Done.
-parsing GTF file: /tmp/nxf.7aYiFT9cHh/tih_rna_sample_00104_23H5VFLT4_s20.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.7aYiFT9cHh/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.7aYiFT9cHh/tih_rna_sample_00104_23H5VFLT4_s20_1.fastp.fastq.gz /tmp/nxf.7aYiFT9cHh/tih_rna_sample_00104_23H5VFLT4_s20_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.7aYiFT9cHh/fi_workdir/tih_rna_sample_00104_23H5VFLT4_s20.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.7aYiFT9cHh/fi_workdir/tih_rna_sample_00104_23H5VFLT4_s20.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00104_23H5VFLT4_s20.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00104_23H5VFLT4_s20.star.sortedByCoord.out.bam
09:38:47 : INFO : Done.
-parsing GTF file: /tmp/nxf.7aYiFT9cHh/fi_workdir/tih_rna_sample_00104_23H5VFLT4_s20.gtf
-parsing /tmp/nxf.7aYiFT9cHh/fi_workdir/tih_rna_sample_00104_23H5VFLT4_s20.star.cSorted.dupsMarked.bam
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[480000] -done parsing /tmp/nxf.7aYiFT9cHh/fi_workdir/tih_rna_sample_00104_23H5VFLT4_s20.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 735,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 8,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 247,
'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 30,
'num_hits: 7 != num_counted_on_fusion_contigs 4 ' => 4,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 14381,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 222,
'num_hits: 7 != num_counted_on_fusion_contigs 5 ' => 10,
'num_hits: 8 != num_counted_on_fusion_contigs 7 ' => 14,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 18,
'num_hits: 7 != num_counted_on_fusion_contigs 1 ' => 1,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 48,
'excessive soft clipping' => 5289,
'per_id < 96' => 18629,
'num_hits: 8 != num_counted_on_fusion_contigs 5 ' => 5,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 1468,
' ** passed ** ' => 1169,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 4,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 3485,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 798,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 206,
'num_hits: 7 != num_counted_on_fusion_contigs 6 ' => 6,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 102,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 1196
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.7aYiFT9cHh/fi_workdir/tih_rna_sample_00104_23H5VFLT4_s20.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[417000] -fusion SPANNING read extraction for scaff: RRBP1--BFSP1
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[13000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 3775
};
EM: Starting log likelihood: -913.650736
EM: Round [1] log likelihood: -913.650736
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.7aYiFT9cHh/tih_rna_sample_00104_23H5VFLT4_s20.consolidated.bam into /tmp/nxf.7aYiFT9cHh/tih_rna_sample_00104_23H5VFLT4_s20.consolidated.bam.read_coords
CMD: touch /tmp/nxf.7aYiFT9cHh/tih_rna_sample_00104_23H5VFLT4_s20.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.7aYiFT9cHh/tih_rna_sample_00104_23H5VFLT4_s20.consolidated.bam.read_coords > /tmp/nxf.7aYiFT9cHh/tih_rna_sample_00104_23H5VFLT4_s20.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.7aYiFT9cHh/tih_rna_sample_00104_23H5VFLT4_s20.consolidated.bam.frag_coords > /tmp/nxf.7aYiFT9cHh/tih_rna_sample_00104_23H5VFLT4_s20.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.7aYiFT9cHh/fi_workdir/tih_rna_sample_00104_23H5VFLT4_s20.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.7aYiFT9cHh/fi_workdir/tih_rna_sample_00104_23H5VFLT4_s20.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.7aYiFT9cHh/fi_workdir/tih_rna_sample_00104_23H5VFLT4_s20.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.7aYiFT9cHh/tih_rna_sample_00104_23H5VFLT4_s20.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.7aYiFT9cHh/tih_rna_sample_00104_23H5VFLT4_s20.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -898.883724
EM: Round [1] log likelihood: -898.883724
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.7aYiFT9cHh/tih_rna_sample_00104_23H5VFLT4_s20_1.fastp.fastq.gz: 207159670
Warning - not locating file: /tmp/nxf.7aYiFT9cHh/tih_rna_sample_00104_23H5VFLT4_s20.gmap_trinity_GG.fusions.gff3.bed
ls: cannot access 'IGV_inputs': No such file or directory