File Info

Filename
.command.err
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/b99b2f9c16ab4e1a228c4b954ef28c/.command.err
Size
17.0 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2)
Attempt

Content

View in new tab 
Done.
-parsing GTF file: /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.EWpmWH8u8E/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.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam 1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index 1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam
11:26:18 : INFO : Done.
-parsing GTF file: /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.gtf
-parsing /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam

[10000]   
[20000]   
[30000]   
[40000]   
[50000]   
[60000]   
[70000]   
[80000]   
[90000]   
[100000]   
[110000]   
[120000]   
[130000]   
[140000]   
[150000]   
[160000]   
[170000]   
[180000]   
[190000]   
[200000]   
[210000]   
[220000]   
[230000]   
[240000]   
[250000]   
[260000]   
[270000]   
[280000]   
[290000]   
[300000]   
[310000]   
[320000]   
[330000]   
[340000]   
[350000]   
[360000]   
[370000]   
[380000]   
[390000]   
[400000]   
[410000]   
[420000]   -done parsing /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 25,
          ' ** passed ** ' => 7550,
          'small anchor length' => 180,
          'per_id < 96' => 1551,
          'seq-similar region overlap' => 188,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 2,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 18,
          'excessive soft clipping' => 2132,
          'num genes matched < 2' => 2
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   
[57000]   
[58000]   
[59000]   
[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   -fusion SPANNING read extraction for scaff: TLK2--LINC01347

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 43027,
          'lacks exon overlap' => 875
        };
EM: Starting log likelihood: -1584.148289
EM: Round [1] log likelihood: -1584.073883
EM: Round [2] log likelihood: -1584.039919
EM: Round [3] log likelihood: -1584.008277
EM: Round [4] log likelihood: -1583.978302
EM: Round [5] log likelihood: -1583.949876
EM: Round [6] log likelihood: -1583.922899
EM: Round [7] log likelihood: -1583.897279
EM: Round [8] log likelihood: -1583.872932
EM: Round [9] log likelihood: -1583.849781
EM: Round [10] log likelihood: -1583.827753
EM: Round [11] log likelihood: -1583.806783
EM: Round [12] log likelihood: -1583.786810
EM: Round [13] log likelihood: -1583.767777
EM: Round [14] log likelihood: -1583.749631
EM: Round [15] log likelihood: -1583.732325
EM: Round [16] log likelihood: -1583.715811
EM: Round [17] log likelihood: -1583.700049
EM: Round [18] log likelihood: -1583.684998
EM: Round [19] log likelihood: -1583.670621
EM: Round [20] log likelihood: -1583.656883
EM: Round [21] log likelihood: -1583.643752
EM: Round [22] log likelihood: -1583.631198
EM: Round [23] log likelihood: -1583.619191
EM: Round [24] log likelihood: -1583.607705
EM: Round [25] log likelihood: -1583.596715
EM: Round [26] log likelihood: -1583.586195
EM: Round [27] log likelihood: -1583.576125
EM: Round [28] log likelihood: -1583.566483
EM: Round [29] log likelihood: -1583.557248
EM: Round [30] log likelihood: -1583.548401
EM: Round [31] log likelihood: -1583.539925
EM: Round [32] log likelihood: -1583.531803
EM: Round [33] log likelihood: -1583.524018
EM: Round [34] log likelihood: -1583.516556
EM: Round [35] log likelihood: -1583.509401
EM: Round [36] log likelihood: -1583.502541
EM: Round [37] log likelihood: -1583.495961
EM: Round [38] log likelihood: -1583.489650
EM: Round [39] log likelihood: -1583.483596
EM: Round [40] log likelihood: -1583.477788
EM: Round [41] log likelihood: -1583.472215
EM: Round [42] log likelihood: -1583.466866
EM: Round [43] log likelihood: -1583.461733
EM: Round [44] log likelihood: -1583.456807
EM: Round [45] log likelihood: -1583.452077
EM: Round [46] log likelihood: -1583.447536
EM: Round [47] log likelihood: -1583.443177
EM: Round [48] log likelihood: -1583.438991
EM: Round [49] log likelihood: -1583.434971
EM: Round [50] log likelihood: -1583.431111
EM: Round [51] log likelihood: -1583.427403
EM: Round [52] log likelihood: -1583.423841
EM: Round [53] log likelihood: -1583.420420
EM: Round [54] log likelihood: -1583.417134
EM: Round [55] log likelihood: -1583.413977
EM: Round [56] log likelihood: -1583.410943
EM: Round [57] log likelihood: -1583.408028
EM: Round [58] log likelihood: -1583.405228
EM: Round [59] log likelihood: -1583.402536
EM: Round [60] log likelihood: -1583.399950
EM: Round [61] log likelihood: -1583.397464
EM: Round [62] log likelihood: -1583.395076
EM: Round [63] log likelihood: -1583.392780
EM: Round [64] log likelihood: -1583.390573
EM: Round [65] log likelihood: -1583.388451
EM: Round [66] log likelihood: -1583.386412
EM: Round [67] log likelihood: -1583.384452
EM: Round [68] log likelihood: -1583.382568
EM: Round [69] log likelihood: -1583.380756
EM: Round [70] log likelihood: -1583.379014
EM: Round [71] log likelihood: -1583.377339
EM: Round [72] log likelihood: -1583.375729
EM: Round [73] log likelihood: -1583.374181
EM: Round [74] log likelihood: -1583.372693
EM: Round [75] log likelihood: -1583.371261
EM: Round [76] log likelihood: -1583.369885
EM: Round [77] log likelihood: -1583.368561
EM: Round [78] log likelihood: -1583.367289
EM: Round [79] log likelihood: -1583.366065
EM: Round [80] log likelihood: -1583.364888
EM: Round [81] log likelihood: -1583.363756
EM: Round [82] log likelihood: -1583.362667
EM: Round [83] log likelihood: -1583.361620
EM: Round [84] log likelihood: -1583.360613
EM: Round [85] log likelihood: -1583.359644
EM: Round [86] log likelihood: -1583.358713
EM: Round [87] log likelihood: -1583.357817
EM: Round [88] log likelihood: -1583.356955
EM: Round [89] log likelihood: -1583.356126
EM: Round [90] log likelihood: -1583.355329
EM: Round [91] log likelihood: -1583.354562
EM: Round [92] log likelihood: -1583.353824
EM: Round [93] log likelihood: -1583.353115
EM: Round [94] log likelihood: -1583.352432
EM: Round [95] log likelihood: -1583.351775
EM: Round [96] log likelihood: -1583.351144
EM: Round [97] log likelihood: -1583.350536
EM: Round [98] log likelihood: -1583.349952
EM: Round [99] log likelihood: -1583.349389
EM: Round [100] log likelihood: -1583.348848
EM: Round [101] log likelihood: -1583.348328
EM: Round [102] log likelihood: -1583.347827
EM: Round [103] log likelihood: -1583.347346
EM: Round [104] log likelihood: -1583.346883
EM: Round [105] log likelihood: -1583.346437
EM: Round [106] log likelihood: -1583.346008
EM: Round [107] log likelihood: -1583.345595
EM: Round [108] log likelihood: -1583.345199
EM: Round [109] log likelihood: -1583.344817
EM: Round [110] log likelihood: -1583.344449
EM: Round [111] log likelihood: -1583.344096
EM: Round [112] log likelihood: -1583.343756
EM: Round [113] log likelihood: -1583.343429
EM: Round [114] log likelihood: -1583.343114
EM: Round [115] log likelihood: -1583.342811
EM: Round [116] log likelihood: -1583.342520
EM: Round [117] log likelihood: -1583.342239
EM: Round [118] log likelihood: -1583.341970
EM: Round [119] log likelihood: -1583.341710
EM: Round [120] log likelihood: -1583.341460
EM: Round [121] log likelihood: -1583.341220
EM: Round [122] log likelihood: -1583.340989
EM: Round [123] log likelihood: -1583.340767
EM: Round [124] log likelihood: -1583.340553
EM: Round [125] log likelihood: -1583.340347
EM: Round [126] log likelihood: -1583.340149
EM: Round [127] log likelihood: -1583.339958
EM: Round [128] log likelihood: -1583.339775
EM: Round [129] log likelihood: -1583.339598
EM: Round [130] log likelihood: -1583.339429
EM: Round [131] log likelihood: -1583.339265
EM: Round [132] log likelihood: -1583.339108
EM: Round [133] log likelihood: -1583.338957
EM: Round [134] log likelihood: -1583.338811
EM: Round [135] log likelihood: -1583.338671
EM: Round [136] log likelihood: -1583.338537
EM: Round [137] log likelihood: -1583.338407
EM: Round [138] log likelihood: -1583.338282
EM: Round [139] log likelihood: -1583.338162
EM: Round [140] log likelihood: -1583.338047
EM: Round [141] log likelihood: -1583.337936
EM: Round [142] log likelihood: -1583.337829
EM: Round [143] log likelihood: -1583.337726
EM: Round [144] log likelihood: -1583.337627
EM: Stopping iterations at round 144 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam into /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords

CMD: touch /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords > /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.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.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.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.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -1464.916540
EM: Round [1] log likelihood: -1464.877460
EM: Round [2] log likelihood: -1464.876909
EM: Round [3] log likelihood: -1464.876901
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz: 280329213
Warning - not locating file: /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.gmap_trinity_GG.fusions.gff3.bed
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 [ENSG00000214837.8]
ls: cannot access 'IGV_inputs': No such file or directory