Done.
-parsing GTF file: /tmp/nxf.zyhqoIjoIy/aih-tih-sc-8c7069-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.zyhqoIjoIy/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.zyhqoIjoIy/aih-tih-sc-8c7069-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.zyhqoIjoIy/aih-tih-sc-8c7069-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.zyhqoIjoIy/fi_workdir/aih-tih-sc-8c7069-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.zyhqoIjoIy/fi_workdir/aih-tih-sc-8c7069-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-8c7069-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-8c7069-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
10:23:58 : INFO : Done.
-parsing GTF file: /tmp/nxf.zyhqoIjoIy/fi_workdir/aih-tih-sc-8c7069-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.zyhqoIjoIy/fi_workdir/aih-tih-sc-8c7069-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
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[2400000] -done parsing /tmp/nxf.zyhqoIjoIy/fi_workdir/aih-tih-sc-8c7069-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 80,
'low complexity anchor region' => 78,
'excessive soft clipping' => 17068,
'small anchor length' => 27,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 147,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 105,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 328,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 410,
'per_id < 96' => 9854,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 625,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 164,
'num genes matched < 2' => 22,
'seq-similar region overlap' => 62,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 573,
' ** passed ** ' => 4749
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.zyhqoIjoIy/fi_workdir/aih-tih-sc-8c7069-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[16000] -fusion SPANNING read extraction for scaff: AC004596.1--HROB
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[175000] -fusion SPANNING read extraction for scaff: BAG6--STPG4
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[61000] -fusion SPANNING read extraction for scaff: CLPTM1L--DNAH5
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[35000] -fusion SPANNING read extraction for scaff: COBLL1--AC079248.1
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[41000] -fusion SPANNING read extraction for scaff: HSF2--PPP4R1
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[60000] -fusion SPANNING read extraction for scaff: JPT2--CRAMP1
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[67000] -fusion SPANNING read extraction for scaff: MGAT3--TAB1
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[34000] -fusion SPANNING read extraction for scaff: MKLN1--DPP6
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[92000] -fusion SPANNING read extraction for scaff: NEB--FMNL2
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[16000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1
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[15000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
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[18000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
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[315000] -fusion SPANNING read extraction for scaff: PTK2--AGO2
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[32000] -fusion SPANNING read extraction for scaff: RALGPS1--PBX3
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[28000] -fusion SPANNING read extraction for scaff: RBPMS--AC090095.1
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[28000] -fusion SPANNING read extraction for scaff: RBPMS--AC090132.1
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[52000] -fusion SPANNING read extraction for scaff: RNF19B--AL031602.1
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[37000] -fusion SPANNING read extraction for scaff: RSU1--RBM20
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[44000] -fusion SPANNING read extraction for scaff: SNX9--SPAG16
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[13000] -fusion SPANNING read extraction for scaff: STON1--GTF2A1L
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[37000] -fusion SPANNING read extraction for scaff: TANK--ITGA4
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[39000] -fusion SPANNING read extraction for scaff: TET1--FHAD1
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[44000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[12000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[110000] -fusion SPANNING read extraction for scaff: TRIP12--C12orf29
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[397000] -fusion SPANNING read extraction for scaff: TRPS1--AC025366.1
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[26000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[9000] -fusion SPANNING read extraction for scaff: ZNRD1ASP--RNF39
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[19000] -fusion SPANNING read extraction for scaff: ZYG11B--AL033530.1
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 19553,
'seq similar region alignment' => 16187
};
EM: Starting log likelihood: -7135.723421
EM: Round [1] log likelihood: -7135.625757
EM: Round [2] log likelihood: -7135.602924
EM: Round [3] log likelihood: -7135.583388
EM: Round [4] log likelihood: -7135.564548
EM: Round [5] log likelihood: -7135.546286
EM: Round [6] log likelihood: -7135.528576
EM: Round [7] log likelihood: -7135.511399
EM: Round [8] log likelihood: -7135.494732
EM: Round [9] log likelihood: -7135.478557
EM: Round [10] log likelihood: -7135.462855
EM: Round [11] log likelihood: -7135.447610
EM: Round [12] log likelihood: -7135.432804
EM: Round [13] log likelihood: -7135.418421
EM: Round [14] log likelihood: -7135.404448
EM: Round [15] log likelihood: -7135.390869
EM: Round [16] log likelihood: -7135.377670
EM: Round [17] log likelihood: -7135.364839
EM: Round [18] log likelihood: -7135.352363
EM: Round [19] log likelihood: -7135.340231
EM: Round [20] log likelihood: -7135.328430
EM: Round [21] log likelihood: -7135.316950
EM: Round [22] log likelihood: -7135.305780
EM: Round [23] log likelihood: -7135.294910
EM: Round [24] log likelihood: -7135.284332
EM: Round [25] log likelihood: -7135.274034
EM: Round [26] log likelihood: -7135.264009
EM: Round [27] log likelihood: -7135.254248
EM: Round [28] log likelihood: -7135.244743
EM: Round [29] log likelihood: -7135.235486
EM: Round [30] log likelihood: -7135.226469
EM: Round [31] log likelihood: -7135.217685
EM: Round [32] log likelihood: -7135.209127
EM: Round [33] log likelihood: -7135.200789
EM: Round [34] log likelihood: -7135.192663
EM: Round [35] log likelihood: -7135.184744
EM: Round [36] log likelihood: -7135.177026
EM: Round [37] log likelihood: -7135.169502
EM: Round [38] log likelihood: -7135.162167
EM: Round [39] log likelihood: -7135.155016
EM: Round [40] log likelihood: -7135.148044
EM: Round [41] log likelihood: -7135.141245
EM: Round [42] log likelihood: -7135.134614
EM: Round [43] log likelihood: -7135.128147
EM: Round [44] log likelihood: -7135.121840
EM: Round [45] log likelihood: -7135.115687
EM: Round [46] log likelihood: -7135.109685
EM: Round [47] log likelihood: -7135.103829
EM: Round [48] log likelihood: -7135.098116
EM: Round [49] log likelihood: -7135.092542
EM: Round [50] log likelihood: -7135.087102
EM: Round [51] log likelihood: -7135.081793
EM: Round [52] log likelihood: -7135.076613
EM: Round [53] log likelihood: -7135.071556
EM: Round [54] log likelihood: -7135.066621
EM: Round [55] log likelihood: -7135.061804
EM: Round [56] log likelihood: -7135.057101
EM: Round [57] log likelihood: -7135.052511
EM: Round [58] log likelihood: -7135.048029
EM: Round [59] log likelihood: -7135.043653
EM: Round [60] log likelihood: -7135.039381
EM: Round [61] log likelihood: -7135.035209
EM: Round [62] log likelihood: -7135.031136
EM: Round [63] log likelihood: -7135.027158
EM: Round [64] log likelihood: -7135.023273
EM: Round [65] log likelihood: -7135.019479
EM: Round [66] log likelihood: -7135.015774
EM: Round [67] log likelihood: -7135.012154
EM: Round [68] log likelihood: -7135.008620
EM: Round [69] log likelihood: -7135.005167
EM: Round [70] log likelihood: -7135.001794
EM: Round [71] log likelihood: -7134.998499
EM: Round [72] log likelihood: -7134.995280
EM: Round [73] log likelihood: -7134.992136
EM: Round [74] log likelihood: -7134.989064
EM: Round [75] log likelihood: -7134.986062
EM: Round [76] log likelihood: -7134.983130
EM: Round [77] log likelihood: -7134.980265
EM: Round [78] log likelihood: -7134.977465
EM: Round [79] log likelihood: -7134.974729
EM: Round [80] log likelihood: -7134.972056
EM: Round [81] log likelihood: -7134.969443
EM: Round [82] log likelihood: -7134.966891
EM: Round [83] log likelihood: -7134.964396
EM: Round [84] log likelihood: -7134.961958
EM: Round [85] log likelihood: -7134.959575
EM: Round [86] log likelihood: -7134.957246
EM: Round [87] log likelihood: -7134.954970
EM: Round [88] log likelihood: -7134.952745
EM: Round [89] log likelihood: -7134.950571
EM: Round [90] log likelihood: -7134.948445
EM: Round [91] log likelihood: -7134.946368
EM: Round [92] log likelihood: -7134.944337
EM: Round [93] log likelihood: -7134.942352
EM: Round [94] log likelihood: -7134.940411
EM: Round [95] log likelihood: -7134.938514
EM: Round [96] log likelihood: -7134.936660
EM: Round [97] log likelihood: -7134.934847
EM: Round [98] log likelihood: -7134.933075
EM: Round [99] log likelihood: -7134.931342
EM: Round [100] log likelihood: -7134.929648
EM: Round [101] log likelihood: -7134.927992
EM: Round [102] log likelihood: -7134.926373
EM: Round [103] log likelihood: -7134.924790
EM: Round [104] log likelihood: -7134.923242
EM: Round [105] log likelihood: -7134.921729
EM: Round [106] log likelihood: -7134.920249
EM: Round [107] log likelihood: -7134.918802
EM: Round [108] log likelihood: -7134.917387
EM: Round [109] log likelihood: -7134.916004
EM: Round [110] log likelihood: -7134.914651
EM: Round [111] log likelihood: -7134.913329
EM: Round [112] log likelihood: -7134.912035
EM: Round [113] log likelihood: -7134.910770
EM: Round [114] log likelihood: -7134.909534
EM: Round [115] log likelihood: -7134.908324
EM: Round [116] log likelihood: -7134.907141
EM: Round [117] log likelihood: -7134.905985
EM: Round [118] log likelihood: -7134.904854
EM: Round [119] log likelihood: -7134.903747
EM: Round [120] log likelihood: -7134.902666
EM: Round [121] log likelihood: -7134.901608
EM: Round [122] log likelihood: -7134.900573
EM: Round [123] log likelihood: -7134.899561
EM: Round [124] log likelihood: -7134.898571
EM: Round [125] log likelihood: -7134.897604
EM: Round [126] log likelihood: -7134.896657
EM: Round [127] log likelihood: -7134.895731
EM: Round [128] log likelihood: -7134.894826
EM: Round [129] log likelihood: -7134.893940
EM: Round [130] log likelihood: -7134.893074
EM: Round [131] log likelihood: -7134.892227
EM: Round [132] log likelihood: -7134.891398
EM: Round [133] log likelihood: -7134.890587
EM: Round [134] log likelihood: -7134.889795
EM: Round [135] log likelihood: -7134.889019
EM: Round [136] log likelihood: -7134.888261
EM: Round [137] log likelihood: -7134.887519
EM: Round [138] log likelihood: -7134.886793
EM: Round [139] log likelihood: -7134.886084
EM: Round [140] log likelihood: -7134.885389
EM: Round [141] log likelihood: -7134.884710
EM: Round [142] log likelihood: -7134.884046
EM: Round [143] log likelihood: -7134.883396
EM: Round [144] log likelihood: -7134.882761
EM: Round [145] log likelihood: -7134.882139
EM: Round [146] log likelihood: -7134.881531
EM: Round [147] log likelihood: -7134.880936
EM: Round [148] log likelihood: -7134.880354
EM: Round [149] log likelihood: -7134.879785
EM: Round [150] log likelihood: -7134.879228
EM: Round [151] log likelihood: -7134.878683
EM: Round [152] log likelihood: -7134.878150
EM: Round [153] log likelihood: -7134.877629
EM: Round [154] log likelihood: -7134.877119
EM: Round [155] log likelihood: -7134.876620
EM: Round [156] log likelihood: -7134.876132
EM: Round [157] log likelihood: -7134.875655
EM: Round [158] log likelihood: -7134.875188
EM: Round [159] log likelihood: -7134.874731
EM: Round [160] log likelihood: -7134.874284
EM: Round [161] log likelihood: -7134.873847
EM: Round [162] log likelihood: -7134.873419
EM: Round [163] log likelihood: -7134.873001
EM: Round [164] log likelihood: -7134.872591
EM: Round [165] log likelihood: -7134.872191
EM: Round [166] log likelihood: -7134.871799
EM: Round [167] log likelihood: -7134.871416
EM: Round [168] log likelihood: -7134.871041
EM: Round [169] log likelihood: -7134.870674
EM: Round [170] log likelihood: -7134.870315
EM: Round [171] log likelihood: -7134.869964
EM: Round [172] log likelihood: -7134.869620
EM: Round [173] log likelihood: -7134.869284
EM: Round [174] log likelihood: -7134.868955
EM: Round [175] log likelihood: -7134.868634
EM: Round [176] log likelihood: -7134.868319
EM: Round [177] log likelihood: -7134.868011
EM: Round [178] log likelihood: -7134.867710
EM: Round [179] log likelihood: -7134.867415
EM: Round [180] log likelihood: -7134.867127
EM: Round [181] log likelihood: -7134.866845
EM: Round [182] log likelihood: -7134.866569
EM: Round [183] log likelihood: -7134.866299
EM: Round [184] log likelihood: -7134.866035
EM: Round [185] log likelihood: -7134.865777
EM: Round [186] log likelihood: -7134.865524
EM: Round [187] log likelihood: -7134.865276
EM: Round [188] log likelihood: -7134.865034
EM: Round [189] log likelihood: -7134.864797
EM: Round [190] log likelihood: -7134.864566
EM: Round [191] log likelihood: -7134.864339
EM: Round [192] log likelihood: -7134.864117
EM: Round [193] log likelihood: -7134.863900
EM: Round [194] log likelihood: -7134.863688
EM: Round [195] log likelihood: -7134.863480
EM: Round [196] log likelihood: -7134.863277
EM: Round [197] log likelihood: -7134.863078
EM: Round [198] log likelihood: -7134.862884
EM: Round [199] log likelihood: -7134.862694
EM: Round [200] log likelihood: -7134.862507
EM: Round [201] log likelihood: -7134.862325
EM: Round [202] log likelihood: -7134.862147
EM: Round [203] log likelihood: -7134.861973
EM: Round [204] log likelihood: -7134.861802
EM: Round [205] log likelihood: -7134.861635
EM: Round [206] log likelihood: -7134.861472
EM: Round [207] log likelihood: -7134.861312
EM: Round [208] log likelihood: -7134.861155
EM: Round [209] log likelihood: -7134.861002
EM: Round [210] log likelihood: -7134.860853
EM: Round [211] log likelihood: -7134.860706
EM: Round [212] log likelihood: -7134.860563
EM: Round [213] log likelihood: -7134.860423
EM: Round [214] log likelihood: -7134.860285
EM: Round [215] log likelihood: -7134.860151
EM: Round [216] log likelihood: -7134.860020
EM: Round [217] log likelihood: -7134.859891
EM: Round [218] log likelihood: -7134.859766
EM: Round [219] log likelihood: -7134.859643
EM: Round [220] log likelihood: -7134.859522
EM: Round [221] log likelihood: -7134.859405
EM: Round [222] log likelihood: -7134.859289
EM: Round [223] log likelihood: -7134.859177
EM: Round [224] log likelihood: -7134.859066
EM: Round [225] log likelihood: -7134.858958
EM: Round [226] log likelihood: -7134.858853
EM: Round [227] log likelihood: -7134.858749
EM: Round [228] log likelihood: -7134.858648
EM: Round [229] log likelihood: -7134.858549
EM: Stopping iterations at round 229 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.zyhqoIjoIy/aih-tih-sc-8c7069-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.zyhqoIjoIy/aih-tih-sc-8c7069-R1_A23YTGFLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.zyhqoIjoIy/aih-tih-sc-8c7069-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.zyhqoIjoIy/aih-tih-sc-8c7069-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.zyhqoIjoIy/aih-tih-sc-8c7069-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.zyhqoIjoIy/aih-tih-sc-8c7069-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.zyhqoIjoIy/aih-tih-sc-8c7069-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.zyhqoIjoIy/fi_workdir/aih-tih-sc-8c7069-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.zyhqoIjoIy/fi_workdir/aih-tih-sc-8c7069-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.zyhqoIjoIy/fi_workdir/aih-tih-sc-8c7069-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.zyhqoIjoIy/aih-tih-sc-8c7069-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.zyhqoIjoIy/aih-tih-sc-8c7069-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -6837.439891
EM: Round [1] log likelihood: -6837.362939
EM: Round [2] log likelihood: -6837.360166
EM: Round [3] log likelihood: -6837.360067
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.zyhqoIjoIy/aih-tih-sc-8c7069-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 240287619
Warning - not locating file: /tmp/nxf.zyhqoIjoIy/aih-tih-sc-8c7069-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000253122.1]
WARNING, no entry stored in dbm for [ENSG00000253122.1]
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 [ENSG00000267394.1]
WARNING, no entry stored in dbm for [ENSG00000267394.1]
WARNING, no entry stored in dbm for [ENSG00000267394.1]
WARNING, no entry stored in dbm for [ENSG00000267394.1]
WARNING, no entry stored in dbm for [ENSG00000241767.2]
WARNING, no entry stored in dbm for [ENSG00000204623.9]
WARNING, no entry stored in dbm for [ENSG00000285407.1]
ls: cannot access 'IGV_inputs': No such file or directory