Done.
-parsing GTF file: /tmp/nxf.zb6cyYghM6/aih-tih-sc-656590-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.zb6cyYghM6/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.zb6cyYghM6/aih-tih-sc-656590-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.zb6cyYghM6/aih-tih-sc-656590-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.zb6cyYghM6/fi_workdir/aih-tih-sc-656590-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.zb6cyYghM6/fi_workdir/aih-tih-sc-656590-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-656590-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-656590-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
11:35:44 : INFO : Done.
-parsing GTF file: /tmp/nxf.zb6cyYghM6/fi_workdir/aih-tih-sc-656590-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.zb6cyYghM6/fi_workdir/aih-tih-sc-656590-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
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[1450000] -done parsing /tmp/nxf.zb6cyYghM6/fi_workdir/aih-tih-sc-656590-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'excessive soft clipping' => 9169,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2,
'num genes matched < 2' => 247,
'exons hit < 2' => 5,
'low complexity anchor region' => 1,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 34,
'per_id < 96' => 5013,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 20,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 66,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 4,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 52,
' ** passed ** ' => 2109
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.zb6cyYghM6/fi_workdir/aih-tih-sc-656590-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[81000] -fusion SPANNING read extraction for scaff: AC010904.1--ZC3H7B
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[17000] -fusion SPANNING read extraction for scaff: AMDHD1--ACAD11
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[217000] -fusion SPANNING read extraction for scaff: AP1B1--AL929601.3
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[33000] -fusion SPANNING read extraction for scaff: ARHGAP12--FOLR3
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[61000] -fusion SPANNING read extraction for scaff: KIF24--NOL6
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[64000] -fusion SPANNING read extraction for scaff: NFX1--ARNT2
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[139000] -fusion SPANNING read extraction for scaff: RNASE10--STON2
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[7000] -fusion SPANNING read extraction for scaff: RNASE10--CD38
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[130000] -fusion SPANNING read extraction for scaff: RPL30P11--ATF7IP
[1000]
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[9000] -fusion SPANNING read extraction for scaff: RPL34P19--FOLR3
[1000] -fusion SPANNING read extraction for scaff: SEPTIN14--AL672310.1
[1000]
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[69000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[37000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[41000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A
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[7000] -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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[50000] -fusion SPANNING read extraction for scaff: UNC13B--B4GALT1
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 109,
'lacks exon overlap' => 12326
};
EM: Starting log likelihood: -3959.860791
EM: Round [1] log likelihood: -3958.072329
EM: Round [2] log likelihood: -3957.865876
EM: Round [3] log likelihood: -3957.833845
EM: Round [4] log likelihood: -3957.828145
EM: Round [5] log likelihood: -3957.827022
EM: Round [6] log likelihood: -3957.826784
EM: Round [7] log likelihood: -3957.826732
EM: Stopping iterations at round 7 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.zb6cyYghM6/aih-tih-sc-656590-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.zb6cyYghM6/aih-tih-sc-656590-R1_A23YTGFLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.zb6cyYghM6/aih-tih-sc-656590-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.zb6cyYghM6/aih-tih-sc-656590-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.zb6cyYghM6/aih-tih-sc-656590-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.zb6cyYghM6/aih-tih-sc-656590-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.zb6cyYghM6/aih-tih-sc-656590-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.zb6cyYghM6/fi_workdir/aih-tih-sc-656590-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.zb6cyYghM6/fi_workdir/aih-tih-sc-656590-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.zb6cyYghM6/fi_workdir/aih-tih-sc-656590-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.zb6cyYghM6/aih-tih-sc-656590-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.zb6cyYghM6/aih-tih-sc-656590-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -3828.314431
EM: Round [1] log likelihood: -3828.183593
EM: Round [2] log likelihood: -3828.182724
EM: Round [3] log likelihood: -3828.182716
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.zb6cyYghM6/aih-tih-sc-656590-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 267695729
Warning - not locating file: /tmp/nxf.zb6cyYghM6/aih-tih-sc-656590-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000238035.8]
WARNING, no entry stored in dbm for [ENSG00000250546.6]
WARNING, no entry stored in dbm for [ENSG00000287868.1]
WARNING, no entry stored in dbm for [ENSG00000287868.1]
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 [ENSG00000275563.1]
WARNING, no entry stored in dbm for [ENSG00000275563.1]
WARNING, no entry stored in dbm for [ENSG00000250258.1]
WARNING, no entry stored in dbm for [ENSG00000230423.3]
WARNING, no entry stored in dbm for [ENSG00000176659.9]
WARNING, no entry stored in dbm for [ENSG00000176659.9]
WARNING, no entry stored in dbm for [ENSG00000276888.1]
WARNING, no entry stored in dbm for [ENSG00000276888.1]
WARNING, no entry stored in dbm for [ENSG00000276888.1]
WARNING, no entry stored in dbm for [ENSG00000251209.9]
WARNING, no entry stored in dbm for [ENSG00000251209.9]
WARNING, no entry stored in dbm for [ENSG00000251209.9]
WARNING, no entry stored in dbm for [ENSG00000236666.1]
ls: cannot access 'IGV_inputs': No such file or directory