File Info

Filename
.command.err
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/827d7392ee1fce390f9c10885a196f/.command.err
Size
14.4 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (aih-tih-sc-33eb27-R1_A23WJ53LT4_1)
Attempt

Content

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Done.
-parsing GTF file: /tmp/nxf.DRPknUgkJU/aih-tih-sc-33eb27-R1_A23WJ53LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.DRPknUgkJU/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.DRPknUgkJU/aih-tih-sc-33eb27-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.DRPknUgkJU/aih-tih-sc-33eb27-R1_A23WJ53LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.DRPknUgkJU/fi_workdir/aih-tih-sc-33eb27-R1_A23WJ53LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.DRPknUgkJU/fi_workdir/aih-tih-sc-33eb27-R1_A23WJ53LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-33eb27-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-33eb27-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
11:11:53 : INFO : Done.
-parsing GTF file: /tmp/nxf.DRPknUgkJU/fi_workdir/aih-tih-sc-33eb27-R1_A23WJ53LT4_1.gtf
-parsing /tmp/nxf.DRPknUgkJU/fi_workdir/aih-tih-sc-33eb27-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam

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[540000]   -done parsing /tmp/nxf.DRPknUgkJU/fi_workdir/aih-tih-sc-33eb27-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          ' ** passed ** ' => 2605,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 16,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 12,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 4,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 70,
          'small anchor length' => 2,
          'per_id < 96' => 3881,
          'excessive soft clipping' => 3960
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.DRPknUgkJU/fi_workdir/aih-tih-sc-33eb27-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[44000]   -fusion SPANNING read extraction for scaff: AGPAT3--GRM5

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[89000]   -fusion SPANNING read extraction for scaff: ANKH--HNRNPKP5

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[67000]   -fusion SPANNING read extraction for scaff: KCNN4--LYPD5

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[18000]   -fusion SPANNING read extraction for scaff: RIPK4--KCNJ6

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[94000]   -fusion SPANNING read extraction for scaff: TCF7L2--AL158212.1

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

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[7000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[16000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[97000]   -fusion SPANNING read extraction for scaff: WASH3P--IQSEC3

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[75000]   -fusion SPANNING read extraction for scaff: WASHC1--IQSEC3
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 4589
        };
EM: Starting log likelihood: -2513.969563
EM: Round [1] log likelihood: -2510.102922
EM: Round [2] log likelihood: -2507.295587
EM: Round [3] log likelihood: -2505.172351
EM: Round [4] log likelihood: -2503.536242
EM: Round [5] log likelihood: -2502.258752
EM: Round [6] log likelihood: -2501.251445
EM: Round [7] log likelihood: -2500.451240
EM: Round [8] log likelihood: -2499.811896
EM: Round [9] log likelihood: -2499.298781
EM: Round [10] log likelihood: -2498.885517
EM: Round [11] log likelihood: -2498.551739
EM: Round [12] log likelihood: -2498.281556
EM: Round [13] log likelihood: -2498.062459
EM: Round [14] log likelihood: -2497.884533
EM: Round [15] log likelihood: -2497.739872
EM: Round [16] log likelihood: -2497.622148
EM: Round [17] log likelihood: -2497.526270
EM: Round [18] log likelihood: -2497.448137
EM: Round [19] log likelihood: -2497.384433
EM: Round [20] log likelihood: -2497.332472
EM: Round [21] log likelihood: -2497.290074
EM: Round [22] log likelihood: -2497.255471
EM: Round [23] log likelihood: -2497.227223
EM: Round [24] log likelihood: -2497.204159
EM: Round [25] log likelihood: -2497.185325
EM: Round [26] log likelihood: -2497.169943
EM: Round [27] log likelihood: -2497.157379
EM: Round [28] log likelihood: -2497.147116
EM: Round [29] log likelihood: -2497.138732
EM: Round [30] log likelihood: -2497.131883
EM: Round [31] log likelihood: -2497.126288
EM: Round [32] log likelihood: -2497.121716
EM: Round [33] log likelihood: -2497.117981
EM: Round [34] log likelihood: -2497.114929
EM: Round [35] log likelihood: -2497.112435
EM: Round [36] log likelihood: -2497.110398
EM: Round [37] log likelihood: -2497.108733
EM: Round [38] log likelihood: -2497.107373
EM: Round [39] log likelihood: -2497.106261
EM: Round [40] log likelihood: -2497.105353
EM: Round [41] log likelihood: -2497.104611
EM: Round [42] log likelihood: -2497.104004
EM: Round [43] log likelihood: -2497.103509
EM: Round [44] log likelihood: -2497.103104
EM: Round [45] log likelihood: -2497.102773
EM: Round [46] log likelihood: -2497.102502
EM: Round [47] log likelihood: -2497.102281
EM: Round [48] log likelihood: -2497.102101
EM: Round [49] log likelihood: -2497.101953
EM: Round [50] log likelihood: -2497.101833
EM: Round [51] log likelihood: -2497.101734
EM: Stopping iterations at round 51 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.DRPknUgkJU/aih-tih-sc-33eb27-R1_A23WJ53LT4_1.consolidated.bam into /tmp/nxf.DRPknUgkJU/aih-tih-sc-33eb27-R1_A23WJ53LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.DRPknUgkJU/aih-tih-sc-33eb27-R1_A23WJ53LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.DRPknUgkJU/aih-tih-sc-33eb27-R1_A23WJ53LT4_1.consolidated.bam.read_coords > /tmp/nxf.DRPknUgkJU/aih-tih-sc-33eb27-R1_A23WJ53LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.DRPknUgkJU/aih-tih-sc-33eb27-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.DRPknUgkJU/aih-tih-sc-33eb27-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.DRPknUgkJU/fi_workdir/aih-tih-sc-33eb27-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.DRPknUgkJU/fi_workdir/aih-tih-sc-33eb27-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.DRPknUgkJU/fi_workdir/aih-tih-sc-33eb27-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.DRPknUgkJU/aih-tih-sc-33eb27-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.DRPknUgkJU/aih-tih-sc-33eb27-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2480.997607
EM: Round [1] log likelihood: -2480.937593
EM: Round [2] log likelihood: -2480.936229
EM: Round [3] log likelihood: -2480.936198
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.DRPknUgkJU/aih-tih-sc-33eb27-R1_A23WJ53LT4_1_1.fastp.fastq.gz: 296769183
Warning - not locating file: /tmp/nxf.DRPknUgkJU/aih-tih-sc-33eb27-R1_A23WJ53LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000185596.16]
WARNING, no entry stored in dbm for [ENSG00000185596.16]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
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 [ENSG00000230092.7]
WARNING, no entry stored in dbm for [ENSG00000225292.2]
WARNING, no entry stored in dbm for [ENSG00000250662.1]
ls: cannot access 'IGV_inputs': No such file or directory