Done.
-parsing GTF file: /tmp/nxf.CrbCeZphpP/659_bR4-T1-TRNA-1_B23MHV2LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.CrbCeZphpP/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.CrbCeZphpP/659_bR4-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.CrbCeZphpP/659_bR4-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.CrbCeZphpP/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.CrbCeZphpP/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
11:16:02 : INFO : Done.
-parsing GTF file: /tmp/nxf.CrbCeZphpP/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.CrbCeZphpP/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
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[3390000] -done parsing /tmp/nxf.CrbCeZphpP/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'per_id < 96' => 18078,
'num genes matched < 2' => 268,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 12,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 4,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 6,
'small anchor length' => 103,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 365,
' ** passed ** ' => 12333,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 32,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 9,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 12,
'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 10,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 28,
'seq-similar region overlap' => 321,
'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 1,
'low complexity anchor region' => 15,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 109,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 3,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 98,
'excessive soft clipping' => 23592
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.CrbCeZphpP/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
[1000] -fusion SPANNING read extraction for scaff: AC007785.3--IGFL2
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[16000] -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L
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[36000] -fusion SPANNING read extraction for scaff: AC091132.4--AC103810.6
[1000] -fusion SPANNING read extraction for scaff: AC217774.1--CRHR1
[1000] -fusion SPANNING read extraction for scaff: AC217774.2--CRHR1
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[26000] -fusion SPANNING read extraction for scaff: AL512590.2--CCDC180
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[167000] -fusion SPANNING read extraction for scaff: ATP11A--STK26
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[179000] -fusion SPANNING read extraction for scaff: BCL2--ZNF521
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[87000] -fusion SPANNING read extraction for scaff: DOCK9--SERPINE2
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[60000] -fusion SPANNING read extraction for scaff: DTNB--SERPINE2
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[39000] -fusion SPANNING read extraction for scaff: DTNB--USP21P1
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[56000] -fusion SPANNING read extraction for scaff: MED14--FTH1P19
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[56000] -fusion SPANNING read extraction for scaff: MED14--FTH1P27
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[48000] -fusion SPANNING read extraction for scaff: PARP8--LINC00276
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[9000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA11
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[15000] -fusion SPANNING read extraction for scaff: PMS2P6--CCDC146
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[43000] -fusion SPANNING read extraction for scaff: PPP1R13B--ZNF138
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[138000] -fusion SPANNING read extraction for scaff: PPP2R2B--GLS
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[67000] -fusion SPANNING read extraction for scaff: R3HDM1--RNF144A
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[74000] -fusion SPANNING read extraction for scaff: RMND5A--KDM3A
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[20000] -fusion SPANNING read extraction for scaff: RNF144A--AC068725.1
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[54000] -fusion SPANNING read extraction for scaff: ROCK2--ZNF385B
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[55000] -fusion SPANNING read extraction for scaff: RUNDC3B--ADAM22
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[12000] -fusion SPANNING read extraction for scaff: SLC25A12--AC092623.1
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[60000] -fusion SPANNING read extraction for scaff: SLC25A12--MGAT5
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[113000] -fusion SPANNING read extraction for scaff: SLFN11--SLFN12
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[66000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[16000] -fusion SPANNING read extraction for scaff: TDRD9--ZNF107
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[45000] -fusion SPANNING read extraction for scaff: TLK2--AL669831.1
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[8000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[19000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[28000] -fusion SPANNING read extraction for scaff: TYW1--ZNF138
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[66000] -fusion SPANNING read extraction for scaff: ZNF521--RN7SL97P
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[32000] -fusion SPANNING read extraction for scaff: ZNF680--TMEM248
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[10000] -fusion SPANNING read extraction for scaff: ZNF92--TDRD9
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[8000] -fusion SPANNING read extraction for scaff: ZNF92--RNU6-1254P
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[8000] -fusion SPANNING read extraction for scaff: ZNF92--LINC02604
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 37138,
'lacks exon overlap' => 32670
};
EM: Starting log likelihood: -16820.626102
EM: Round [1] log likelihood: -16802.831924
EM: Round [2] log likelihood: -16795.814987
EM: Round [3] log likelihood: -16791.689085
EM: Round [4] log likelihood: -16788.918673
EM: Round [5] log likelihood: -16786.917632
EM: Round [6] log likelihood: -16785.405455
EM: Round [7] log likelihood: -16784.228113
EM: Round [8] log likelihood: -16783.292326
EM: Round [9] log likelihood: -16782.537359
EM: Round [10] log likelihood: -16781.921455
EM: Round [11] log likelihood: -16781.414695
EM: Round [12] log likelihood: -16780.994943
EM: Round [13] log likelihood: -16780.645406
EM: Round [14] log likelihood: -16780.353086
EM: Round [15] log likelihood: -16780.107752
EM: Round [16] log likelihood: -16779.901252
EM: Round [17] log likelihood: -16779.727011
EM: Round [18] log likelihood: -16779.579684
EM: Round [19] log likelihood: -16779.454891
EM: Round [20] log likelihood: -16779.349022
EM: Round [21] log likelihood: -16779.259085
EM: Round [22] log likelihood: -16779.182590
EM: Round [23] log likelihood: -16779.117460
EM: Round [24] log likelihood: -16779.061951
EM: Round [25] log likelihood: -16779.014603
EM: Round [26] log likelihood: -16778.974183
EM: Round [27] log likelihood: -16778.939652
EM: Round [28] log likelihood: -16778.910134
EM: Round [29] log likelihood: -16778.884884
EM: Round [30] log likelihood: -16778.863274
EM: Round [31] log likelihood: -16778.844769
EM: Round [32] log likelihood: -16778.828916
EM: Round [33] log likelihood: -16778.815328
EM: Round [34] log likelihood: -16778.803677
EM: Round [35] log likelihood: -16778.793683
EM: Round [36] log likelihood: -16778.785108
EM: Round [37] log likelihood: -16778.777746
EM: Round [38] log likelihood: -16778.771426
EM: Round [39] log likelihood: -16778.765997
EM: Round [40] log likelihood: -16778.761333
EM: Round [41] log likelihood: -16778.757324
EM: Round [42] log likelihood: -16778.753879
EM: Round [43] log likelihood: -16778.750917
EM: Round [44] log likelihood: -16778.748370
EM: Round [45] log likelihood: -16778.746180
EM: Round [46] log likelihood: -16778.744295
EM: Round [47] log likelihood: -16778.742674
EM: Round [48] log likelihood: -16778.741279
EM: Round [49] log likelihood: -16778.740078
EM: Round [50] log likelihood: -16778.739044
EM: Round [51] log likelihood: -16778.738154
EM: Round [52] log likelihood: -16778.737388
EM: Round [53] log likelihood: -16778.736729
EM: Round [54] log likelihood: -16778.736161
EM: Round [55] log likelihood: -16778.735671
EM: Round [56] log likelihood: -16778.735250
EM: Round [57] log likelihood: -16778.734887
EM: Round [58] log likelihood: -16778.734574
EM: Round [59] log likelihood: -16778.734305
EM: Round [60] log likelihood: -16778.734073
EM: Round [61] log likelihood: -16778.733873
EM: Round [62] log likelihood: -16778.733701
EM: Round [63] log likelihood: -16778.733552
EM: Round [64] log likelihood: -16778.733424
EM: Round [65] log likelihood: -16778.733314
EM: Round [66] log likelihood: -16778.733219
EM: Stopping iterations at round 66 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.CrbCeZphpP/659_bR4-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.CrbCeZphpP/659_bR4-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.CrbCeZphpP/659_bR4-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.CrbCeZphpP/659_bR4-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.CrbCeZphpP/659_bR4-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.CrbCeZphpP/659_bR4-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.CrbCeZphpP/659_bR4-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.CrbCeZphpP/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_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.CrbCeZphpP/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_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.CrbCeZphpP/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.CrbCeZphpP/659_bR4-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.CrbCeZphpP/659_bR4-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -16426.239044
EM: Round [1] log likelihood: -16424.947176
EM: Round [2] log likelihood: -16424.926850
EM: Round [3] log likelihood: -16424.926271
EM: Round [4] log likelihood: -16424.926254
EM: Stopping iterations at round 4 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.CrbCeZphpP/659_bR4-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 290821167
Warning - not locating file: /tmp/nxf.CrbCeZphpP/659_bR4-T1-TRNA-1_B23MHV2LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000228327.3]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286065.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
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 [ENSG00000285548.1]
WARNING, no entry stored in dbm for [ENSG00000285548.1]
WARNING, no entry stored in dbm for [ENSG00000285548.1]
WARNING, no entry stored in dbm for [ENSG00000285548.1]
WARNING, no entry stored in dbm for [ENSG00000268401.2]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
WARNING, no entry stored in dbm for [ENSG00000267198.1]
WARNING, no entry stored in dbm for [ENSG00000272134.1]
WARNING, no entry stored in dbm for [ENSG00000267198.1]
WARNING, no entry stored in dbm for [ENSG00000272134.1]
WARNING, no entry stored in dbm for [ENSG00000204650.14]
ls: cannot access 'IGV_inputs': No such file or directory