Error, chr discrepancy in gtf info for chr20 ENSEMBL exon 29297095 29297246 . - . gene_id "5_8S_rRNA^ENSG00000283568.1"; transcript_id "ENST00000637374.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.9-201"; exon_number 1; exon_id "ENSE00003799614.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000283568.1"; orig_coord_info "chr20,29297095,29297246,-";
Error, chr discrepancy in gtf info for chr20 ENSEMBL exon 29741510 29741661 . - . gene_id "5_8S_rRNA^ENSG00000283291.1"; transcript_id "ENST00000638132.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.8-201"; exon_number 1; exon_id "ENSE00003794628.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000283291.1"; orig_coord_info "chr20,29741510,29741661,-";
Error, chr discrepancy in gtf info for chr20 ENSEMBL exon 30484925 30485076 . - . gene_id "5_8S_rRNA^ENSG00000275877.1"; transcript_id "ENST00000614365.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.3-201"; exon_number 1; exon_id "ENSE00003742842.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000275877.1"; orig_coord_info "chr20,30484925,30485076,-";
Error, chr discrepancy in gtf info for chr21 ENSEMBL exon 8256781 8256933 . + . gene_id "5_8S_rRNA^ENSG00000277739.1"; transcript_id "ENST00000610460.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.5-201"; exon_number 1; exon_id "ENSE00003746458.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000277739.1"; orig_coord_info "chr21,8256781,8256933,+";
Error, chr discrepancy in gtf info for chr22 ENSEMBL exon 11249809 11249959 . - . gene_id "5_8S_rRNA^ENSG00000276871.1"; transcript_id "ENST00000612732.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.4-201"; exon_number 1; exon_id "ENSE00003735240.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000276871.1"; orig_coord_info "chr22,11249809,11249959,-";
Done.
-parsing GTF file: /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.C0cAtwyrvW/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.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
22:29:15 : INFO : Done.
-parsing GTF file: /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
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[4290000] -done parsing /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'seq-similar region overlap' => 304,
'num genes matched < 2' => 89,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 35,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 277,
'per_id < 96' => 15186,
'excessive soft clipping' => 31810,
' ** passed ** ' => 5684,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 64,
'small anchor length' => 13,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 24,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 34,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 12,
'low complexity anchor region' => 6
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[78000] -fusion SPANNING read extraction for scaff: AATF--AC243830.2
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[78000] -fusion SPANNING read extraction for scaff: AATF--AC243830.3
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[5000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1
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[80000] -fusion SPANNING read extraction for scaff: AKAP7--PTPRK
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[90000] -fusion SPANNING read extraction for scaff: AMOTL2--ME1
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[12000] -fusion SPANNING read extraction for scaff: ATXN8OS--KLHL1
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[14000] -fusion SPANNING read extraction for scaff: C1QTNF3--AMACR
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[38000] -fusion SPANNING read extraction for scaff: CACNB1--ADAP2
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[20000] -fusion SPANNING read extraction for scaff: CILK1--AL033504.1
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[108000] -fusion SPANNING read extraction for scaff: ERBB4--AL020994.1
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[32000] -fusion SPANNING read extraction for scaff: EXT1--AC084114.1
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[36000] -fusion SPANNING read extraction for scaff: EXT1--MED30
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[47000] -fusion SPANNING read extraction for scaff: FLACC1--TRAK2
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[52000] -fusion SPANNING read extraction for scaff: FSIP1--AC013652.1
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[11000] -fusion SPANNING read extraction for scaff: KLRC4--KLRK1
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[427000] -fusion SPANNING read extraction for scaff: NF1--IKZF3
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[92000] -fusion SPANNING read extraction for scaff: NFKB2--DENND10
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[57000] -fusion SPANNING read extraction for scaff: NPEPPSP1--AC003101.1
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[57000] -fusion SPANNING read extraction for scaff: NPEPPSP1--MIR4725
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[212000] -fusion SPANNING read extraction for scaff: NSD3--5_8S_rRNA
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[212000] -fusion SPANNING read extraction for scaff: NSD3--CR383658.1
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[56000] -fusion SPANNING read extraction for scaff: PAPSS1--HADH
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[28000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
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[29000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
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[19000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1
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[19000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2
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[20000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13
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[424000] -fusion SPANNING read extraction for scaff: PGAP3--MED1
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[115000] -fusion SPANNING read extraction for scaff: PHF12--LINC02693
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[120000] -fusion SPANNING read extraction for scaff: PHF12--RPL21P120
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[74000] -fusion SPANNING read extraction for scaff: PTPRK--TRDN
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[46000] -fusion SPANNING read extraction for scaff: RANBP9--AKAP7
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[20000] -fusion SPANNING read extraction for scaff: RAPGEF5--UNC5D
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[160000] -fusion SPANNING read extraction for scaff: RAPGEF5--EGFR
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[248000] -fusion SPANNING read extraction for scaff: RERE--SHANK2
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[6000] -fusion SPANNING read extraction for scaff: RIMS1--TRDN
[1000] -fusion SPANNING read extraction for scaff: RNU4-66P--TRDN
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[8000] -fusion SPANNING read extraction for scaff: RNU6-54P--KLHL1
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[66000] -fusion SPANNING read extraction for scaff: SMG7--CACNA1E
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[82000] -fusion SPANNING read extraction for scaff: STK4--ARHGEF3
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[13000] -fusion SPANNING read extraction for scaff: STON1--GTF2A1L
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[97000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[41000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[42000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A
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[41000] -fusion SPANNING read extraction for scaff: TMTC2--ACSS3
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[89000] -fusion SPANNING read extraction for scaff: TRAK1--ULK4
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[372000] -fusion SPANNING read extraction for scaff: TRPS1--LINC00824
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[22000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 23403,
'lacks exon overlap' => 39837
};
EM: Starting log likelihood: -9056.657967
EM: Round [1] log likelihood: -9054.735816
EM: Round [2] log likelihood: -9054.320558
EM: Round [3] log likelihood: -9053.953688
EM: Round [4] log likelihood: -9053.626148
EM: Round [5] log likelihood: -9053.332702
EM: Round [6] log likelihood: -9053.068981
EM: Round [7] log likelihood: -9052.831304
EM: Round [8] log likelihood: -9052.616550
EM: Round [9] log likelihood: -9052.422051
EM: Round [10] log likelihood: -9052.245515
EM: Round [11] log likelihood: -9052.084964
EM: Round [12] log likelihood: -9051.938676
EM: Round [13] log likelihood: -9051.805151
EM: Round [14] log likelihood: -9051.683076
EM: Round [15] log likelihood: -9051.571295
EM: Round [16] log likelihood: -9051.468787
EM: Round [17] log likelihood: -9051.374649
EM: Round [18] log likelihood: -9051.288079
EM: Round [19] log likelihood: -9051.208361
EM: Round [20] log likelihood: -9051.134859
EM: Round [21] log likelihood: -9051.067000
EM: Round [22] log likelihood: -9051.004272
EM: Round [23] log likelihood: -9050.946213
EM: Round [24] log likelihood: -9050.892410
EM: Round [25] log likelihood: -9050.842488
EM: Round [26] log likelihood: -9050.796107
EM: Round [27] log likelihood: -9050.752964
EM: Round [28] log likelihood: -9050.712779
EM: Round [29] log likelihood: -9050.675301
EM: Round [30] log likelihood: -9050.640302
EM: Round [31] log likelihood: -9050.607574
EM: Round [32] log likelihood: -9050.576928
EM: Round [33] log likelihood: -9050.548192
EM: Round [34] log likelihood: -9050.521209
EM: Round [35] log likelihood: -9050.495836
EM: Round [36] log likelihood: -9050.471942
EM: Round [37] log likelihood: -9050.449409
EM: Round [38] log likelihood: -9050.428127
EM: Round [39] log likelihood: -9050.407996
EM: Round [40] log likelihood: -9050.388927
EM: Round [41] log likelihood: -9050.370834
EM: Round [42] log likelihood: -9050.353643
EM: Round [43] log likelihood: -9050.337284
EM: Round [44] log likelihood: -9050.321692
EM: Round [45] log likelihood: -9050.306809
EM: Round [46] log likelihood: -9050.292582
EM: Round [47] log likelihood: -9050.278960
EM: Round [48] log likelihood: -9050.265900
EM: Round [49] log likelihood: -9050.253360
EM: Round [50] log likelihood: -9050.241302
EM: Round [51] log likelihood: -9050.229692
EM: Round [52] log likelihood: -9050.218496
EM: Round [53] log likelihood: -9050.207687
EM: Round [54] log likelihood: -9050.197236
EM: Round [55] log likelihood: -9050.187121
EM: Round [56] log likelihood: -9050.177317
EM: Round [57] log likelihood: -9050.167803
EM: Round [58] log likelihood: -9050.158562
EM: Round [59] log likelihood: -9050.149575
EM: Round [60] log likelihood: -9050.140826
EM: Round [61] log likelihood: -9050.132300
EM: Round [62] log likelihood: -9050.123983
EM: Round [63] log likelihood: -9050.115863
EM: Round [64] log likelihood: -9050.107929
EM: Round [65] log likelihood: -9050.100169
EM: Round [66] log likelihood: -9050.092573
EM: Round [67] log likelihood: -9050.085133
EM: Round [68] log likelihood: -9050.077841
EM: Round [69] log likelihood: -9050.070687
EM: Round [70] log likelihood: -9050.063667
EM: Round [71] log likelihood: -9050.056771
EM: Round [72] log likelihood: -9050.049996
EM: Round [73] log likelihood: -9050.043335
EM: Round [74] log likelihood: -9050.036782
EM: Round [75] log likelihood: -9050.030334
EM: Round [76] log likelihood: -9050.023985
EM: Round [77] log likelihood: -9050.017732
EM: Round [78] log likelihood: -9050.011571
EM: Round [79] log likelihood: -9050.005497
EM: Round [80] log likelihood: -9049.999508
EM: Round [81] log likelihood: -9049.993601
EM: Round [82] log likelihood: -9049.987773
EM: Round [83] log likelihood: -9049.982020
EM: Round [84] log likelihood: -9049.976342
EM: Round [85] log likelihood: -9049.970735
EM: Round [86] log likelihood: -9049.965197
EM: Round [87] log likelihood: -9049.959726
EM: Round [88] log likelihood: -9049.954320
EM: Round [89] log likelihood: -9049.948978
EM: Round [90] log likelihood: -9049.943697
EM: Round [91] log likelihood: -9049.938477
EM: Round [92] log likelihood: -9049.933315
EM: Round [93] log likelihood: -9049.928211
EM: Round [94] log likelihood: -9049.923162
EM: Round [95] log likelihood: -9049.918168
EM: Round [96] log likelihood: -9049.913228
EM: Round [97] log likelihood: -9049.908340
EM: Round [98] log likelihood: -9049.903504
EM: Round [99] log likelihood: -9049.898717
EM: Round [100] log likelihood: -9049.893981
EM: Round [101] log likelihood: -9049.889292
EM: Round [102] log likelihood: -9049.884651
EM: Round [103] log likelihood: -9049.880057
EM: Round [104] log likelihood: -9049.875509
EM: Round [105] log likelihood: -9049.871006
EM: Round [106] log likelihood: -9049.866547
EM: Round [107] log likelihood: -9049.862132
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EM: Round [568] log likelihood: -9049.346537
EM: Round [569] log likelihood: -9049.346413
EM: Round [570] log likelihood: -9049.346290
EM: Round [571] log likelihood: -9049.346167
EM: Round [572] log likelihood: -9049.346046
EM: Round [573] log likelihood: -9049.345925
EM: Round [574] log likelihood: -9049.345805
EM: Round [575] log likelihood: -9049.345686
EM: Round [576] log likelihood: -9049.345568
EM: Round [577] log likelihood: -9049.345451
EM: Round [578] log likelihood: -9049.345334
EM: Round [579] log likelihood: -9049.345219
EM: Round [580] log likelihood: -9049.345104
EM: Round [581] log likelihood: -9049.344990
EM: Round [582] log likelihood: -9049.344877
EM: Round [583] log likelihood: -9049.344765
EM: Round [584] log likelihood: -9049.344653
EM: Round [585] log likelihood: -9049.344542
EM: Round [586] log likelihood: -9049.344432
EM: Round [587] log likelihood: -9049.344323
EM: Round [588] log likelihood: -9049.344215
EM: Round [589] log likelihood: -9049.344107
EM: Round [590] log likelihood: -9049.344001
EM: Round [591] log likelihood: -9049.343895
EM: Round [592] log likelihood: -9049.343789
EM: Round [593] log likelihood: -9049.343685
EM: Round [594] log likelihood: -9049.343581
EM: Round [595] log likelihood: -9049.343478
EM: Round [596] log likelihood: -9049.343376
EM: Round [597] log likelihood: -9049.343274
EM: Round [598] log likelihood: -9049.343173
EM: Round [599] log likelihood: -9049.343073
EM: Round [600] log likelihood: -9049.342974
EM: Stopping iterations at round 600 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-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.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-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.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-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.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -8641.808258
EM: Round [1] log likelihood: -8641.160562
EM: Round [2] log likelihood: -8641.160249
EM: Round [3] log likelihood: -8641.160249
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296397279
Warning - not locating file: /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000212719.13]
WARNING, no entry stored in dbm for [ENSG00000212719.13]
WARNING, no entry stored in dbm for [ENSG00000212719.13]
WARNING, no entry stored in dbm for [ENSG00000212719.13]
WARNING, no entry stored in dbm for [ENSG00000212719.13]
WARNING, no entry stored in dbm for [ENSG00000212719.13]
WARNING, no entry stored in dbm for [ENSG00000212719.13]
WARNING, no entry stored in dbm for [ENSG00000212719.13]
WARNING, no entry stored in dbm for [ENSG00000212719.13]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000212719.13]
WARNING, no entry stored in dbm for [ENSG00000212719.13]
WARNING, no entry stored in dbm for [ENSG00000223726.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000254275.6]
WARNING, no entry stored in dbm for [ENSG00000274487.2]
WARNING, no entry stored in dbm for [ENSG00000228768.3]
ls: cannot access 'IGV_inputs': No such file or directory