Done.
-parsing GTF file: /tmp/nxf.BAl7gZ6CTL/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.BAl7gZ6CTL/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.BAl7gZ6CTL/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.BAl7gZ6CTL/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.BAl7gZ6CTL/fi_workdir/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.BAl7gZ6CTL/fi_workdir/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
11:37:08 : INFO : Done.
-parsing GTF file: /tmp/nxf.BAl7gZ6CTL/fi_workdir/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.BAl7gZ6CTL/fi_workdir/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
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[780000] -done parsing /tmp/nxf.BAl7gZ6CTL/fi_workdir/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'seq-similar region overlap' => 232,
'num genes matched < 2' => 12,
'small anchor length' => 3,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 6,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 33,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 46,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 24,
' ** passed ** ' => 2339,
'per_id < 96' => 2928,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 3,
'excessive soft clipping' => 4891,
'low complexity anchor region' => 31,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 4
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.BAl7gZ6CTL/fi_workdir/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[108000] -fusion SPANNING read extraction for scaff: CSMD3--RNU4-37P
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[108000] -fusion SPANNING read extraction for scaff: CSMD3--LINC02237
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[109000] -fusion SPANNING read extraction for scaff: GDPD1--SETD2
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[72000] -fusion SPANNING read extraction for scaff: GUSBP13--NAIP
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[41000] -fusion SPANNING read extraction for scaff: PARD6B--RASSF2
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[29000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1
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[30000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
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[31000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
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[111000] -fusion SPANNING read extraction for scaff: SETD2--CA4
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[21000] -fusion SPANNING read extraction for scaff: SFMBT1--RFT1
[1000]
[2000] -fusion SPANNING read extraction for scaff: SORCS1--AL353740.1
[1000]
[2000] -fusion SPANNING read extraction for scaff: SORCS1--LINC02661
[1000]
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[4000] -fusion SPANNING read extraction for scaff: SREK1IP1--RGS7BP
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[33000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[6000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[16000] -fusion SPANNING read extraction for scaff: TTC39C--ISM1
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[13000] -fusion SPANNING read extraction for scaff: TTC39C--AL121782.1
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[17000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 3446,
'seq similar region alignment' => 25791
};
EM: Starting log likelihood: -2751.836266
EM: Round [1] log likelihood: -2751.064566
EM: Round [2] log likelihood: -2750.426526
EM: Round [3] log likelihood: -2749.882730
EM: Round [4] log likelihood: -2749.416482
EM: Round [5] log likelihood: -2749.014938
EM: Round [6] log likelihood: -2748.667828
EM: Round [7] log likelihood: -2748.366831
EM: Round [8] log likelihood: -2748.105122
EM: Round [9] log likelihood: -2747.877056
EM: Round [10] log likelihood: -2747.677917
EM: Round [11] log likelihood: -2747.503744
EM: Round [12] log likelihood: -2747.351186
EM: Round [13] log likelihood: -2747.217391
EM: Round [14] log likelihood: -2747.099922
EM: Round [15] log likelihood: -2746.996689
EM: Round [16] log likelihood: -2746.905892
EM: Round [17] log likelihood: -2746.825974
EM: Round [18] log likelihood: -2746.755586
EM: Round [19] log likelihood: -2746.693557
EM: Round [20] log likelihood: -2746.638868
EM: Round [21] log likelihood: -2746.590630
EM: Round [22] log likelihood: -2746.548066
EM: Round [23] log likelihood: -2746.510495
EM: Round [24] log likelihood: -2746.477322
EM: Round [25] log likelihood: -2746.448025
EM: Round [26] log likelihood: -2746.422145
EM: Round [27] log likelihood: -2746.399279
EM: Round [28] log likelihood: -2746.379072
EM: Round [29] log likelihood: -2746.361212
EM: Round [30] log likelihood: -2746.345425
EM: Round [31] log likelihood: -2746.331468
EM: Round [32] log likelihood: -2746.319127
EM: Round [33] log likelihood: -2746.308215
EM: Round [34] log likelihood: -2746.298566
EM: Round [35] log likelihood: -2746.290031
EM: Round [36] log likelihood: -2746.282484
EM: Round [37] log likelihood: -2746.275807
EM: Round [38] log likelihood: -2746.269902
EM: Round [39] log likelihood: -2746.264678
EM: Round [40] log likelihood: -2746.260057
EM: Round [41] log likelihood: -2746.255969
EM: Round [42] log likelihood: -2746.252353
EM: Round [43] log likelihood: -2746.249153
EM: Round [44] log likelihood: -2746.246322
EM: Round [45] log likelihood: -2746.243818
EM: Round [46] log likelihood: -2746.241602
EM: Round [47] log likelihood: -2746.239641
EM: Round [48] log likelihood: -2746.237906
EM: Round [49] log likelihood: -2746.236372
EM: Round [50] log likelihood: -2746.235014
EM: Round [51] log likelihood: -2746.233812
EM: Round [52] log likelihood: -2746.232749
EM: Round [53] log likelihood: -2746.231808
EM: Round [54] log likelihood: -2746.230975
EM: Round [55] log likelihood: -2746.230239
EM: Round [56] log likelihood: -2746.229587
EM: Round [57] log likelihood: -2746.229010
EM: Round [58] log likelihood: -2746.228500
EM: Round [59] log likelihood: -2746.228048
EM: Round [60] log likelihood: -2746.227649
EM: Round [61] log likelihood: -2746.227295
EM: Round [62] log likelihood: -2746.226982
EM: Round [63] log likelihood: -2746.226705
EM: Round [64] log likelihood: -2746.226460
EM: Round [65] log likelihood: -2746.226244
EM: Round [66] log likelihood: -2746.226052
EM: Round [67] log likelihood: -2746.225882
EM: Round [68] log likelihood: -2746.225732
EM: Round [69] log likelihood: -2746.225599
EM: Round [70] log likelihood: -2746.225481
EM: Round [71] log likelihood: -2746.225377
EM: Round [72] log likelihood: -2746.225285
EM: Stopping iterations at round 72 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.BAl7gZ6CTL/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.BAl7gZ6CTL/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.BAl7gZ6CTL/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.BAl7gZ6CTL/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.BAl7gZ6CTL/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.BAl7gZ6CTL/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.BAl7gZ6CTL/aih-tih-sc-f0dbdf-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.BAl7gZ6CTL/fi_workdir/aih-tih-sc-f0dbdf-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.BAl7gZ6CTL/fi_workdir/aih-tih-sc-f0dbdf-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.BAl7gZ6CTL/fi_workdir/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.BAl7gZ6CTL/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.BAl7gZ6CTL/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2574.397102
EM: Round [1] log likelihood: -2574.377943
EM: Round [2] log likelihood: -2574.377526
EM: Round [3] log likelihood: -2574.377517
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.BAl7gZ6CTL/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296382314
Warning - not locating file: /tmp/nxf.BAl7gZ6CTL/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000242858.1]
WARNING, no entry stored in dbm for [ENSG00000198237.8]
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 [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
ls: cannot access 'IGV_inputs': No such file or directory