Done.
-parsing GTF file: /tmp/nxf.ldzfF6eIHp/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.ldzfF6eIHp/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.ldzfF6eIHp/659_b7Z-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.ldzfF6eIHp/659_b7Z-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.ldzfF6eIHp/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.ldzfF6eIHp/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
23:38:35 : INFO : Done.
-parsing GTF file: /tmp/nxf.ldzfF6eIHp/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.ldzfF6eIHp/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
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[950000] -done parsing /tmp/nxf.ldzfF6eIHp/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 6,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 44,
'per_id < 96' => 4578,
' ** passed ** ' => 22574,
'exons hit < 2' => 5,
'low complexity anchor region' => 63,
'excessive soft clipping' => 5605,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 8,
'seq-similar region overlap' => 319,
'small anchor length' => 186,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 10,
'num genes matched < 2' => 5,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 12
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.ldzfF6eIHp/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[77000] -fusion SPANNING read extraction for scaff: AC124944.2--SDHAP1
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[15000] -fusion SPANNING read extraction for scaff: AGAP12P--FRMPD2
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[39000] -fusion SPANNING read extraction for scaff: ATIC--AC092844.1
-fusion SPANNING read extraction for scaff: CCDC169--SOHLH2
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[19000] -fusion SPANNING read extraction for scaff: CDK19--RPF2
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[37000] -fusion SPANNING read extraction for scaff: CFLAR-AS1--PIP5K1B
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[26000] -fusion SPANNING read extraction for scaff: CRYZL2P--SEC16B
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[112000] -fusion SPANNING read extraction for scaff: ETV6--FAR2
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[12000] -fusion SPANNING read extraction for scaff: FBXO25--AC240565.1
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[22000] -fusion SPANNING read extraction for scaff: FSIP1--AC013652.1
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[63000] -fusion SPANNING read extraction for scaff: HGD--GTF2E1
[1000] -fusion SPANNING read extraction for scaff: KLRC4--KLRK1
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[7000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8
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[17000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6
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[33000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3
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[20000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11
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[13000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7
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[17000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9
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[16000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12
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[26000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[7000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
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[15000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[19000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[31000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[16000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[14000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[19000] -fusion SPANNING read extraction for scaff: RPF2--CDK19
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[45000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[27000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[27000] -fusion SPANNING read extraction for scaff: TLK2--LINC01347
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[21000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 31195,
'lacks exon overlap' => 10568
};
EM: Starting log likelihood: -7641.278033
EM: Round [1] log likelihood: -7629.279192
EM: Round [2] log likelihood: -7626.130149
EM: Round [3] log likelihood: -7623.537641
EM: Round [4] log likelihood: -7621.367491
EM: Round [5] log likelihood: -7619.532791
EM: Round [6] log likelihood: -7617.968805
EM: Round [7] log likelihood: -7616.626142
EM: Round [8] log likelihood: -7615.466392
EM: Round [9] log likelihood: -7614.459208
EM: Round [10] log likelihood: -7613.580276
EM: Round [11] log likelihood: -7612.809882
EM: Round [12] log likelihood: -7612.131867
EM: Round [13] log likelihood: -7611.532860
EM: Round [14] log likelihood: -7611.001704
EM: Round [15] log likelihood: -7610.529024
EM: Round [16] log likelihood: -7610.106891
EM: Round [17] log likelihood: -7609.728562
EM: Round [18] log likelihood: -7609.388282
EM: Round [19] log likelihood: -7609.081117
EM: Round [20] log likelihood: -7608.802825
EM: Round [21] log likelihood: -7608.549751
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EM: Round [940] log likelihood: -7599.385384
EM: Round [941] log likelihood: -7599.385224
EM: Round [942] log likelihood: -7599.385064
EM: Round [943] log likelihood: -7599.384905
EM: Round [944] log likelihood: -7599.384748
EM: Round [945] log likelihood: -7599.384591
EM: Round [946] log likelihood: -7599.384434
EM: Round [947] log likelihood: -7599.384279
EM: Round [948] log likelihood: -7599.384125
EM: Round [949] log likelihood: -7599.383971
EM: Round [950] log likelihood: -7599.383818
EM: Round [951] log likelihood: -7599.383666
EM: Round [952] log likelihood: -7599.383515
EM: Round [953] log likelihood: -7599.383365
EM: Round [954] log likelihood: -7599.383215
EM: Round [955] log likelihood: -7599.383066
EM: Round [956] log likelihood: -7599.382918
EM: Round [957] log likelihood: -7599.382771
EM: Round [958] log likelihood: -7599.382625
EM: Round [959] log likelihood: -7599.382479
EM: Round [960] log likelihood: -7599.382334
EM: Round [961] log likelihood: -7599.382190
EM: Round [962] log likelihood: -7599.382047
EM: Round [963] log likelihood: -7599.381905
EM: Round [964] log likelihood: -7599.381763
EM: Round [965] log likelihood: -7599.381622
EM: Round [966] log likelihood: -7599.381482
EM: Round [967] log likelihood: -7599.381342
EM: Round [968] log likelihood: -7599.381204
EM: Round [969] log likelihood: -7599.381066
EM: Round [970] log likelihood: -7599.380929
EM: Round [971] log likelihood: -7599.380792
EM: Round [972] log likelihood: -7599.380657
EM: Round [973] log likelihood: -7599.380522
EM: Round [974] log likelihood: -7599.380387
EM: Round [975] log likelihood: -7599.380254
EM: Round [976] log likelihood: -7599.380121
EM: Round [977] log likelihood: -7599.379989
EM: Round [978] log likelihood: -7599.379858
EM: Round [979] log likelihood: -7599.379727
EM: Round [980] log likelihood: -7599.379597
EM: Round [981] log likelihood: -7599.379468
EM: Round [982] log likelihood: -7599.379339
EM: Round [983] log likelihood: -7599.379211
EM: Round [984] log likelihood: -7599.379084
EM: Round [985] log likelihood: -7599.378957
EM: Round [986] log likelihood: -7599.378832
EM: Round [987] log likelihood: -7599.378707
EM: Round [988] log likelihood: -7599.378582
EM: Round [989] log likelihood: -7599.378458
EM: Round [990] log likelihood: -7599.378335
EM: Round [991] log likelihood: -7599.378213
EM: Round [992] log likelihood: -7599.378091
EM: Round [993] log likelihood: -7599.377970
EM: Round [994] log likelihood: -7599.377849
EM: Round [995] log likelihood: -7599.377729
EM: Round [996] log likelihood: -7599.377610
EM: Round [997] log likelihood: -7599.377492
EM: Round [998] log likelihood: -7599.377374
EM: Round [999] log likelihood: -7599.377256
EM: Round [1000] log likelihood: -7599.377140
EM: Round [1001] log likelihood: -7599.377024
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.ldzfF6eIHp/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.ldzfF6eIHp/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.ldzfF6eIHp/659_b7Z-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.ldzfF6eIHp/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.ldzfF6eIHp/659_b7Z-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.ldzfF6eIHp/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.ldzfF6eIHp/659_b7Z-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.ldzfF6eIHp/fi_workdir/659_b7Z-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.ldzfF6eIHp/fi_workdir/659_b7Z-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.ldzfF6eIHp/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.ldzfF6eIHp/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.ldzfF6eIHp/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -5270.044808
EM: Round [1] log likelihood: -5269.567155
EM: Round [2] log likelihood: -5269.566565
EM: Round [3] log likelihood: -5269.566563
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.ldzfF6eIHp/659_b7Z-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 296305715
Warning - not locating file: /tmp/nxf.ldzfF6eIHp/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gmap_trinity_GG.fusions.gff3.bed
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 [ENSG00000265018.6]
WARNING, no entry stored in dbm for [ENSG00000260261.2]
WARNING, no entry stored in dbm for [ENSG00000185485.14]
WARNING, no entry stored in dbm for [ENSG00000260261.2]
WARNING, no entry stored in dbm for [ENSG00000185485.14]
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 [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
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 [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000226312.7]
ls: cannot access 'IGV_inputs': No such file or directory