.command.err - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (aih-tih-sc-a97ce1-R1_A23YTGFLT4_1)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/38114a04234a664b1fab0f6d6aa811/.command.err
Size: 19.2 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (aih-tih-sc-a97ce1-R1_A23YTGFLT4_1)
Attempt
Content

Done.
-parsing GTF file: /tmp/nxf.SJUubQnIeE/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.SJUubQnIeE/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.SJUubQnIeE/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.SJUubQnIeE/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.SJUubQnIeE/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.SJUubQnIeE/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
09:56:11 : INFO : Done.
-parsing GTF file: /tmp/nxf.SJUubQnIeE/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.SJUubQnIeE/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

[10000]   
[20000]   
[30000]   
[40000]   
[50000]   
[60000]   
[70000]   
[80000]   
[90000]   
[100000]   
[110000]   
[120000]   
[130000]   
[140000]   
[150000]   -done parsing /tmp/nxf.SJUubQnIeE/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 30,
          'low complexity anchor region' => 1,
          'seq-similar region overlap' => 37,
          'exons hit < 2' => 3,
          ' ** passed ** ' => 1222,
          'per_id < 96' => 567,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 11,
          'excessive soft clipping' => 1108
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.SJUubQnIeE/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.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]   
[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]   -fusion SPANNING read extraction for scaff: AC004980.3--UPK3BL1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   -fusion SPANNING read extraction for scaff: PRCP--RAB30

[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]   -fusion SPANNING read extraction for scaff: TLK2--AL669831.1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 10336,
          'lacks exon overlap' => 1704
        };
EM: Starting log likelihood: -732.721321
EM: Round [1] log likelihood: -732.705762
EM: Round [2] log likelihood: -732.690570
EM: Round [3] log likelihood: -732.675733
EM: Round [4] log likelihood: -732.661239
EM: Round [5] log likelihood: -732.647080
EM: Round [6] log likelihood: -732.633244
EM: Round [7] log likelihood: -732.619722
EM: Round [8] log likelihood: -732.606506
EM: Round [9] log likelihood: -732.593585
EM: Round [10] log likelihood: -732.580952
EM: Round [11] log likelihood: -732.568599
EM: Round [12] log likelihood: -732.556517
EM: Round [13] log likelihood: -732.544700
EM: Round [14] log likelihood: -732.533139
EM: Round [15] log likelihood: -732.521828
EM: Round [16] log likelihood: -732.510761
EM: Round [17] log likelihood: -732.499929
EM: Round [18] log likelihood: -732.489328
EM: Round [19] log likelihood: -732.478952
EM: Round [20] log likelihood: -732.468793
EM: Round [21] log likelihood: -732.458847
EM: Round [22] log likelihood: -732.449109
EM: Round [23] log likelihood: -732.439572
EM: Round [24] log likelihood: -732.430232
EM: Round [25] log likelihood: -732.421084
EM: Round [26] log likelihood: -732.412123
EM: Round [27] log likelihood: -732.403344
EM: Round [28] log likelihood: -732.394743
EM: Round [29] log likelihood: -732.386316
EM: Round [30] log likelihood: -732.378058
EM: Round [31] log likelihood: -732.369965
EM: Round [32] log likelihood: -732.362034
EM: Round [33] log likelihood: -732.354260
EM: Round [34] log likelihood: -732.346640
EM: Round [35] log likelihood: -732.339170
EM: Round [36] log likelihood: -732.331847
EM: Round [37] log likelihood: -732.324667
EM: Round [38] log likelihood: -732.317627
EM: Round [39] log likelihood: -732.310723
EM: Round [40] log likelihood: -732.303954
EM: Round [41] log likelihood: -732.297315
EM: Round [42] log likelihood: -732.290803
EM: Round [43] log likelihood: -732.284417
EM: Round [44] log likelihood: -732.278152
EM: Round [45] log likelihood: -732.272007
EM: Round [46] log likelihood: -732.265978
EM: Round [47] log likelihood: -732.260064
EM: Round [48] log likelihood: -732.254261
EM: Round [49] log likelihood: -732.248568
EM: Round [50] log likelihood: -732.242981
EM: Round [51] log likelihood: -732.237499
EM: Round [52] log likelihood: -732.232119
EM: Round [53] log likelihood: -732.226840
EM: Round [54] log likelihood: -732.221658
EM: Round [55] log likelihood: -732.216573
EM: Round [56] log likelihood: -732.211581
EM: Round [57] log likelihood: -732.206681
EM: Round [58] log likelihood: -732.201872
EM: Round [59] log likelihood: -732.197151
EM: Round [60] log likelihood: -732.192516
EM: Round [61] log likelihood: -732.187966
EM: Round [62] log likelihood: -732.183498
EM: Round [63] log likelihood: -732.179112
EM: Round [64] log likelihood: -732.174805
EM: Round [65] log likelihood: -732.170577
EM: Round [66] log likelihood: -732.166424
EM: Round [67] log likelihood: -732.162347
EM: Round [68] log likelihood: -732.158343
EM: Round [69] log likelihood: -732.154410
EM: Round [70] log likelihood: -732.150548
EM: Round [71] log likelihood: -732.146756
EM: Round [72] log likelihood: -732.143031
EM: Round [73] log likelihood: -732.139372
EM: Round [74] log likelihood: -732.135778
EM: Round [75] log likelihood: -732.132248
EM: Round [76] log likelihood: -732.128781
EM: Round [77] log likelihood: -732.125375
EM: Round [78] log likelihood: -732.122029
EM: Round [79] log likelihood: -732.118742
EM: Round [80] log likelihood: -732.115513
EM: Round [81] log likelihood: -732.112341
EM: Round [82] log likelihood: -732.109224
EM: Round [83] log likelihood: -732.106162
EM: Round [84] log likelihood: -732.103154
EM: Round [85] log likelihood: -732.100198
EM: Round [86] log likelihood: -732.097294
EM: Round [87] log likelihood: -732.094440
EM: Round [88] log likelihood: -732.091636
EM: Round [89] log likelihood: -732.088880
EM: Round [90] log likelihood: -732.086173
EM: Round [91] log likelihood: -732.083512
EM: Round [92] log likelihood: -732.080897
EM: Round [93] log likelihood: -732.078328
EM: Round [94] log likelihood: -732.075803
EM: Round [95] log likelihood: -732.073321
EM: Round [96] log likelihood: -732.070882
EM: Round [97] log likelihood: -732.068485
EM: Round [98] log likelihood: -732.066129
EM: Round [99] log likelihood: -732.063813
EM: Round [100] log likelihood: -732.061537
EM: Round [101] log likelihood: -732.059300
EM: Round [102] log likelihood: -732.057102
EM: Round [103] log likelihood: -732.054941
EM: Round [104] log likelihood: -732.052816
EM: Round [105] log likelihood: -732.050728
EM: Round [106] log likelihood: -732.048676
EM: Round [107] log likelihood: -732.046658
EM: Round [108] log likelihood: -732.044675
EM: Round [109] log likelihood: -732.042725
EM: Round [110] log likelihood: -732.040808
EM: Round [111] log likelihood: -732.038924
EM: Round [112] log likelihood: -732.037071
EM: Round [113] log likelihood: -732.035250
EM: Round [114] log likelihood: -732.033460
EM: Round [115] log likelihood: -732.031700
EM: Round [116] log likelihood: -732.029970
EM: Round [117] log likelihood: -732.028268
EM: Round [118] log likelihood: -732.026596
EM: Round [119] log likelihood: -732.024951
EM: Round [120] log likelihood: -732.023334
EM: Round [121] log likelihood: -732.021744
EM: Round [122] log likelihood: -732.020181
EM: Round [123] log likelihood: -732.018644
EM: Round [124] log likelihood: -732.017133
EM: Round [125] log likelihood: -732.015648
EM: Round [126] log likelihood: -732.014187
EM: Round [127] log likelihood: -732.012750
EM: Round [128] log likelihood: -732.011337
EM: Round [129] log likelihood: -732.009948
EM: Round [130] log likelihood: -732.008582
EM: Round [131] log likelihood: -732.007239
EM: Round [132] log likelihood: -732.005919
EM: Round [133] log likelihood: -732.004620
EM: Round [134] log likelihood: -732.003343
EM: Round [135] log likelihood: -732.002087
EM: Round [136] log likelihood: -732.000852
EM: Round [137] log likelihood: -731.999637
EM: Round [138] log likelihood: -731.998443
EM: Round [139] log likelihood: -731.997268
EM: Round [140] log likelihood: -731.996113
EM: Round [141] log likelihood: -731.994977
EM: Round [142] log likelihood: -731.993860
EM: Round [143] log likelihood: -731.992761
EM: Round [144] log likelihood: -731.991681
EM: Round [145] log likelihood: -731.990618
EM: Round [146] log likelihood: -731.989573
EM: Round [147] log likelihood: -731.988545
EM: Round [148] log likelihood: -731.987534
EM: Round [149] log likelihood: -731.986540
EM: Round [150] log likelihood: -731.985562
EM: Round [151] log likelihood: -731.984601
EM: Round [152] log likelihood: -731.983655
EM: Round [153] log likelihood: -731.982725
EM: Round [154] log likelihood: -731.981810
EM: Round [155] log likelihood: -731.980910
EM: Round [156] log likelihood: -731.980024
EM: Round [157] log likelihood: -731.979154
EM: Round [158] log likelihood: -731.978297
EM: Round [159] log likelihood: -731.977455
EM: Round [160] log likelihood: -731.976627
EM: Round [161] log likelihood: -731.975812
EM: Round [162] log likelihood: -731.975010
EM: Round [163] log likelihood: -731.974222
EM: Round [164] log likelihood: -731.973447
EM: Round [165] log likelihood: -731.972684
EM: Round [166] log likelihood: -731.971934
EM: Round [167] log likelihood: -731.971196
EM: Round [168] log likelihood: -731.970470
EM: Round [169] log likelihood: -731.969756
EM: Round [170] log likelihood: -731.969054
EM: Round [171] log likelihood: -731.968363
EM: Round [172] log likelihood: -731.967683
EM: Round [173] log likelihood: -731.967015
EM: Round [174] log likelihood: -731.966357
EM: Round [175] log likelihood: -731.965710
EM: Round [176] log likelihood: -731.965074
EM: Round [177] log likelihood: -731.964448
EM: Round [178] log likelihood: -731.963832
EM: Round [179] log likelihood: -731.963227
EM: Round [180] log likelihood: -731.962631
EM: Round [181] log likelihood: -731.962045
EM: Round [182] log likelihood: -731.961468
EM: Round [183] log likelihood: -731.960901
EM: Round [184] log likelihood: -731.960343
EM: Round [185] log likelihood: -731.959794
EM: Round [186] log likelihood: -731.959254
EM: Round [187] log likelihood: -731.958723
EM: Round [188] log likelihood: -731.958201
EM: Round [189] log likelihood: -731.957687
EM: Round [190] log likelihood: -731.957181
EM: Round [191] log likelihood: -731.956684
EM: Round [192] log likelihood: -731.956194
EM: Round [193] log likelihood: -731.955713
EM: Round [194] log likelihood: -731.955239
EM: Round [195] log likelihood: -731.954773
EM: Round [196] log likelihood: -731.954315
EM: Round [197] log likelihood: -731.953864
EM: Round [198] log likelihood: -731.953421
EM: Round [199] log likelihood: -731.952984
EM: Round [200] log likelihood: -731.952555
EM: Round [201] log likelihood: -731.952132
EM: Round [202] log likelihood: -731.951717
EM: Round [203] log likelihood: -731.951308
EM: Round [204] log likelihood: -731.950906
EM: Round [205] log likelihood: -731.950510
EM: Round [206] log likelihood: -731.950121
EM: Round [207] log likelihood: -731.949738
EM: Round [208] log likelihood: -731.949361
EM: Round [209] log likelihood: -731.948991
EM: Round [210] log likelihood: -731.948626
EM: Round [211] log likelihood: -731.948267
EM: Round [212] log likelihood: -731.947914
EM: Round [213] log likelihood: -731.947567
EM: Round [214] log likelihood: -731.947225
EM: Round [215] log likelihood: -731.946889
EM: Round [216] log likelihood: -731.946559
EM: Round [217] log likelihood: -731.946233
EM: Round [218] log likelihood: -731.945913
EM: Round [219] log likelihood: -731.945598
EM: Round [220] log likelihood: -731.945289
EM: Round [221] log likelihood: -731.944984
EM: Round [222] log likelihood: -731.944684
EM: Round [223] log likelihood: -731.944389
EM: Round [224] log likelihood: -731.944099
EM: Round [225] log likelihood: -731.943813
EM: Round [226] log likelihood: -731.943532
EM: Round [227] log likelihood: -731.943255
EM: Round [228] log likelihood: -731.942984
EM: Round [229] log likelihood: -731.942716
EM: Round [230] log likelihood: -731.942453
EM: Round [231] log likelihood: -731.942194
EM: Round [232] log likelihood: -731.941939
EM: Round [233] log likelihood: -731.941688
EM: Round [234] log likelihood: -731.941441
EM: Round [235] log likelihood: -731.941199
EM: Round [236] log likelihood: -731.940960
EM: Round [237] log likelihood: -731.940725
EM: Round [238] log likelihood: -731.940494
EM: Round [239] log likelihood: -731.940266
EM: Round [240] log likelihood: -731.940042
EM: Round [241] log likelihood: -731.939822
EM: Round [242] log likelihood: -731.939605
EM: Round [243] log likelihood: -731.939392
EM: Round [244] log likelihood: -731.939183
EM: Round [245] log likelihood: -731.938976
EM: Round [246] log likelihood: -731.938773
EM: Round [247] log likelihood: -731.938573
EM: Round [248] log likelihood: -731.938377
EM: Round [249] log likelihood: -731.938184
EM: Round [250] log likelihood: -731.937993
EM: Round [251] log likelihood: -731.937806
EM: Round [252] log likelihood: -731.937622
EM: Round [253] log likelihood: -731.937441
EM: Round [254] log likelihood: -731.937262
EM: Round [255] log likelihood: -731.937087
EM: Round [256] log likelihood: -731.936914
EM: Round [257] log likelihood: -731.936744
EM: Round [258] log likelihood: -731.936577
EM: Round [259] log likelihood: -731.936413
EM: Round [260] log likelihood: -731.936251
EM: Round [261] log likelihood: -731.936092
EM: Round [262] log likelihood: -731.935935
EM: Round [263] log likelihood: -731.935781
EM: Round [264] log likelihood: -731.935630
EM: Round [265] log likelihood: -731.935480
EM: Round [266] log likelihood: -731.935334
EM: Round [267] log likelihood: -731.935189
EM: Round [268] log likelihood: -731.935047
EM: Round [269] log likelihood: -731.934907
EM: Round [270] log likelihood: -731.934770
EM: Round [271] log likelihood: -731.934634
EM: Round [272] log likelihood: -731.934501
EM: Round [273] log likelihood: -731.934370
EM: Round [274] log likelihood: -731.934241
EM: Round [275] log likelihood: -731.934114
EM: Round [276] log likelihood: -731.933989
EM: Round [277] log likelihood: -731.933867
EM: Round [278] log likelihood: -731.933746
EM: Round [279] log likelihood: -731.933627
EM: Round [280] log likelihood: -731.933510
EM: Round [281] log likelihood: -731.933395
EM: Round [282] log likelihood: -731.933281
EM: Round [283] log likelihood: -731.933170
EM: Round [284] log likelihood: -731.933060
EM: Round [285] log likelihood: -731.932952
EM: Round [286] log likelihood: -731.932846
EM: Round [287] log likelihood: -731.932742
EM: Round [288] log likelihood: -731.932639
EM: Round [289] log likelihood: -731.932538
EM: Round [290] log likelihood: -731.932438
EM: Stopping iterations at round 290 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.SJUubQnIeE/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.SJUubQnIeE/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.SJUubQnIeE/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.SJUubQnIeE/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.SJUubQnIeE/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.SJUubQnIeE/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.SJUubQnIeE/aih-tih-sc-a97ce1-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.SJUubQnIeE/fi_workdir/aih-tih-sc-a97ce1-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.SJUubQnIeE/fi_workdir/aih-tih-sc-a97ce1-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.SJUubQnIeE/fi_workdir/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.SJUubQnIeE/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.SJUubQnIeE/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -719.400948
EM: Round [1] log likelihood: -719.400948
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.SJUubQnIeE/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 216439276
Warning - not locating file: /tmp/nxf.SJUubQnIeE/aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000230305.2]
WARNING, no entry stored in dbm for [ENSG00000228327.3]
WARNING, no entry stored in dbm for [ENSG00000228327.3]
ls: cannot access 'IGV_inputs': No such file or directory