Done.
-parsing GTF file: /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.mozZzLS8CN/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.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00146_B23WHTKLT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00146_B23WHTKLT4_2.star.sortedByCoord.out.bam
11:43:27 : INFO : Done.
-parsing GTF file: /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.gtf
-parsing /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam
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[900000] -done parsing /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'seq-similar region overlap' => 15,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 4,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 10,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 210,
' ** passed ** ' => 8209,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 9,
'per_id < 96' => 3268,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 82,
'excessive soft clipping' => 11193,
'exons hit < 2' => 6,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 92,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 613,
'small anchor length' => 29,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 958,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 12,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 15,
'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 5,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 1846,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 12,
'low complexity anchor region' => 13,
'num genes matched < 2' => 51
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[79000] -fusion SPANNING read extraction for scaff: FSIP1--AC013652.1
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[79000] -fusion SPANNING read extraction for scaff: IGL-@-ext--PRR7-AS1
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[34000] -fusion SPANNING read extraction for scaff: PCDHA5--PCDHA13
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[29000] -fusion SPANNING read extraction for scaff: PCDHA5--PCDHAC2
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[31000] -fusion SPANNING read extraction for scaff: PCDHA5--PCDHAC1
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[46000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13
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[43000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1
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[32000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[17000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[119000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[136000] -fusion SPANNING read extraction for scaff: ZFHX3--LINC01572
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 28464,
'seq similar region alignment' => 18606
};
EM: Starting log likelihood: -6205.277206
EM: Round [1] log likelihood: -6200.753596
EM: Round [2] log likelihood: -6200.724714
EM: Round [3] log likelihood: -6200.715455
EM: Round [4] log likelihood: -6200.706321
EM: Round [5] log likelihood: -6200.697273
EM: Round [6] log likelihood: -6200.688309
EM: Round [7] log likelihood: -6200.679428
EM: Round [8] log likelihood: -6200.670630
EM: Round [9] log likelihood: -6200.661912
EM: Round [10] log likelihood: -6200.653275
EM: Round [11] log likelihood: -6200.644718
EM: Round [12] log likelihood: -6200.636238
EM: Round [13] log likelihood: -6200.627837
EM: Round [14] log likelihood: -6200.619511
EM: Round [15] log likelihood: -6200.611262
EM: Round [16] log likelihood: -6200.603087
EM: Round [17] log likelihood: -6200.594985
EM: Round [18] log likelihood: -6200.586957
EM: Round [19] log likelihood: -6200.579001
EM: Round [20] log likelihood: -6200.571116
EM: Round [21] log likelihood: -6200.563302
EM: Round [22] log likelihood: -6200.555557
EM: Round [23] log likelihood: -6200.547881
EM: Round [24] log likelihood: -6200.540273
EM: Round [25] log likelihood: -6200.532733
EM: Round [26] log likelihood: -6200.525259
EM: Round [27] log likelihood: -6200.517851
EM: Round [28] log likelihood: -6200.510507
EM: Round [29] log likelihood: -6200.503229
EM: Round [30] log likelihood: -6200.496013
EM: Round [31] log likelihood: -6200.488861
EM: Round [32] log likelihood: -6200.481771
EM: Round [33] log likelihood: -6200.474742
EM: Round [34] log likelihood: -6200.467774
EM: Round [35] log likelihood: -6200.460866
EM: Round [36] log likelihood: -6200.454018
EM: Round [37] log likelihood: -6200.447228
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EM: Round [499] log likelihood: -6199.578645
EM: Round [500] log likelihood: -6199.578376
EM: Round [501] log likelihood: -6199.578110
EM: Round [502] log likelihood: -6199.577845
EM: Round [503] log likelihood: -6199.577582
EM: Round [504] log likelihood: -6199.577320
EM: Round [505] log likelihood: -6199.577061
EM: Round [506] log likelihood: -6199.576803
EM: Round [507] log likelihood: -6199.576546
EM: Round [508] log likelihood: -6199.576291
EM: Round [509] log likelihood: -6199.576038
EM: Round [510] log likelihood: -6199.575787
EM: Round [511] log likelihood: -6199.575537
EM: Round [512] log likelihood: -6199.575288
EM: Round [513] log likelihood: -6199.575042
EM: Round [514] log likelihood: -6199.574797
EM: Round [515] log likelihood: -6199.574553
EM: Round [516] log likelihood: -6199.574311
EM: Round [517] log likelihood: -6199.574070
EM: Round [518] log likelihood: -6199.573832
EM: Round [519] log likelihood: -6199.573594
EM: Round [520] log likelihood: -6199.573358
EM: Round [521] log likelihood: -6199.573124
EM: Round [522] log likelihood: -6199.572891
EM: Round [523] log likelihood: -6199.572660
EM: Round [524] log likelihood: -6199.572430
EM: Round [525] log likelihood: -6199.572201
EM: Round [526] log likelihood: -6199.571974
EM: Round [527] log likelihood: -6199.571749
EM: Round [528] log likelihood: -6199.571525
EM: Round [529] log likelihood: -6199.571302
EM: Round [530] log likelihood: -6199.571081
EM: Round [531] log likelihood: -6199.570861
EM: Round [532] log likelihood: -6199.570643
EM: Round [533] log likelihood: -6199.570426
EM: Round [534] log likelihood: -6199.570210
EM: Round [535] log likelihood: -6199.569996
EM: Round [536] log likelihood: -6199.569783
EM: Round [537] log likelihood: -6199.569572
EM: Round [538] log likelihood: -6199.569361
EM: Round [539] log likelihood: -6199.569153
EM: Round [540] log likelihood: -6199.568945
EM: Round [541] log likelihood: -6199.568739
EM: Round [542] log likelihood: -6199.568534
EM: Round [543] log likelihood: -6199.568331
EM: Round [544] log likelihood: -6199.568128
EM: Round [545] log likelihood: -6199.567927
EM: Round [546] log likelihood: -6199.567728
EM: Round [547] log likelihood: -6199.567529
EM: Round [548] log likelihood: -6199.567332
EM: Round [549] log likelihood: -6199.567137
EM: Round [550] log likelihood: -6199.566942
EM: Round [551] log likelihood: -6199.566749
EM: Round [552] log likelihood: -6199.566557
EM: Round [553] log likelihood: -6199.566366
EM: Round [554] log likelihood: -6199.566176
EM: Round [555] log likelihood: -6199.565988
EM: Round [556] log likelihood: -6199.565800
EM: Round [557] log likelihood: -6199.565614
EM: Round [558] log likelihood: -6199.565429
EM: Round [559] log likelihood: -6199.565246
EM: Round [560] log likelihood: -6199.565063
EM: Round [561] log likelihood: -6199.564882
EM: Round [562] log likelihood: -6199.564702
EM: Round [563] log likelihood: -6199.564523
EM: Round [564] log likelihood: -6199.564345
EM: Round [565] log likelihood: -6199.564168
EM: Round [566] log likelihood: -6199.563992
EM: Round [567] log likelihood: -6199.563818
EM: Round [568] log likelihood: -6199.563644
EM: Round [569] log likelihood: -6199.563472
EM: Round [570] log likelihood: -6199.563301
EM: Round [571] log likelihood: -6199.563131
EM: Round [572] log likelihood: -6199.562962
EM: Round [573] log likelihood: -6199.562794
EM: Round [574] log likelihood: -6199.562627
EM: Round [575] log likelihood: -6199.562461
EM: Round [576] log likelihood: -6199.562296
EM: Round [577] log likelihood: -6199.562133
EM: Round [578] log likelihood: -6199.561970
EM: Round [579] log likelihood: -6199.561808
EM: Round [580] log likelihood: -6199.561648
EM: Round [581] log likelihood: -6199.561488
EM: Round [582] log likelihood: -6199.561330
EM: Round [583] log likelihood: -6199.561172
EM: Round [584] log likelihood: -6199.561016
EM: Round [585] log likelihood: -6199.560860
EM: Round [586] log likelihood: -6199.560706
EM: Round [587] log likelihood: -6199.560552
EM: Round [588] log likelihood: -6199.560399
EM: Round [589] log likelihood: -6199.560248
EM: Round [590] log likelihood: -6199.560097
EM: Round [591] log likelihood: -6199.559948
EM: Round [592] log likelihood: -6199.559799
EM: Round [593] log likelihood: -6199.559651
EM: Round [594] log likelihood: -6199.559504
EM: Round [595] log likelihood: -6199.559358
EM: Round [596] log likelihood: -6199.559213
EM: Round [597] log likelihood: -6199.559069
EM: Round [598] log likelihood: -6199.558926
EM: Round [599] log likelihood: -6199.558784
EM: Round [600] log likelihood: -6199.558643
EM: Round [601] log likelihood: -6199.558502
EM: Round [602] log likelihood: -6199.558363
EM: Round [603] log likelihood: -6199.558224
EM: Round [604] log likelihood: -6199.558086
EM: Round [605] log likelihood: -6199.557949
EM: Round [606] log likelihood: -6199.557813
EM: Round [607] log likelihood: -6199.557678
EM: Round [608] log likelihood: -6199.557544
EM: Round [609] log likelihood: -6199.557411
EM: Round [610] log likelihood: -6199.557278
EM: Round [611] log likelihood: -6199.557146
EM: Round [612] log likelihood: -6199.557015
EM: Round [613] log likelihood: -6199.556885
EM: Round [614] log likelihood: -6199.556756
EM: Round [615] log likelihood: -6199.556628
EM: Round [616] log likelihood: -6199.556500
EM: Round [617] log likelihood: -6199.556373
EM: Round [618] log likelihood: -6199.556247
EM: Round [619] log likelihood: -6199.556122
EM: Round [620] log likelihood: -6199.555998
EM: Round [621] log likelihood: -6199.555874
EM: Round [622] log likelihood: -6199.555752
EM: Round [623] log likelihood: -6199.555629
EM: Round [624] log likelihood: -6199.555508
EM: Round [625] log likelihood: -6199.555388
EM: Round [626] log likelihood: -6199.555268
EM: Round [627] log likelihood: -6199.555149
EM: Round [628] log likelihood: -6199.555031
EM: Round [629] log likelihood: -6199.554914
EM: Round [630] log likelihood: -6199.554797
EM: Round [631] log likelihood: -6199.554681
EM: Round [632] log likelihood: -6199.554566
EM: Round [633] log likelihood: -6199.554451
EM: Round [634] log likelihood: -6199.554338
EM: Round [635] log likelihood: -6199.554224
EM: Round [636] log likelihood: -6199.554112
EM: Round [637] log likelihood: -6199.554001
EM: Round [638] log likelihood: -6199.553890
EM: Round [639] log likelihood: -6199.553780
EM: Round [640] log likelihood: -6199.553670
EM: Round [641] log likelihood: -6199.553561
EM: Round [642] log likelihood: -6199.553453
EM: Round [643] log likelihood: -6199.553346
EM: Round [644] log likelihood: -6199.553239
EM: Round [645] log likelihood: -6199.553133
EM: Round [646] log likelihood: -6199.553028
EM: Round [647] log likelihood: -6199.552923
EM: Round [648] log likelihood: -6199.552819
EM: Round [649] log likelihood: -6199.552716
EM: Round [650] log likelihood: -6199.552613
EM: Round [651] log likelihood: -6199.552511
EM: Round [652] log likelihood: -6199.552409
EM: Round [653] log likelihood: -6199.552309
EM: Round [654] log likelihood: -6199.552209
EM: Round [655] log likelihood: -6199.552109
EM: Stopping iterations at round 655 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.consolidated.bam into /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.consolidated.bam.read_coords
CMD: touch /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.consolidated.bam.read_coords > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.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.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.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.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -5147.304091
EM: Round [1] log likelihood: -5145.617989
EM: Round [2] log likelihood: -5145.615491
EM: Round [3] log likelihood: -5145.615485
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2_1.fastp.fastq.gz: 296087706
Warning - not locating file: /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000273598.1]
WARNING, no entry stored in dbm for [ENSG00000273598.1]
WARNING, no entry stored in dbm for [ENSG00000273598.1]
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 [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
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 [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 [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
ls: cannot access 'IGV_inputs': No such file or directory