Done.
-parsing GTF file: /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.C1XRhGIdM9/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.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam
12:45:14 : INFO : Done.
-parsing GTF file: /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.gtf
-parsing /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam
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[11530000] -done parsing /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'excessive soft clipping' => 82683,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 192,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 640,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 1908,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 224,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 8,
'seq-similar region overlap' => 3,
'per_id < 96' => 42240,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 16,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 111,
'num genes matched < 2' => 137,
'small anchor length' => 24,
'exons hit < 2' => 4,
'low complexity anchor region' => 4,
' ** passed ** ' => 11438,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 9
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[119000] -fusion SPANNING read extraction for scaff: AC136431.1--PKD1P5
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[56000] -fusion SPANNING read extraction for scaff: AHDC1--EYA2
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[224000] -fusion SPANNING read extraction for scaff: BCAT1--KRAS
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[99000] -fusion SPANNING read extraction for scaff: CAPZB--TMCO4
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[67000] -fusion SPANNING read extraction for scaff: CDKL1--MAP4K5
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[201000] -fusion SPANNING read extraction for scaff: CUX1--IFT22
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[11000] -fusion SPANNING read extraction for scaff: DNTTIP1--AC068774.1
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[46000] -fusion SPANNING read extraction for scaff: DSCAML1--FXYD6
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[14000] -fusion SPANNING read extraction for scaff: ENPP3--AKAP7
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[14000] -fusion SPANNING read extraction for scaff: FBXO25--AL669831.1
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[317000] -fusion SPANNING read extraction for scaff: KMT2A--KCNK7
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[68000] -fusion SPANNING read extraction for scaff: KXD1--IFI30
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[157000] -fusion SPANNING read extraction for scaff: LIMS1--VINAC1P
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[510000] -fusion SPANNING read extraction for scaff: LRBA--SH3D19
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[8000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13
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[128000] -fusion SPANNING read extraction for scaff: RIN2--ETV4
-fusion SPANNING read extraction for scaff: RNU7-159P--WTAPP1
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[21000] -fusion SPANNING read extraction for scaff: SELENBP1--TDRKH
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[93000] -fusion SPANNING read extraction for scaff: SEMA4B--CPA6
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[672000] -fusion SPANNING read extraction for scaff: SKIL--PRKCI
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[61000] -fusion SPANNING read extraction for scaff: SLC35A3--AGL
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[404000] -fusion SPANNING read extraction for scaff: SMARCC1--MAP4
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[301000] -fusion SPANNING read extraction for scaff: SPON1--DCAF8
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[81000] -fusion SPANNING read extraction for scaff: STAT2--DNTTIP1
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[67000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[15000] -fusion SPANNING read extraction for scaff: STXBP6--LINC02286
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[50000] -fusion SPANNING read extraction for scaff: TCOF1--IL17B
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[24000] -fusion SPANNING read extraction for scaff: TERF2--AC007663.2
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[37000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[8000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[106000] -fusion SPANNING read extraction for scaff: TMEM131--CRACDL
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[214000] -fusion SPANNING read extraction for scaff: TMEM259--ETV4
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[37000] -fusion SPANNING read extraction for scaff: TRIT1--MYCL
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[33000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[31000] -fusion SPANNING read extraction for scaff: TXNDC15--JADE2
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[38000] -fusion SPANNING read extraction for scaff: TXNDC15--SAR1B
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[498000] -fusion SPANNING read extraction for scaff: UACA--BCAS1
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[56000] -fusion SPANNING read extraction for scaff: YARS1--PHC2
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[386000] -fusion SPANNING read extraction for scaff: ZBTB10--TPD52
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 34651,
'seq similar region alignment' => 11413
};
EM: Starting log likelihood: -23789.672295
EM: Round [1] log likelihood: -23787.393499
EM: Round [2] log likelihood: -23787.198240
EM: Round [3] log likelihood: -23787.128174
EM: Round [4] log likelihood: -23787.098383
EM: Round [5] log likelihood: -23787.085053
EM: Round [6] log likelihood: -23787.078889
EM: Round [7] log likelihood: -23787.075969
EM: Round [8] log likelihood: -23787.074563
EM: Round [9] log likelihood: -23787.073878
EM: Round [10] log likelihood: -23787.073541
EM: Round [11] log likelihood: -23787.073374
EM: Round [12] log likelihood: -23787.073291
EM: Stopping iterations at round 12 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam into /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords
CMD: touch /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_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.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_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.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -23051.659243
EM: Round [1] log likelihood: -23050.634389
EM: Round [2] log likelihood: -23050.623280
EM: Round [3] log likelihood: -23050.623121
EM: Round [4] log likelihood: -23050.623119
EM: Stopping iterations at round 4 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz: 295399288
Warning - not locating file: /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000228327.3]
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 [ENSG00000286546.1]
WARNING, no entry stored in dbm for [ENSG00000286546.1]
WARNING, no entry stored in dbm for [ENSG00000286546.1]
WARNING, no entry stored in dbm for [ENSG00000286546.1]
WARNING, no entry stored in dbm for [ENSG00000286546.1]
WARNING, no entry stored in dbm for [ENSG00000260126.2]
WARNING, no entry stored in dbm for [ENSG00000254681.6]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000249923.1]
WARNING, no entry stored in dbm for [ENSG00000287388.1]
WARNING, no entry stored in dbm for [ENSG00000258098.2]
WARNING, no entry stored in dbm for [ENSG00000258098.2]
WARNING, no entry stored in dbm for [ENSG00000267053.8]
WARNING, no entry stored in dbm for [ENSG00000267053.8]
WARNING, no entry stored in dbm for [ENSG00000181984.11]
WARNING, no entry stored in dbm for [ENSG00000283698.1]
WARNING, no entry stored in dbm for [ENSG00000283698.1]
WARNING, no entry stored in dbm for [ENSG00000283698.1]
WARNING, no entry stored in dbm for [ENSG00000225422.4]
WARNING, no entry stored in dbm for [ENSG00000225422.4]
WARNING, no entry stored in dbm for [ENSG00000248515.2]
WARNING, no entry stored in dbm for [ENSG00000248515.2]
WARNING, no entry stored in dbm for [ENSG00000248515.2]
WARNING, no entry stored in dbm for [ENSG00000248515.2]
WARNING, no entry stored in dbm for [ENSG00000236866.5]
WARNING, no entry stored in dbm for [ENSG00000236866.5]
ls: cannot access 'IGV_inputs': No such file or directory