Done.
-parsing GTF file: /tmp/nxf.qJa8iViOLW/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.qJa8iViOLW/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.qJa8iViOLW/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.qJa8iViOLW/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.qJa8iViOLW/fi_workdir/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.qJa8iViOLW/fi_workdir/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
22:34:38 : INFO : Done.
-parsing GTF file: /tmp/nxf.qJa8iViOLW/fi_workdir/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.qJa8iViOLW/fi_workdir/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
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[420000] -done parsing /tmp/nxf.qJa8iViOLW/fi_workdir/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'exons hit < 2' => 3,
'excessive soft clipping' => 2133,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 3,
'small anchor length' => 37,
' ** passed ** ' => 6074,
'seq-similar region overlap' => 108,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 18,
'per_id < 96' => 1848
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.qJa8iViOLW/fi_workdir/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[49000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[9000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[22000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[25000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[19000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[21000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[41000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[31000] -fusion SPANNING read extraction for scaff: STON1--GTF2A1L
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[28000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[21000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 1276,
'seq similar region alignment' => 34175
};
EM: Starting log likelihood: -2596.168221
EM: Round [1] log likelihood: -2595.772215
EM: Round [2] log likelihood: -2595.451622
EM: Round [3] log likelihood: -2595.188948
EM: Round [4] log likelihood: -2594.972131
EM: Round [5] log likelihood: -2594.792107
EM: Round [6] log likelihood: -2594.641920
EM: Round [7] log likelihood: -2594.516138
EM: Round [8] log likelihood: -2594.410461
EM: Round [9] log likelihood: -2594.321442
EM: Round [10] log likelihood: -2594.246290
EM: Round [11] log likelihood: -2594.182731
EM: Round [12] log likelihood: -2594.128895
EM: Round [13] log likelihood: -2594.083235
EM: Round [14] log likelihood: -2594.044468
EM: Round [15] log likelihood: -2594.011524
EM: Round [16] log likelihood: -2593.983507
EM: Round [17] log likelihood: -2593.959664
EM: Round [18] log likelihood: -2593.939362
EM: Round [19] log likelihood: -2593.922067
EM: Round [20] log likelihood: -2593.907328
EM: Round [21] log likelihood: -2593.894764
EM: Round [22] log likelihood: -2593.884049
EM: Round [23] log likelihood: -2593.874910
EM: Round [24] log likelihood: -2593.867113
EM: Round [25] log likelihood: -2593.860460
EM: Round [26] log likelihood: -2593.854782
EM: Round [27] log likelihood: -2593.849936
EM: Round [28] log likelihood: -2593.845799
EM: Round [29] log likelihood: -2593.842268
EM: Round [30] log likelihood: -2593.839253
EM: Round [31] log likelihood: -2593.836679
EM: Round [32] log likelihood: -2593.834480
EM: Round [33] log likelihood: -2593.832603
EM: Round [34] log likelihood: -2593.831000
EM: Round [35] log likelihood: -2593.829631
EM: Round [36] log likelihood: -2593.828462
EM: Round [37] log likelihood: -2593.827464
EM: Round [38] log likelihood: -2593.826611
EM: Round [39] log likelihood: -2593.825883
EM: Round [40] log likelihood: -2593.825261
EM: Round [41] log likelihood: -2593.824730
EM: Round [42] log likelihood: -2593.824276
EM: Round [43] log likelihood: -2593.823889
EM: Round [44] log likelihood: -2593.823558
EM: Round [45] log likelihood: -2593.823275
EM: Round [46] log likelihood: -2593.823033
EM: Round [47] log likelihood: -2593.822827
EM: Round [48] log likelihood: -2593.822651
EM: Round [49] log likelihood: -2593.822500
EM: Round [50] log likelihood: -2593.822372
EM: Round [51] log likelihood: -2593.822262
EM: Round [52] log likelihood: -2593.822168
EM: Stopping iterations at round 52 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.qJa8iViOLW/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.qJa8iViOLW/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.qJa8iViOLW/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.qJa8iViOLW/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.qJa8iViOLW/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.qJa8iViOLW/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.qJa8iViOLW/aih-tih-sc-d1f1a3-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.qJa8iViOLW/fi_workdir/aih-tih-sc-d1f1a3-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.qJa8iViOLW/fi_workdir/aih-tih-sc-d1f1a3-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.qJa8iViOLW/fi_workdir/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.qJa8iViOLW/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.qJa8iViOLW/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2389.747946
EM: Round [1] log likelihood: -2389.747946
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.qJa8iViOLW/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 297220257
Warning - not locating file: /tmp/nxf.qJa8iViOLW/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
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 [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000186148.13]
WARNING, no entry stored in dbm for [ENSG00000186148.13]
WARNING, no entry stored in dbm for [ENSG00000186148.13]
WARNING, no entry stored in dbm for [ENSG00000068781.21]
WARNING, no entry stored in dbm for [ENSG00000068781.21]
ls: cannot access 'IGV_inputs': No such file or directory