Done.
-parsing GTF file: /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.k6iMamKp4Y/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.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00766_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00766_B23MVV7LT4_1.star.sortedByCoord.out.bam
10:05:08 : INFO : Done.
-parsing GTF file: /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
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[1040000] -done parsing /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
'seq-similar region overlap' => 547,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 56,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 4,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 1,
' ** passed ** ' => 1147,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 8,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 81,
'per_id < 96' => 5998,
'small anchor length' => 2,
'low complexity anchor region' => 3,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 7,
'num genes matched < 2' => 30,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 18,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 8,
'excessive soft clipping' => 10146,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 16
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_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: PCDHA11--PCDHA13
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[60000] -fusion SPANNING read extraction for scaff: RRP36--PEX6
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[9000]
[10000]
[11000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 39001,
'lacks exon overlap' => 11793
};
EM: Starting log likelihood: -1192.060136
EM: Round [1] log likelihood: -1192.049448
EM: Round [2] log likelihood: -1192.039108
EM: Round [3] log likelihood: -1192.029099
EM: Round [4] log likelihood: -1192.019409
EM: Round [5] log likelihood: -1192.010024
EM: Round [6] log likelihood: -1192.000932
EM: Round [7] log likelihood: -1191.992121
EM: Round [8] log likelihood: -1191.983581
EM: Round [9] log likelihood: -1191.975300
EM: Round [10] log likelihood: -1191.967269
EM: Round [11] log likelihood: -1191.959478
EM: Round [12] log likelihood: -1191.951919
EM: Round [13] log likelihood: -1191.944582
EM: Round [14] log likelihood: -1191.937460
EM: Round [15] log likelihood: -1191.930546
EM: Round [16] log likelihood: -1191.923830
EM: Round [17] log likelihood: -1191.917308
EM: Round [18] log likelihood: -1191.910971
EM: Round [19] log likelihood: -1191.904813
EM: Round [20] log likelihood: -1191.898829
EM: Round [21] log likelihood: -1191.893012
EM: Round [22] log likelihood: -1191.887357
EM: Round [23] log likelihood: -1191.881859
EM: Round [24] log likelihood: -1191.876511
EM: Round [25] log likelihood: -1191.871310
EM: Round [26] log likelihood: -1191.866251
EM: Round [27] log likelihood: -1191.861329
EM: Round [28] log likelihood: -1191.856539
EM: Round [29] log likelihood: -1191.851878
EM: Round [30] log likelihood: -1191.847341
EM: Round [31] log likelihood: -1191.842925
EM: Round [32] log likelihood: -1191.838626
EM: Round [33] log likelihood: -1191.834441
EM: Round [34] log likelihood: -1191.830365
EM: Round [35] log likelihood: -1191.826395
EM: Round [36] log likelihood: -1191.822529
EM: Round [37] log likelihood: -1191.818764
EM: Round [38] log likelihood: -1191.815096
EM: Round [39] log likelihood: -1191.811522
EM: Round [40] log likelihood: -1191.808040
EM: Round [41] log likelihood: -1191.804647
EM: Round [42] log likelihood: -1191.801340
EM: Round [43] log likelihood: -1191.798118
EM: Round [44] log likelihood: -1191.794977
EM: Round [45] log likelihood: -1191.791915
EM: Round [46] log likelihood: -1191.788931
EM: Round [47] log likelihood: -1191.786021
EM: Round [48] log likelihood: -1191.783184
EM: Round [49] log likelihood: -1191.780418
EM: Round [50] log likelihood: -1191.777721
EM: Round [51] log likelihood: -1191.775091
EM: Round [52] log likelihood: -1191.772526
EM: Round [53] log likelihood: -1191.770024
EM: Round [54] log likelihood: -1191.767584
EM: Round [55] log likelihood: -1191.765204
EM: Round [56] log likelihood: -1191.762882
EM: Round [57] log likelihood: -1191.760617
EM: Round [58] log likelihood: -1191.758408
EM: Round [59] log likelihood: -1191.756252
EM: Round [60] log likelihood: -1191.754148
EM: Round [61] log likelihood: -1191.752096
EM: Round [62] log likelihood: -1191.750093
EM: Round [63] log likelihood: -1191.748139
EM: Round [64] log likelihood: -1191.746232
EM: Round [65] log likelihood: -1191.744370
EM: Round [66] log likelihood: -1191.742553
EM: Round [67] log likelihood: -1191.740780
EM: Round [68] log likelihood: -1191.739050
EM: Round [69] log likelihood: -1191.737360
EM: Round [70] log likelihood: -1191.735711
EM: Round [71] log likelihood: -1191.734101
EM: Round [72] log likelihood: -1191.732530
EM: Round [73] log likelihood: -1191.730996
EM: Round [74] log likelihood: -1191.729498
EM: Round [75] log likelihood: -1191.728036
EM: Round [76] log likelihood: -1191.726608
EM: Round [77] log likelihood: -1191.725214
EM: Round [78] log likelihood: -1191.723852
EM: Round [79] log likelihood: -1191.722523
EM: Round [80] log likelihood: -1191.721225
EM: Round [81] log likelihood: -1191.719958
EM: Round [82] log likelihood: -1191.718720
EM: Round [83] log likelihood: -1191.717511
EM: Round [84] log likelihood: -1191.716331
EM: Round [85] log likelihood: -1191.715178
EM: Round [86] log likelihood: -1191.714052
EM: Round [87] log likelihood: -1191.712952
EM: Round [88] log likelihood: -1191.711878
EM: Round [89] log likelihood: -1191.710828
EM: Round [90] log likelihood: -1191.709804
EM: Round [91] log likelihood: -1191.708803
EM: Round [92] log likelihood: -1191.707825
EM: Round [93] log likelihood: -1191.706870
EM: Round [94] log likelihood: -1191.705936
EM: Round [95] log likelihood: -1191.705025
EM: Round [96] log likelihood: -1191.704135
EM: Round [97] log likelihood: -1191.703265
EM: Round [98] log likelihood: -1191.702415
EM: Round [99] log likelihood: -1191.701585
EM: Round [100] log likelihood: -1191.700774
EM: Round [101] log likelihood: -1191.699981
EM: Round [102] log likelihood: -1191.699207
EM: Round [103] log likelihood: -1191.698450
EM: Round [104] log likelihood: -1191.697711
EM: Round [105] log likelihood: -1191.696989
EM: Round [106] log likelihood: -1191.696284
EM: Round [107] log likelihood: -1191.695594
EM: Round [108] log likelihood: -1191.694921
EM: Round [109] log likelihood: -1191.694262
EM: Round [110] log likelihood: -1191.693619
EM: Round [111] log likelihood: -1191.692991
EM: Round [112] log likelihood: -1191.692376
EM: Round [113] log likelihood: -1191.691776
EM: Round [114] log likelihood: -1191.691190
EM: Round [115] log likelihood: -1191.690617
EM: Round [116] log likelihood: -1191.690057
EM: Round [117] log likelihood: -1191.689509
EM: Round [118] log likelihood: -1191.688975
EM: Round [119] log likelihood: -1191.688452
EM: Round [120] log likelihood: -1191.687941
EM: Round [121] log likelihood: -1191.687442
EM: Round [122] log likelihood: -1191.686954
EM: Round [123] log likelihood: -1191.686477
EM: Round [124] log likelihood: -1191.686011
EM: Round [125] log likelihood: -1191.685556
EM: Round [126] log likelihood: -1191.685111
EM: Round [127] log likelihood: -1191.684676
EM: Round [128] log likelihood: -1191.684251
EM: Round [129] log likelihood: -1191.683835
EM: Round [130] log likelihood: -1191.683429
EM: Round [131] log likelihood: -1191.683032
EM: Round [132] log likelihood: -1191.682644
EM: Round [133] log likelihood: -1191.682265
EM: Round [134] log likelihood: -1191.681894
EM: Round [135] log likelihood: -1191.681532
EM: Round [136] log likelihood: -1191.681178
EM: Round [137] log likelihood: -1191.680832
EM: Round [138] log likelihood: -1191.680493
EM: Round [139] log likelihood: -1191.680163
EM: Round [140] log likelihood: -1191.679840
EM: Round [141] log likelihood: -1191.679524
EM: Round [142] log likelihood: -1191.679215
EM: Round [143] log likelihood: -1191.678913
EM: Round [144] log likelihood: -1191.678618
EM: Round [145] log likelihood: -1191.678330
EM: Round [146] log likelihood: -1191.678048
EM: Round [147] log likelihood: -1191.677772
EM: Round [148] log likelihood: -1191.677503
EM: Round [149] log likelihood: -1191.677239
EM: Round [150] log likelihood: -1191.676982
EM: Round [151] log likelihood: -1191.676730
EM: Round [152] log likelihood: -1191.676484
EM: Round [153] log likelihood: -1191.676244
EM: Round [154] log likelihood: -1191.676009
EM: Round [155] log likelihood: -1191.675779
EM: Round [156] log likelihood: -1191.675554
EM: Round [157] log likelihood: -1191.675335
EM: Round [158] log likelihood: -1191.675120
EM: Round [159] log likelihood: -1191.674910
EM: Round [160] log likelihood: -1191.674705
EM: Round [161] log likelihood: -1191.674505
EM: Round [162] log likelihood: -1191.674309
EM: Round [163] log likelihood: -1191.674117
EM: Round [164] log likelihood: -1191.673930
EM: Round [165] log likelihood: -1191.673746
EM: Round [166] log likelihood: -1191.673567
EM: Round [167] log likelihood: -1191.673392
EM: Round [168] log likelihood: -1191.673221
EM: Round [169] log likelihood: -1191.673054
EM: Round [170] log likelihood: -1191.672890
EM: Round [171] log likelihood: -1191.672730
EM: Round [172] log likelihood: -1191.672574
EM: Round [173] log likelihood: -1191.672421
EM: Round [174] log likelihood: -1191.672272
EM: Round [175] log likelihood: -1191.672126
EM: Round [176] log likelihood: -1191.671983
EM: Round [177] log likelihood: -1191.671843
EM: Round [178] log likelihood: -1191.671707
EM: Round [179] log likelihood: -1191.671574
EM: Round [180] log likelihood: -1191.671443
EM: Round [181] log likelihood: -1191.671316
EM: Round [182] log likelihood: -1191.671191
EM: Round [183] log likelihood: -1191.671069
EM: Round [184] log likelihood: -1191.670950
EM: Round [185] log likelihood: -1191.670833
EM: Round [186] log likelihood: -1191.670719
EM: Round [187] log likelihood: -1191.670608
EM: Round [188] log likelihood: -1191.670499
EM: Round [189] log likelihood: -1191.670393
EM: Round [190] log likelihood: -1191.670289
EM: Round [191] log likelihood: -1191.670187
EM: Round [192] log likelihood: -1191.670088
EM: Stopping iterations at round 192 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -1131.300251
EM: Round [1] log likelihood: -1131.300251
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1_1.fastp.fastq.gz: 202924806
Warning - not locating file: /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.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 [ENSG00000277125.1]
WARNING, no entry stored in dbm for [ENSG00000277125.1]
ls: cannot access 'IGV_inputs': No such file or directory