] log likelihood: -961.018872
EM: Round [13] log likelihood: -961.008919
EM: Round [14] log likelihood: -960.999491
EM: Round [15] log likelihood: -960.990555
EM: Round [16] log likelihood: -960.982081
EM: Round [17] log likelihood: -960.974043
EM: Round [18] log likelihood: -960.966414
EM: Round [19] log likelihood: -960.959171
EM: Round [20] log likelihood: -960.952292
EM: Round [21] log likelihood: -960.945755
EM: Round [22] log likelihood: -960.939543
EM: Round [23] log likelihood: -960.933637
EM: Round [24] log likelihood: -960.928019
EM: Round [25] log likelihood: -960.922676
EM: Round [26] log likelihood: -960.917591
EM: Round [27] log likelihood: -960.912752
EM: Round [28] log likelihood: -960.908144
EM: Round [29] log likelihood: -960.903757
EM: Round [30] log likelihood: -960.899579
EM: Round [31] log likelihood: -960.895598
EM: Round [32] log likelihood: -960.891805
EM: Round [33] log likelihood: -960.888191
EM: Round [34] log likelihood: -960.884746
EM: Round [35] log likelihood: -960.881462
EM: Round [36] log likelihood: -960.878330
EM: Round [37] log likelihood: -960.875344
EM: Round [38] log likelihood: -960.872496
EM: Round [39] log likelihood: -960.869780
EM: Round [40] log likelihood: -960.867188
EM: Round [41] log likelihood: -960.864716
EM: Round [42] log likelihood: -960.862356
EM: Round [43] log likelihood: -960.860105
EM: Round [44] log likelihood: -960.857956
EM: Round [45] log likelihood: -960.855905
EM: Round [46] log likelihood: -960.853946
EM: Round [47] log likelihood: -960.852077
EM: Round [48] log likelihood: -960.850292
EM: Round [49] log likelihood: -960.848588
EM: Round [50] log likelihood: -960.846960
EM: Round [51] log likelihood: -960.845406
EM: Round [52] log likelihood: -960.843922
EM: Round [53] log likelihood: -960.842504
EM: Round [54] log likelihood: -960.841150
EM: Round [55] log likelihood: -960.839856
EM: Round [56] log likelihood: -960.838620
EM: Round [57] log likelihood: -960.837439
EM: Round [58] log likelihood: -960.836311
EM: Round [59] log likelihood: -960.835234
EM: Round [60] log likelihood: -960.834204
EM: Round [61] log likelihood: -960.833220
EM: Round [62] log likelihood: -960.832279
EM: Round [63] log likelihood: -960.831380
EM: Round [64] log likelihood: -960.830521
EM: Round [65] log likelihood: -960.829701
EM: Round [66] log likelihood: -960.828916
EM: Round [67] log likelihood: -960.828166
EM: Round [68] log likelihood: -960.827450
EM: Round [69] log likelihood: -960.826764
EM: Round [70] log likelihood: -960.826110
EM: Round [71] log likelihood: -960.825484
EM: Round [72] log likelihood: -960.824885
EM: Round [73] log likelihood: -960.824313
EM: Round [74] log likelihood: -960.823766
EM: Round [75] log likelihood: -960.823244
EM: Round [76] log likelihood: -960.822744
EM: Round [77] log likelihood: -960.822266
EM: Round [78] log likelihood: -960.821809
EM: Round [79] log likelihood: -960.821372
EM: Round [80] log likelihood: -960.820955
EM: Round [81] log likelihood: -960.820555
EM: Round [82] log likelihood: -960.820173
EM: Round [83] log likelihood: -960.819808
EM: Round [84] log likelihood: -960.819459
EM: Round [85] log likelihood: -960.819125
EM: Round [86] log likelihood: -960.818806
EM: Round [87] log likelihood: -960.818501
EM: Round [88] log likelihood: -960.818209
EM: Round [89] log likelihood: -960.817930
EM: Round [90] log likelihood: -960.817663
EM: Round [91] log likelihood: -960.817408
EM: Round [92] log likelihood: -960.817164
EM: Round [93] log likelihood: -960.816931
EM: Round [94] log likelihood: -960.816708
EM: Round [95] log likelihood: -960.816494
EM: Round [96] log likelihood: -960.816290
EM: Round [97] log likelihood: -960.816095
EM: Round [98] log likelihood: -960.815908
EM: Round [99] log likelihood: -960.815730
EM: Round [100] log likelihood: -960.815559
EM: Round [101] log likelihood: -960.815396
EM: Round [102] log likelihood: -960.815240
EM: Round [103] log likelihood: -960.815090
EM: Round [104] log likelihood: -960.814947
EM: Round [105] log likelihood: -960.814811
EM: Round [106] log likelihood: -960.814680
EM: Round [107] log likelihood: -960.814555
EM: Round [108] log likelihood: -960.814436
EM: Round [109] log likelihood: -960.814321
EM: Round [110] log likelihood: -960.814212
EM: Round [111] log likelihood: -960.814108
EM: Round [112] log likelihood: -960.814008
EM: Stopping iterations at round 112 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.Oz0e6MmjbU/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.Oz0e6MmjbU/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.Oz0e6MmjbU/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.Oz0e6MmjbU/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.Oz0e6MmjbU/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.Oz0e6MmjbU/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.Oz0e6MmjbU/aih-tih-sc-96d0f6-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.Oz0e6MmjbU/fi_workdir/aih-tih-sc-96d0f6-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.Oz0e6MmjbU/fi_workdir/aih-tih-sc-96d0f6-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.Oz0e6MmjbU/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.Oz0e6MmjbU/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.Oz0e6MmjbU/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -907.467560
EM: Round [1] log likelihood: -907.416349
EM: Round [2] log likelihood: -907.416338
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.Oz0e6MmjbU/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296375716
Warning - not locating file: /tmp/nxf.Oz0e6MmjbU/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
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]
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 [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000228546.2]
WARNING, no entry stored in dbm for [ENSG00000250778.1]
WARNING, no entry stored in dbm for [ENSG00000228546.2]
WARNING, no entry stored in dbm for [ENSG00000250778.1]
ls: cannot access 'IGV_inputs': No such file or directory