Done.
-parsing GTF file: /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.XV5eT4t5u0/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.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32_1.fastp.fastq.gz /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00090_23H5VFLT4_s32.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00090_23H5VFLT4_s32.star.sortedByCoord.out.bam
11:13:39 : INFO : Done.
-parsing GTF file: /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.gtf
-parsing /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam
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[350000] -done parsing /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 12,
'excessive soft clipping' => 2690,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 6,
' ** passed ** ' => 1171,
'low complexity anchor region' => 2,
'seq-similar region overlap' => 36,
'small anchor length' => 22,
'per_id < 96' => 2261,
'num genes matched < 2' => 26,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 148
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[75000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[17000] -fusion SPANNING read extraction for scaff: SUMF1--AC087857.1
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[16000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 5117,
'lacks exon overlap' => 5000
};
EM: Starting log likelihood: -1155.104925
EM: Round [1] log likelihood: -1154.946850
EM: Round [2] log likelihood: -1154.808689
EM: Round [3] log likelihood: -1154.687378
EM: Round [4] log likelihood: -1154.580446
EM: Round [5] log likelihood: -1154.485872
EM: Round [6] log likelihood: -1154.401988
EM: Round [7] log likelihood: -1154.327399
EM: Round [8] log likelihood: -1154.260931
EM: Round [9] log likelihood: -1154.201586
EM: Round [10] log likelihood: -1154.148513
EM: Round [11] log likelihood: -1154.100978
EM: Round [12] log likelihood: -1154.058348
EM: Round [13] log likelihood: -1154.020073
EM: Round [14] log likelihood: -1153.985673
EM: Round [15] log likelihood: -1153.954726
EM: Round [16] log likelihood: -1153.926863
EM: Round [17] log likelihood: -1153.901759
EM: Round [18] log likelihood: -1153.879126
EM: Round [19] log likelihood: -1153.858708
EM: Round [20] log likelihood: -1153.840280
EM: Round [21] log likelihood: -1153.823638
EM: Round [22] log likelihood: -1153.808605
EM: Round [23] log likelihood: -1153.795018
EM: Round [24] log likelihood: -1153.782736
EM: Round [25] log likelihood: -1153.771628
EM: Round [26] log likelihood: -1153.761580
EM: Round [27] log likelihood: -1153.752489
EM: Round [28] log likelihood: -1153.744261
EM: Round [29] log likelihood: -1153.736813
EM: Round [30] log likelihood: -1153.730070
EM: Round [31] log likelihood: -1153.723964
EM: Round [32] log likelihood: -1153.718434
EM: Round [33] log likelihood: -1153.713425
EM: Round [34] log likelihood: -1153.708888
EM: Round [35] log likelihood: -1153.704777
EM: Round [36] log likelihood: -1153.701052
EM: Round [37] log likelihood: -1153.697676
EM: Round [38] log likelihood: -1153.694617
EM: Round [39] log likelihood: -1153.691845
EM: Round [40] log likelihood: -1153.689332
EM: Round [41] log likelihood: -1153.687054
EM: Round [42] log likelihood: -1153.684990
EM: Round [43] log likelihood: -1153.683118
EM: Round [44] log likelihood: -1153.681421
EM: Round [45] log likelihood: -1153.679883
EM: Round [46] log likelihood: -1153.678488
EM: Round [47] log likelihood: -1153.677223
EM: Round [48] log likelihood: -1153.676077
EM: Round [49] log likelihood: -1153.675037
EM: Round [50] log likelihood: -1153.674094
EM: Round [51] log likelihood: -1153.673240
EM: Round [52] log likelihood: -1153.672464
EM: Round [53] log likelihood: -1153.671761
EM: Round [54] log likelihood: -1153.671124
EM: Round [55] log likelihood: -1153.670546
EM: Round [56] log likelihood: -1153.670022
EM: Round [57] log likelihood: -1153.669546
EM: Round [58] log likelihood: -1153.669115
EM: Round [59] log likelihood: -1153.668724
EM: Round [60] log likelihood: -1153.668370
EM: Round [61] log likelihood: -1153.668048
EM: Round [62] log likelihood: -1153.667757
EM: Round [63] log likelihood: -1153.667492
EM: Round [64] log likelihood: -1153.667252
EM: Round [65] log likelihood: -1153.667035
EM: Round [66] log likelihood: -1153.666837
EM: Round [67] log likelihood: -1153.666659
EM: Round [68] log likelihood: -1153.666496
EM: Round [69] log likelihood: -1153.666349
EM: Round [70] log likelihood: -1153.666216
EM: Round [71] log likelihood: -1153.666095
EM: Round [72] log likelihood: -1153.665985
EM: Round [73] log likelihood: -1153.665885
EM: Stopping iterations at round 73 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.consolidated.bam into /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.consolidated.bam.read_coords
CMD: touch /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.consolidated.bam.read_coords > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.consolidated.bam.frag_coords > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.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.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.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.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -1118.542712
EM: Round [1] log likelihood: -1118.542712
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32_1.fastp.fastq.gz: 296131405
Warning - not locating file: /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.gmap_trinity_GG.fusions.gff3.bed
ls: cannot access 'IGV_inputs': No such file or directory