Done.
-parsing GTF file: /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.HEmYH06Pph/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.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
12:29:32 : INFO : Done.
-parsing GTF file: /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
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[3390000] -done parsing /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 115,
'num_hits: 7 != num_counted_on_fusion_contigs 3 ' => 12,
'per_id < 96' => 11798,
'seq-similar region overlap' => 1606,
'num genes matched < 2' => 57,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
'small anchor length' => 243,
' ** passed ** ' => 42912,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 111,
'num_hits: 10 != num_counted_on_fusion_contigs 8 ' => 16,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 505,
'excessive soft clipping' => 20078,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 6,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 68,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 48,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 102,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 40,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 1,
'num_hits: 9 != num_counted_on_fusion_contigs 3 ' => 30,
'low complexity anchor region' => 26
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[1000] -fusion SPANNING read extraction for scaff: AC138035.1--SEPTIN14
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[9000] -fusion SPANNING read extraction for scaff: AL512590.2--CCDC180
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[565000] -fusion SPANNING read extraction for scaff: EWSR1--FLI1
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[87000] -fusion SPANNING read extraction for scaff: GUSB--NAIPP4
[1000]
[2000] -fusion SPANNING read extraction for scaff: KLRC4--KLRK1
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[106000] -fusion SPANNING read extraction for scaff: MCM3AP--MTRNR2L12
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[192000] -fusion SPANNING read extraction for scaff: NKX2-2--NOC4L
[1000]
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[64000]
[65000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
[1000]
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[70000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1
[1000]
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[74000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
[1000]
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[71000]
[72000]
[73000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC1
[1000]
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[67000]
[68000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC2
[1000]
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[77000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHA13
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[70000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2
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[79000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13
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[75000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1
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[17000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA8
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[13000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGB6
[1000]
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[13000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGC5
[1000]
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[7000]
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[12000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGC4
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[39000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA11
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[13000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA9
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[87000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA10
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[73000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGC3
[1000]
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[24000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA12
[1000]
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[17000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA8
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[14000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGB6
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[14000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC5
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[12000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC4
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[40000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA11
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[13000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA9
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[87000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA10
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[74000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC3
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[25000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA12
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[103000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGB7
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[16000] -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGA8
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[13000] -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGB6
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[13000] -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGC5
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[11000] -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGC4
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[39000] -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGA11
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[12000] -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGA9
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[86000] -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGA10
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[73000] -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGC3
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[24000] -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGA12
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[102000] -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGB7
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[39000] -fusion SPANNING read extraction for scaff: SDHAP1--SMBD1P
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[44000] -fusion SPANNING read extraction for scaff: SOGA3--KIAA0408
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[58000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[45000] -fusion SPANNING read extraction for scaff: TAS2R14--PRR4
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[39000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[46000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A
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[8000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[15000] -fusion SPANNING read extraction for scaff: TMED7--TICAM2
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[33000] -fusion SPANNING read extraction for scaff: TMEM244--ARHGAP18
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[44000] -fusion SPANNING read extraction for scaff: TRIM59--IFT80
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[19000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[12000] -fusion SPANNING read extraction for scaff: UBE2Q2P2--GOLGA6L10
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 234322,
'lacks exon overlap' => 28530
};
EM: Starting log likelihood: -22686.086059
EM: Round [1] log likelihood: -22641.631506
EM: Round [2] log likelihood: -22633.143414
EM: Round [3] log likelihood: -22626.490431
EM: Round [4] log likelihood: -22621.165259
EM: Round [5] log likelihood: -22616.865958
EM: Round [6] log likelihood: -22613.366415
EM: Round [7] log likelihood: -22610.494775
EM: Round [8] log likelihood: -22608.119160
EM: Round [9] log likelihood: -22606.137742
EM: Round [10] log likelihood: -22604.471645
EM: Round [11] log likelihood: -22603.059691
EM: Round [12] log likelihood: -22601.854381
EM: Round [13] log likelihood: -22600.818726
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EM: Round [930] log likelihood: -22588.552838
EM: Round [931] log likelihood: -22588.552727
EM: Round [932] log likelihood: -22588.552616
EM: Round [933] log likelihood: -22588.552505
EM: Round [934] log likelihood: -22588.552396
EM: Round [935] log likelihood: -22588.552286
EM: Round [936] log likelihood: -22588.552178
EM: Round [937] log likelihood: -22588.552070
EM: Round [938] log likelihood: -22588.551962
EM: Round [939] log likelihood: -22588.551855
EM: Round [940] log likelihood: -22588.551748
EM: Round [941] log likelihood: -22588.551642
EM: Round [942] log likelihood: -22588.551537
EM: Round [943] log likelihood: -22588.551432
EM: Round [944] log likelihood: -22588.551327
EM: Round [945] log likelihood: -22588.551223
EM: Round [946] log likelihood: -22588.551120
EM: Round [947] log likelihood: -22588.551017
EM: Round [948] log likelihood: -22588.550914
EM: Round [949] log likelihood: -22588.550812
EM: Round [950] log likelihood: -22588.550711
EM: Round [951] log likelihood: -22588.550610
EM: Round [952] log likelihood: -22588.550509
EM: Round [953] log likelihood: -22588.550409
EM: Stopping iterations at round 953 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -16195.754994
EM: Round [1] log likelihood: -16191.619086
EM: Round [2] log likelihood: -16191.592622
EM: Round [3] log likelihood: -16191.592107
EM: Round [4] log likelihood: -16191.592094
EM: Stopping iterations at round 4 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 295934893
Warning - not locating file: /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000284627.1]
WARNING, no entry stored in dbm for [ENSG00000284627.1]
WARNING, no entry stored in dbm for [ENSG00000284627.1]
WARNING, no entry stored in dbm for [ENSG00000284627.1]
WARNING, no entry stored in dbm for [ENSG00000236438.7]
WARNING, no entry stored in dbm for [ENSG00000259429.5]
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]
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 [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 [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000238035.8]
WARNING, no entry stored in dbm for [ENSG00000238035.8]
WARNING, no entry stored in dbm for [ENSG00000238035.8]
WARNING, no entry stored in dbm for [ENSG00000251634.2]
WARNING, no entry stored in dbm for [ENSG00000286833.1]
WARNING, no entry stored in dbm for [ENSG00000286833.1]
WARNING, no entry stored in dbm for [ENSG00000261318.1]
WARNING, no entry stored in dbm for [ENSG00000261318.1]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
WARNING, no entry stored in dbm for [ENSG00000185485.14]
WARNING, no entry stored in dbm for [ENSG00000283426.1]
WARNING, no entry stored in dbm for [ENSG00000267198.1]
WARNING, no entry stored in dbm for [ENSG00000131484.4]
ls: cannot access 'IGV_inputs': No such file or directory