.command.err - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (aih-tih-sc-38a0a3-R1_A23WJ53LT4_1)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/f5e4c8b354529c59180bb73dbb6d00/.command.err
Size: 11.1 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (aih-tih-sc-38a0a3-R1_A23WJ53LT4_1)
Attempt
Content

Done.
-parsing GTF file: /tmp/nxf.iF3FKqFePk/aih-tih-sc-38a0a3-R1_A23WJ53LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.iF3FKqFePk/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.iF3FKqFePk/aih-tih-sc-38a0a3-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.iF3FKqFePk/aih-tih-sc-38a0a3-R1_A23WJ53LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.iF3FKqFePk/fi_workdir/aih-tih-sc-38a0a3-R1_A23WJ53LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.iF3FKqFePk/fi_workdir/aih-tih-sc-38a0a3-R1_A23WJ53LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-38a0a3-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-38a0a3-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
11:23:51 : INFO : Done.
-parsing GTF file: /tmp/nxf.iF3FKqFePk/fi_workdir/aih-tih-sc-38a0a3-R1_A23WJ53LT4_1.gtf
-parsing /tmp/nxf.iF3FKqFePk/fi_workdir/aih-tih-sc-38a0a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam

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[120000]   -done parsing /tmp/nxf.iF3FKqFePk/fi_workdir/aih-tih-sc-38a0a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 35,
          'small anchor length' => 12,
          'seq-similar region overlap' => 23,
          ' ** passed ** ' => 1427,
          'per_id < 96' => 445,
          'excessive soft clipping' => 989,
          'num genes matched < 2' => 10
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.iF3FKqFePk/fi_workdir/aih-tih-sc-38a0a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[19000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1
-fusion SPANNING read extraction for scaff: LINC00381--NKAIN2

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[7000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

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[8000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

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

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[13000]   -fusion SPANNING read extraction for scaff: PMS2P6--CCDC146

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[22000]   -fusion SPANNING read extraction for scaff: STON1--GTF2A1L

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[22000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[4000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[19000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 5744,
          'lacks exon overlap' => 762
        };
EM: Starting log likelihood: -1968.251691
EM: Round [1] log likelihood: -1967.880041
EM: Round [2] log likelihood: -1967.793002
EM: Round [3] log likelihood: -1967.714731
EM: Round [4] log likelihood: -1967.643966
EM: Round [5] log likelihood: -1967.579838
EM: Round [6] log likelihood: -1967.521601
EM: Round [7] log likelihood: -1967.468617
EM: Round [8] log likelihood: -1967.420332
EM: Round [9] log likelihood: -1967.376263
EM: Round [10] log likelihood: -1967.335988
EM: Round [11] log likelihood: -1967.299138
EM: Round [12] log likelihood: -1967.265383
EM: Round [13] log likelihood: -1967.234433
EM: Round [14] log likelihood: -1967.206031
EM: Round [15] log likelihood: -1967.179945
EM: Round [16] log likelihood: -1967.155968
EM: Round [17] log likelihood: -1967.133916
EM: Round [18] log likelihood: -1967.113621
EM: Round [19] log likelihood: -1967.094932
EM: Round [20] log likelihood: -1967.077715
EM: Round [21] log likelihood: -1967.061845
EM: Round [22] log likelihood: -1967.047211
EM: Round [23] log likelihood: -1967.033711
EM: Round [24] log likelihood: -1967.021253
EM: Round [25] log likelihood: -1967.009752
EM: Round [26] log likelihood: -1966.999132
EM: Round [27] log likelihood: -1966.989323
EM: Round [28] log likelihood: -1966.980260
EM: Round [29] log likelihood: -1966.971885
EM: Round [30] log likelihood: -1966.964143
EM: Round [31] log likelihood: -1966.956985
EM: Round [32] log likelihood: -1966.950367
EM: Round [33] log likelihood: -1966.944246
EM: Round [34] log likelihood: -1966.938583
EM: Round [35] log likelihood: -1966.933345
EM: Round [36] log likelihood: -1966.928498
EM: Round [37] log likelihood: -1966.924013
EM: Round [38] log likelihood: -1966.919861
EM: Round [39] log likelihood: -1966.916019
EM: Round [40] log likelihood: -1966.912462
EM: Round [41] log likelihood: -1966.909170
EM: Round [42] log likelihood: -1966.906121
EM: Round [43] log likelihood: -1966.903298
EM: Round [44] log likelihood: -1966.900684
EM: Round [45] log likelihood: -1966.898264
EM: Round [46] log likelihood: -1966.896022
EM: Round [47] log likelihood: -1966.893946
EM: Round [48] log likelihood: -1966.892023
EM: Round [49] log likelihood: -1966.890242
EM: Round [50] log likelihood: -1966.888592
EM: Round [51] log likelihood: -1966.887064
EM: Round [52] log likelihood: -1966.885648
EM: Round [53] log likelihood: -1966.884336
EM: Round [54] log likelihood: -1966.883121
EM: Round [55] log likelihood: -1966.881995
EM: Round [56] log likelihood: -1966.880952
EM: Round [57] log likelihood: -1966.879986
EM: Round [58] log likelihood: -1966.879090
EM: Round [59] log likelihood: -1966.878261
EM: Round [60] log likelihood: -1966.877492
EM: Round [61] log likelihood: -1966.876780
EM: Round [62] log likelihood: -1966.876119
EM: Round [63] log likelihood: -1966.875508
EM: Round [64] log likelihood: -1966.874941
EM: Round [65] log likelihood: -1966.874416
EM: Round [66] log likelihood: -1966.873929
EM: Round [67] log likelihood: -1966.873478
EM: Round [68] log likelihood: -1966.873060
EM: Round [69] log likelihood: -1966.872673
EM: Round [70] log likelihood: -1966.872314
EM: Round [71] log likelihood: -1966.871981
EM: Round [72] log likelihood: -1966.871673
EM: Round [73] log likelihood: -1966.871387
EM: Round [74] log likelihood: -1966.871123
EM: Round [75] log likelihood: -1966.870877
EM: Round [76] log likelihood: -1966.870650
EM: Round [77] log likelihood: -1966.870439
EM: Round [78] log likelihood: -1966.870244
EM: Round [79] log likelihood: -1966.870063
EM: Round [80] log likelihood: -1966.869895
EM: Round [81] log likelihood: -1966.869740
EM: Round [82] log likelihood: -1966.869596
EM: Round [83] log likelihood: -1966.869462
EM: Round [84] log likelihood: -1966.869338
EM: Round [85] log likelihood: -1966.869224
EM: Round [86] log likelihood: -1966.869117
EM: Round [87] log likelihood: -1966.869019
EM: Stopping iterations at round 87 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.iF3FKqFePk/aih-tih-sc-38a0a3-R1_A23WJ53LT4_1.consolidated.bam into /tmp/nxf.iF3FKqFePk/aih-tih-sc-38a0a3-R1_A23WJ53LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.iF3FKqFePk/aih-tih-sc-38a0a3-R1_A23WJ53LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.iF3FKqFePk/aih-tih-sc-38a0a3-R1_A23WJ53LT4_1.consolidated.bam.read_coords > /tmp/nxf.iF3FKqFePk/aih-tih-sc-38a0a3-R1_A23WJ53LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.iF3FKqFePk/aih-tih-sc-38a0a3-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.iF3FKqFePk/aih-tih-sc-38a0a3-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.iF3FKqFePk/fi_workdir/aih-tih-sc-38a0a3-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.iF3FKqFePk/fi_workdir/aih-tih-sc-38a0a3-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.iF3FKqFePk/fi_workdir/aih-tih-sc-38a0a3-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.iF3FKqFePk/aih-tih-sc-38a0a3-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.iF3FKqFePk/aih-tih-sc-38a0a3-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -1901.575315
EM: Round [1] log likelihood: -1901.501593
EM: Round [2] log likelihood: -1901.501430
EM: Round [3] log likelihood: -1901.501429
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.iF3FKqFePk/aih-tih-sc-38a0a3-R1_A23WJ53LT4_1_1.fastp.fastq.gz: 295863290
Warning - not locating file: /tmp/nxf.iF3FKqFePk/aih-tih-sc-38a0a3-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 [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000226240.2]
WARNING, no entry stored in dbm for [ENSG00000226240.2]
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 [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