Done.
-parsing GTF file: /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.0HSd2SUmKP/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.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39_1.fastp.fastq.gz /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00089_23H5VFLT4_s39.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00089_23H5VFLT4_s39.star.sortedByCoord.out.bam
11:05:26 : INFO : Done.
-parsing GTF file: /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.gtf
-parsing /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam
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[1930000] -done parsing /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'excessive soft clipping' => 13184,
'small anchor length' => 49,
'low complexity anchor region' => 16,
'num genes matched < 2' => 11,
'exons hit < 2' => 5,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 1030,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 12,
'per_id < 96' => 7457,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 11,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 33,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 18,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 36,
' ** passed ** ' => 5730,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 16
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
[1000] -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L
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[48000] -fusion SPANNING read extraction for scaff: AVEN--NFATC2
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[42000] -fusion SPANNING read extraction for scaff: FAM135A--AL080275.1
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[7000] -fusion SPANNING read extraction for scaff: FBXO25--AC240565.1
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[83000] -fusion SPANNING read extraction for scaff: MAPK6--TRPM7
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[52000] -fusion SPANNING read extraction for scaff: PRELID3A--AFG3L2
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[26000] -fusion SPANNING read extraction for scaff: PRSS27--TPSB2
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[70000] -fusion SPANNING read extraction for scaff: PTPRK--RSPO3
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[17000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[56000] -fusion SPANNING read extraction for scaff: TMEM87B--MERTK
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[75000] -fusion SPANNING read extraction for scaff: TRPM7--TMOD3
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[82000] -fusion SPANNING read extraction for scaff: WSB2--NOS1
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 36444
};
EM: Starting log likelihood: -9227.192266
EM: Round [1] log likelihood: -9220.058251
EM: Round [2] log likelihood: -9220.032871
EM: Round [3] log likelihood: -9220.032021
EM: Round [4] log likelihood: -9220.031988
EM: Stopping iterations at round 4 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.consolidated.bam into /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.consolidated.bam.read_coords
CMD: touch /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.consolidated.bam.read_coords > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.consolidated.bam.frag_coords > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.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.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.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.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -8960.516585
EM: Round [1] log likelihood: -8956.183808
EM: Round [2] log likelihood: -8956.159390
EM: Round [3] log likelihood: -8956.158540
EM: Round [4] log likelihood: -8956.158507
EM: Stopping iterations at round 4 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39_1.fastp.fastq.gz: 296909533
Warning - not locating file: /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.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 [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
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 [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286065.2]
ls: cannot access 'IGV_inputs': No such file or directory