.command.err - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (aih-tih-sc-da06ce-R1_A23YTGFLT4_1)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/29/3df659aa1d92911457209a4845934b/.command.err
Size: 20.6 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (aih-tih-sc-da06ce-R1_A23YTGFLT4_1)
Attempt
Content

Done.
-parsing GTF file: /tmp/nxf.bZuhpufnsu/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.bZuhpufnsu/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.bZuhpufnsu/aih-tih-sc-da06ce-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.bZuhpufnsu/aih-tih-sc-da06ce-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.bZuhpufnsu/fi_workdir/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.bZuhpufnsu/fi_workdir/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-da06ce-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-da06ce-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
11:52:43 : INFO : Done.
-parsing GTF file: /tmp/nxf.bZuhpufnsu/fi_workdir/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.bZuhpufnsu/fi_workdir/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

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[390000]   -done parsing /tmp/nxf.bZuhpufnsu/fi_workdir/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'excessive soft clipping' => 3821,
          'seq-similar region overlap' => 117,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 2,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 111,
          ' ** passed ** ' => 1666,
          'low complexity anchor region' => 4,
          'per_id < 96' => 1826,
          'num genes matched < 2' => 1,
          'small anchor length' => 54,
          'exons hit < 2' => 1
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.bZuhpufnsu/fi_workdir/aih-tih-sc-da06ce-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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[204000]   -fusion SPANNING read extraction for scaff: CCAR2--AC055854.1

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[26000]   -fusion SPANNING read extraction for scaff: PAPOLA--RBMXP1

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[26000]   -fusion SPANNING read extraction for scaff: PAPOLA--FO393412.1

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[14000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

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[14000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

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[16000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

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[13000]   -fusion SPANNING read extraction for scaff: STON1--GTF2A1L

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[18000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 3756,
          'seq similar region alignment' => 13295
        };
EM: Starting log likelihood: -1869.509848
EM: Round [1] log likelihood: -1869.402485
EM: Round [2] log likelihood: -1869.358123
EM: Round [3] log likelihood: -1869.316906
EM: Round [4] log likelihood: -1869.278339
EM: Round [5] log likelihood: -1869.242166
EM: Round [6] log likelihood: -1869.208168
EM: Round [7] log likelihood: -1869.176154
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EM: Round [10] log likelihood: -1869.090434
EM: Round [11] log likelihood: -1869.064861
EM: Round [12] log likelihood: -1869.040603
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EM: Round [14] log likelihood: -1868.995665
EM: Round [15] log likelihood: -1868.974824
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EM: Round [18] log likelihood: -1868.917986
EM: Round [19] log likelihood: -1868.900741
EM: Round [20] log likelihood: -1868.884262
EM: Round [21] log likelihood: -1868.868503
EM: Round [22] log likelihood: -1868.853424
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EM: Round [66] log likelihood: -1868.537784
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EM: Round [69] log likelihood: -1868.528650
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EM: Round [143] log likelihood: -1868.430706
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EM: Round [149] log likelihood: -1868.427740
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EM: Round [151] log likelihood: -1868.426827
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EM: Round [153] log likelihood: -1868.425948
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EM: Round [155] log likelihood: -1868.425102
EM: Round [156] log likelihood: -1868.424691
EM: Round [157] log likelihood: -1868.424288
EM: Round [158] log likelihood: -1868.423892
EM: Round [159] log likelihood: -1868.423504
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EM: Round [161] log likelihood: -1868.422750
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EM: Round [164] log likelihood: -1868.421670
EM: Round [165] log likelihood: -1868.421324
EM: Round [166] log likelihood: -1868.420984
EM: Round [167] log likelihood: -1868.420651
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EM: Round [169] log likelihood: -1868.420002
EM: Round [170] log likelihood: -1868.419686
EM: Round [171] log likelihood: -1868.419377
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EM: Round [174] log likelihood: -1868.418482
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EM: Round [178] log likelihood: -1868.417363
EM: Round [179] log likelihood: -1868.417096
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EM: Round [188] log likelihood: -1868.414902
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EM: Round [191] log likelihood: -1868.414247
EM: Round [192] log likelihood: -1868.414036
EM: Round [193] log likelihood: -1868.413830
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EM: Round [195] log likelihood: -1868.413427
EM: Round [196] log likelihood: -1868.413231
EM: Round [197] log likelihood: -1868.413039
EM: Round [198] log likelihood: -1868.412850
EM: Round [199] log likelihood: -1868.412665
EM: Round [200] log likelihood: -1868.412483
EM: Round [201] log likelihood: -1868.412304
EM: Round [202] log likelihood: -1868.412128
EM: Round [203] log likelihood: -1868.411955
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EM: Round [205] log likelihood: -1868.411619
EM: Round [206] log likelihood: -1868.411456
EM: Round [207] log likelihood: -1868.411295
EM: Round [208] log likelihood: -1868.411137
EM: Round [209] log likelihood: -1868.410982
EM: Round [210] log likelihood: -1868.410830
EM: Round [211] log likelihood: -1868.410681
EM: Round [212] log likelihood: -1868.410534
EM: Round [213] log likelihood: -1868.410389
EM: Round [214] log likelihood: -1868.410248
EM: Round [215] log likelihood: -1868.410108
EM: Round [216] log likelihood: -1868.409972
EM: Round [217] log likelihood: -1868.409837
EM: Round [218] log likelihood: -1868.409705
EM: Round [219] log likelihood: -1868.409576
EM: Round [220] log likelihood: -1868.409448
EM: Round [221] log likelihood: -1868.409323
EM: Round [222] log likelihood: -1868.409200
EM: Round [223] log likelihood: -1868.409079
EM: Round [224] log likelihood: -1868.408961
EM: Round [225] log likelihood: -1868.408844
EM: Round [226] log likelihood: -1868.408730
EM: Round [227] log likelihood: -1868.408617
EM: Round [228] log likelihood: -1868.408507
EM: Round [229] log likelihood: -1868.408398
EM: Round [230] log likelihood: -1868.408291
EM: Round [231] log likelihood: -1868.408187
EM: Round [232] log likelihood: -1868.408084
EM: Round [233] log likelihood: -1868.407982
EM: Round [234] log likelihood: -1868.407883
EM: Stopping iterations at round 234 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.bZuhpufnsu/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.bZuhpufnsu/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.bZuhpufnsu/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.bZuhpufnsu/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.bZuhpufnsu/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.bZuhpufnsu/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.bZuhpufnsu/aih-tih-sc-da06ce-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.bZuhpufnsu/fi_workdir/aih-tih-sc-da06ce-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.bZuhpufnsu/fi_workdir/aih-tih-sc-da06ce-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.bZuhpufnsu/fi_workdir/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.bZuhpufnsu/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.bZuhpufnsu/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -1825.647436
EM: Round [1] log likelihood: -1825.587519
EM: Round [2] log likelihood: -1825.587314
EM: Round [3] log likelihood: -1825.587314
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.bZuhpufnsu/aih-tih-sc-da06ce-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296209672
Warning - not locating file: /tmp/nxf.bZuhpufnsu/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000253125.1]
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 [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