Done.
-parsing GTF file: /tmp/nxf.K14TOGhkAb/tih_rna_sample_00668_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.K14TOGhkAb/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.K14TOGhkAb/tih_rna_sample_00668_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.K14TOGhkAb/tih_rna_sample_00668_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.K14TOGhkAb/fi_workdir/tih_rna_sample_00668_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.K14TOGhkAb/fi_workdir/tih_rna_sample_00668_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00668_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00668_B23MVV7LT4_1.star.sortedByCoord.out.bam
11:34:40 : INFO : Done.
-parsing GTF file: /tmp/nxf.K14TOGhkAb/fi_workdir/tih_rna_sample_00668_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.K14TOGhkAb/fi_workdir/tih_rna_sample_00668_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
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[4280000] -done parsing /tmp/nxf.K14TOGhkAb/fi_workdir/tih_rna_sample_00668_B23MVV7LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 25,
'exons hit < 2' => 2,
'excessive soft clipping' => 24296,
'seq-similar region overlap' => 1,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 6,
'low complexity anchor region' => 59,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 12,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 1009,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 44,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 132,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 15,
' ** passed ** ' => 12609,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 48,
'per_id < 96' => 16430,
'num genes matched < 2' => 101,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 12,
'small anchor length' => 134
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.K14TOGhkAb/fi_workdir/tih_rna_sample_00668_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[56000] -fusion SPANNING read extraction for scaff: AC011451.3--PODNL1
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[16000] -fusion SPANNING read extraction for scaff: AC015712.1--FAM13C
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[5000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1
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[28000] -fusion SPANNING read extraction for scaff: AC245297.1--AC134879.2
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[581000] -fusion SPANNING read extraction for scaff: ACTBP6--ACTB
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[19000] -fusion SPANNING read extraction for scaff: AGAP12P--FRMPD2
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[27000] -fusion SPANNING read extraction for scaff: AL049812.2--STAU1
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[47000] -fusion SPANNING read extraction for scaff: BLACE--STON2
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[59000] -fusion SPANNING read extraction for scaff: CDC37--ATG4D
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[371000] -fusion SPANNING read extraction for scaff: CTSD--LSP1
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[31000] -fusion SPANNING read extraction for scaff: ELAVL1--MARCHF2
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[62000] -fusion SPANNING read extraction for scaff: EPB41L1--NDRG3
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[54000] -fusion SPANNING read extraction for scaff: FANCI--ABHD2
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[88000] -fusion SPANNING read extraction for scaff: GET3--PODNL1
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[63000] -fusion SPANNING read extraction for scaff: GID4--USP22
[1000] -fusion SPANNING read extraction for scaff: KLRC4--KLRK1
-fusion SPANNING read extraction for scaff: LINC00486--SRARP
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[254000] -fusion SPANNING read extraction for scaff: NCOR1--SAFB
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[335000] -fusion SPANNING read extraction for scaff: NPEPL1--GNAS
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[13000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[10000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
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[18000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[17000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[27000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[19000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[14000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[12000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[42000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[118000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[10000] -fusion SPANNING read extraction for scaff: PIGL--AL139348.1
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[10000] -fusion SPANNING read extraction for scaff: PIGL--AL121910.1
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[534000] -fusion SPANNING read extraction for scaff: PRKCSH--FGFR1
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[280000] -fusion SPANNING read extraction for scaff: PRKCSH--MPRIP
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[47000] -fusion SPANNING read extraction for scaff: PRSS27--TPSB2
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[53000] -fusion SPANNING read extraction for scaff: RBBP4--FAM13C
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[397000] -fusion SPANNING read extraction for scaff: TNRC18--SDK1
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[68000] -fusion SPANNING read extraction for scaff: ZNF823--MAFB
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 22520,
'seq similar region alignment' => 27210
};
EM: Starting log likelihood: -11831.027865
EM: Round [1] log likelihood: -11820.287600
EM: Round [2] log likelihood: -11820.275246
EM: Round [3] log likelihood: -11820.275233
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.K14TOGhkAb/tih_rna_sample_00668_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.K14TOGhkAb/tih_rna_sample_00668_B23MVV7LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.K14TOGhkAb/tih_rna_sample_00668_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.K14TOGhkAb/tih_rna_sample_00668_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.K14TOGhkAb/tih_rna_sample_00668_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.K14TOGhkAb/tih_rna_sample_00668_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.K14TOGhkAb/tih_rna_sample_00668_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.K14TOGhkAb/fi_workdir/tih_rna_sample_00668_B23MVV7LT4_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.K14TOGhkAb/fi_workdir/tih_rna_sample_00668_B23MVV7LT4_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.K14TOGhkAb/fi_workdir/tih_rna_sample_00668_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.K14TOGhkAb/tih_rna_sample_00668_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.K14TOGhkAb/tih_rna_sample_00668_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -10952.601576
EM: Round [1] log likelihood: -10952.097857
EM: Round [2] log likelihood: -10952.097577
EM: Round [3] log likelihood: -10952.097577
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.K14TOGhkAb/tih_rna_sample_00668_B23MVV7LT4_1_1.fastp.fastq.gz: 296814049
Warning - not locating file: /tmp/nxf.K14TOGhkAb/tih_rna_sample_00668_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000283108.1]
WARNING, no entry stored in dbm for [ENSG00000283108.1]
WARNING, no entry stored in dbm for [ENSG00000283108.1]
WARNING, no entry stored in dbm for [ENSG00000265018.6]
WARNING, no entry stored in dbm for [ENSG00000265018.6]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
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 [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000225458.1]
WARNING, no entry stored in dbm for [ENSG00000225458.1]
WARNING, no entry stored in dbm for [ENSG00000216829.6]
WARNING, no entry stored in dbm for [ENSG00000215861.6]
WARNING, no entry stored in dbm for [ENSG00000271375.1]
WARNING, no entry stored in dbm for [ENSG00000204960.7]
WARNING, no entry stored in dbm for [ENSG00000232386.9]
ls: cannot access 'IGV_inputs': No such file or directory