Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/4fd190dad4046b9da18af76c592fcb/tih_rna_sample_00479_B23WHTKLT4_1_1.fastp.fastq.gz
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/88caaae735347dd57d014e6bb2151b/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/88caaae735347dd57d014e6bb2151b/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/30ed0f4b1d94ae2e648234fc84a2be/tih_rna_sample_00479_B23WHTKLT4_1.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/4fd190dad4046b9da18af76c592fcb/tih_rna_sample_00479_B23WHTKLT4_1_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00479_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.3KRbpDehHe/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.3KRbpDehHe/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.14 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00479_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.3KRbpDehHe/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.3KRbpDehHe/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fa /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fa /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fa
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.gtf /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.gtf /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.gtf
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fa /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.gtf > /tmp/nxf.3KRbpDehHe/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fa /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.gtf > /tmp/nxf.3KRbpDehHe/cytoBand.txt
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.gtf > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.bed
-parsing GTF file: /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.gtf
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.gtf > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.bed
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.bed > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.bed > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/tih_rna_sample_00479_B23WHTKLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/tih_rna_sample_00479_B23WHTKLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/tih_rna_sample_00479_B23WHTKLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fa
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.3KRbpDehHe/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00479_B23WHTKLT4_1.star --out_dir /tmp/nxf.3KRbpDehHe/fi_workdir --reads "/tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.3KRbpDehHe/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.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:17:49 ..... started STAR run
Jun 08 10:17:49 ..... loading genome
Jun 08 10:19:36 ... generating Suffix Array index
Jun 08 10:23:27 ... completed Suffix Array index
Jun 08 10:23:27 ..... processing annotations GTF
Jun 08 10:23:27 ..... inserting junctions into the genome indices
Jun 08 10:24:29 ..... started mapping
Jun 08 11:44:43 ..... finished mapping
Jun 08 11:44:45 ..... started sorting BAM
Jun 08 11:44:47 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00479_B23WHTKLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00479_B23WHTKLT4_1.star.sortedByCoord.out.bam
Execution Time = 87.05 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.3KRbpDehHe/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00479_B23WHTKLT4_1.star --out_dir /tmp/nxf.3KRbpDehHe/fi_workdir --reads "/tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:45:16 : INFO : Done.
Execution Time = 0.41 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/mark_dups_reads.index.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.gtf
-parsing /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
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[4510000] -done parsing /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 20,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
' ** passed ** ' => 15697,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 1218,
'num genes matched < 2' => 320,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 9,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 398,
'exons hit < 2' => 17,
'low complexity anchor region' => 31,
'per_id < 96' => 21589,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 143,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 12,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 28,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 45,
'small anchor length' => 14,
'seq-similar region overlap' => 347,
'excessive soft clipping' => 31621,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 20,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 45,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 286
};
-writing fusion junction support info.
Execution Time = 2.53 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[91000] -fusion SPANNING read extraction for scaff: CREBBP--AC008798.3
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[43000] -fusion SPANNING read extraction for scaff: CRYBB2P1--MYO18B
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[128000] -fusion SPANNING read extraction for scaff: EIF4G3--AL445231.1
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[11000] -fusion SPANNING read extraction for scaff: FAM86C1P--RNF121
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[53000] -fusion SPANNING read extraction for scaff: GBF1--BORCS7
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[38000] -fusion SPANNING read extraction for scaff: GK5--IQCB1
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[14000] -fusion SPANNING read extraction for scaff: GNAQ--GNA14
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[45000] -fusion SPANNING read extraction for scaff: GNPTAB--RN7SL88P
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[45000] -fusion SPANNING read extraction for scaff: GNPTAB--LINC02452
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[91000] -fusion SPANNING read extraction for scaff: HIF1A--PRKCH
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[21000] -fusion SPANNING read extraction for scaff: HMGB3P23--ACO1
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[7000] -fusion SPANNING read extraction for scaff: IQCB1--LINC00882
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[30000] -fusion SPANNING read extraction for scaff: KIAA2026--AC025254.1
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[30000] -fusion SPANNING read extraction for scaff: KIAA2026--AC090049.2
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[5000] -fusion SPANNING read extraction for scaff: LDLRAD3--DMD-AS3
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[19000] -fusion SPANNING read extraction for scaff: LDLRAD3--DMD
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[42000] -fusion SPANNING read extraction for scaff: LMNB2--AC004490.1
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[44000] -fusion SPANNING read extraction for scaff: MAP3K1--AC244502.1
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[33000] -fusion SPANNING read extraction for scaff: MCM5--LINC01643
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[33000] -fusion SPANNING read extraction for scaff: MCM5--AL021877.1
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[83000] -fusion SPANNING read extraction for scaff: MECOM--PHC3
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[10000] -fusion SPANNING read extraction for scaff: MGAT3--PHF21B
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[128000] -fusion SPANNING read extraction for scaff: MORF4L1--VAT1L
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[130000] -fusion SPANNING read extraction for scaff: NELFB--EHMT1
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[201000] -fusion SPANNING read extraction for scaff: NF2--WWTR1
[1000] -fusion SPANNING read extraction for scaff: NXPH2--LINC01832
[1000] -fusion SPANNING read extraction for scaff: NXPH2--RPL15P5
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[13000] -fusion SPANNING read extraction for scaff: OSBP2--LRRC8C
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[27000] -fusion SPANNING read extraction for scaff: OTUD3--TTF2
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[10000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
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[9000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1
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[10000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
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[16000] -fusion SPANNING read extraction for scaff: PCDHA2--PCDHAC1
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[17000] -fusion SPANNING read extraction for scaff: PCDHA2--PCDHAC2
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[17000] -fusion SPANNING read extraction for scaff: PCDHA2--PCDHA13
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[25000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHA13
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[25000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC1
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[26000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC2
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[14000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2
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[14000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1
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[15000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13
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[10000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[6000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[5000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[6000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[6000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
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[74000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[6000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[4000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[8000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[109000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[44000] -fusion SPANNING read extraction for scaff: PEPD--AC011474.1
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[112000] -fusion SPANNING read extraction for scaff: PER1--CELSR1
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[7000] -fusion SPANNING read extraction for scaff: PHF21B--Z99755.2
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[58000] -fusion SPANNING read extraction for scaff: PHTF2--PTPN12
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[23000] -fusion SPANNING read extraction for scaff: PITPNM2--CSMD3
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[350000] -fusion SPANNING read extraction for scaff: PKD1--NPIPB2
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[32000] -fusion SPANNING read extraction for scaff: RBM19--YPEL5P3
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[32000] -fusion SPANNING read extraction for scaff: RBM19--RN7SL88P
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[24000] -fusion SPANNING read extraction for scaff: REL--AHSA2P
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[21000] -fusion SPANNING read extraction for scaff: RNA5SP281--ACO1
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[37000] -fusion SPANNING read extraction for scaff: SBF2--GRK7
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[10000] -fusion SPANNING read extraction for scaff: SGF29--NPHS1
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[48000] -fusion SPANNING read extraction for scaff: TANC2--GAS7
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[105000] -fusion SPANNING read extraction for scaff: TIMM44--GRAMD1A
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[24000] -fusion SPANNING read extraction for scaff: TIMM44--AC020907.4
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[42000] -fusion SPANNING read extraction for scaff: TNIK--NAALADL2
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[38000] -fusion SPANNING read extraction for scaff: TOMM70--DCBLD2
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[24000] -fusion SPANNING read extraction for scaff: TP53--LINC02071
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[70000] -fusion SPANNING read extraction for scaff: TTC17--SLC9A9
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[67000] -fusion SPANNING read extraction for scaff: TTC28--ZNRF3
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[22000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[46000] -fusion SPANNING read extraction for scaff: URI1--LIN37
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[96000] -fusion SPANNING read extraction for scaff: URI1--PROSER3
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[23000] -fusion SPANNING read extraction for scaff: ZFPM2--DPYS
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[21000] -fusion SPANNING read extraction for scaff: ZFPM2--AP002847.1
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[64000] -fusion SPANNING read extraction for scaff: ZNF146--ZNF568
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[23000] -fusion SPANNING read extraction for scaff: ZNF536--COX7A1
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 33743,
'seq similar region alignment' => 112104
};
Execution Time = 7.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -23945.220698
EM: Round [1] log likelihood: -23942.726877
EM: Round [2] log likelihood: -23942.570152
EM: Round [3] log likelihood: -23942.436429
EM: Round [4] log likelihood: -23942.319356
EM: Round [5] log likelihood: -23942.216408
EM: Round [6] log likelihood: -23942.125540
EM: Round [7] log likelihood: -23942.045068
EM: Round [8] log likelihood: -23941.973590
EM: Round [9] log likelihood: -23941.909928
EM: Round [10] log likelihood: -23941.853086
EM: Round [11] log likelihood: -23941.802216
EM: Round [12] log likelihood: -23941.756592
EM: Round [13] log likelihood: -23941.715588
EM: Round [14] log likelihood: -23941.678663
EM: Round [15] log likelihood: -23941.645347
EM: Round [16] log likelihood: -23941.615230
EM: Round [17] log likelihood: -23941.587955
EM: Round [18] log likelihood: -23941.563208
EM: Round [19] log likelihood: -23941.540712
EM: Round [20] log likelihood: -23941.520225
EM: Round [21] log likelihood: -23941.501533
EM: Round [22] log likelihood: -23941.484445
EM: Round [23] log likelihood: -23941.468793
EM: Round [24] log likelihood: -23941.454428
EM: Round [25] log likelihood: -23941.441217
EM: Round [26] log likelihood: -23941.429043
EM: Round [27] log likelihood: -23941.417801
EM: Round [28] log likelihood: -23941.407396
EM: Round [29] log likelihood: -23941.397747
EM: Round [30] log likelihood: -23941.388777
EM: Round [31] log likelihood: -23941.380421
EM: Round [32] log likelihood: -23941.372619
EM: Round [33] log likelihood: -23941.365317
EM: Round [34] log likelihood: -23941.358468
EM: Round [35] log likelihood: -23941.352030
EM: Round [36] log likelihood: -23941.345963
EM: Round [37] log likelihood: -23941.340234
EM: Round [38] log likelihood: -23941.334812
EM: Round [39] log likelihood: -23941.329669
EM: Round [40] log likelihood: -23941.324780
EM: Round [41] log likelihood: -23941.320123
EM: Round [42] log likelihood: -23941.315678
EM: Round [43] log likelihood: -23941.311426
EM: Round [44] log likelihood: -23941.307353
EM: Round [45] log likelihood: -23941.303442
EM: Round [46] log likelihood: -23941.299681
EM: Round [47] log likelihood: -23941.296058
EM: Round [48] log likelihood: -23941.292562
EM: Round [49] log likelihood: -23941.289184
EM: Round [50] log likelihood: -23941.285914
EM: Round [51] log likelihood: -23941.282746
EM: Round [52] log likelihood: -23941.279672
EM: Round [53] log likelihood: -23941.276685
EM: Round [54] log likelihood: -23941.273779
EM: Round [55] log likelihood: -23941.270951
EM: Round [56] log likelihood: -23941.268193
EM: Round [57] log likelihood: -23941.265503
EM: Round [58] log likelihood: -23941.262877
EM: Round [59] log likelihood: -23941.260310
EM: Round [60] log likelihood: -23941.257800
EM: Round [61] log likelihood: -23941.255343
EM: Round [62] log likelihood: -23941.252937
EM: Round [63] log likelihood: -23941.250580
EM: Round [64] log likelihood: -23941.248268
EM: Round [65] log likelihood: -23941.246001
EM: Round [66] log likelihood: -23941.243776
EM: Round [67] log likelihood: -23941.241591
EM: Round [68] log likelihood: -23941.239445
EM: Round [69] log likelihood: -23941.237337
EM: Round [70] log likelihood: -23941.235264
EM: Round [71] log likelihood: -23941.233226
EM: Round [72] log likelihood: -23941.231221
EM: Round [73] log likelihood: -23941.229249
EM: Round [74] log likelihood: -23941.227309
EM: Round [75] log likelihood: -23941.225398
EM: Round [76] log likelihood: -23941.223518
EM: Round [77] log likelihood: -23941.221666
EM: Round [78] log likelihood: -23941.219842
EM: Round [79] log likelihood: -23941.218046
EM: Round [80] log likelihood: -23941.216276
EM: Round [81] log likelihood: -23941.214532
EM: Round [82] log likelihood: -23941.212814
EM: Round [83] log likelihood: -23941.211120
EM: Round [84] log likelihood: -23941.209451
EM: Round [85] log likelihood: -23941.207805
EM: Round [86] log likelihood: -23941.206182
EM: Round [87] log likelihood: -23941.204583
EM: Round [88] log likelihood: -23941.203005
EM: Round [89] log likelihood: -23941.201450
EM: Round [90] log likelihood: -23941.199915
EM: Round [91] log likelihood: -23941.198402
EM: Round [92] log likelihood: -23941.196910
EM: Round [93] log likelihood: -23941.195438
EM: Round [94] log likelihood: -23941.193986
EM: Round [95] log likelihood: -23941.192553
EM: Round [96] log likelihood: -23941.191140
EM: Round [97] log likelihood: -23941.189746
EM: Round [98] log likelihood: -23941.188370
EM: Round [99] log likelihood: -23941.187013
EM: Round [100] log likelihood: -23941.185674
EM: Round [101] log likelihood: -23941.184352
EM: Round [102] log likelihood: -23941.183049
EM: Round [103] log likelihood: -23941.181762
EM: Round [104] log likelihood: -23941.180492
EM: Round [105] log likelihood: -23941.179239
EM: Round [106] log likelihood: -23941.178002
EM: Round [107] log likelihood: -23941.176781
EM: Round [108] log likelihood: -23941.175577
EM: Round [109] log likelihood: -23941.174388
EM: Round [110] log likelihood: -23941.173214
EM: Round [111] log likelihood: -23941.172056
EM: Round [112] log likelihood: -23941.170913
EM: Round [113] log likelihood: -23941.169785
EM: Round [114] log likelihood: -23941.168671
EM: Round [115] log likelihood: -23941.167571
EM: Round [116] log likelihood: -23941.166486
EM: Round [117] log likelihood: -23941.165415
EM: Round [118] log likelihood: -23941.164357
EM: Round [119] log likelihood: -23941.163313
EM: Round [120] log likelihood: -23941.162282
EM: Round [121] log likelihood: -23941.161265
EM: Round [122] log likelihood: -23941.160261
EM: Round [123] log likelihood: -23941.159269
EM: Round [124] log likelihood: -23941.158290
EM: Round [125] log likelihood: -23941.157324
EM: Round [126] log likelihood: -23941.156370
EM: Round [127] log likelihood: -23941.155428
EM: Round [128] log likelihood: -23941.154498
EM: Round [129] log likelihood: -23941.153579
EM: Round [130] log likelihood: -23941.152673
EM: Round [131] log likelihood: -23941.151778
EM: Round [132] log likelihood: -23941.150894
EM: Round [133] log likelihood: -23941.150021
EM: Round [134] log likelihood: -23941.149160
EM: Round [135] log likelihood: -23941.148309
EM: Round [136] log likelihood: -23941.147469
EM: Round [137] log likelihood: -23941.146640
EM: Round [138] log likelihood: -23941.145821
EM: Round [139] log likelihood: -23941.145012
EM: Round [140] log likelihood: -23941.144213
EM: Round [141] log likelihood: -23941.143425
EM: Round [142] log likelihood: -23941.142646
EM: Round [143] log likelihood: -23941.141877
EM: Round [144] log likelihood: -23941.141118
EM: Round [145] log likelihood: -23941.140368
EM: Round [146] log likelihood: -23941.139628
EM: Round [147] log likelihood: -23941.138897
EM: Round [148] log likelihood: -23941.138175
EM: Round [149] log likelihood: -23941.137462
EM: Round [150] log likelihood: -23941.136758
EM: Round [151] log likelihood: -23941.136063
EM: Round [152] log likelihood: -23941.135376
EM: Round [153] log likelihood: -23941.134698
EM: Round [154] log likelihood: -23941.134028
EM: Round [155] log likelihood: -23941.133367
EM: Round [156] log likelihood: -23941.132714
EM: Round [157] log likelihood: -23941.132069
EM: Round [158] log likelihood: -23941.131432
EM: Round [159] log likelihood: -23941.130803
EM: Round [160] log likelihood: -23941.130181
EM: Round [161] log likelihood: -23941.129568
EM: Round [162] log likelihood: -23941.128961
EM: Round [163] log likelihood: -23941.128363
EM: Round [164] log likelihood: -23941.127772
EM: Round [165] log likelihood: -23941.127188
EM: Round [166] log likelihood: -23941.126611
EM: Round [167] log likelihood: -23941.126041
EM: Round [168] log likelihood: -23941.125479
EM: Round [169] log likelihood: -23941.124923
EM: Round [170] log likelihood: -23941.124374
EM: Round [171] log likelihood: -23941.123832
EM: Round [172] log likelihood: -23941.123297
EM: Round [173] log likelihood: -23941.122768
EM: Round [174] log likelihood: -23941.122246
EM: Round [175] log likelihood: -23941.121730
EM: Round [176] log likelihood: -23941.121221
EM: Round [177] log likelihood: -23941.120717
EM: Round [178] log likelihood: -23941.120220
EM: Round [179] log likelihood: -23941.119729
EM: Round [180] log likelihood: -23941.119244
EM: Round [181] log likelihood: -23941.118765
EM: Round [182] log likelihood: -23941.118292
EM: Round [183] log likelihood: -23941.117824
EM: Round [184] log likelihood: -23941.117363
EM: Round [185] log likelihood: -23941.116906
EM: Round [186] log likelihood: -23941.116456
EM: Round [187] log likelihood: -23941.116011
EM: Round [188] log likelihood: -23941.115571
EM: Round [189] log likelihood: -23941.115137
EM: Round [190] log likelihood: -23941.114708
EM: Round [191] log likelihood: -23941.114284
EM: Round [192] log likelihood: -23941.113866
EM: Round [193] log likelihood: -23941.113452
EM: Round [194] log likelihood: -23941.113044
EM: Round [195] log likelihood: -23941.112641
EM: Round [196] log likelihood: -23941.112242
EM: Round [197] log likelihood: -23941.111848
EM: Round [198] log likelihood: -23941.111459
EM: Round [199] log likelihood: -23941.111075
EM: Round [200] log likelihood: -23941.110696
EM: Round [201] log likelihood: -23941.110321
EM: Round [202] log likelihood: -23941.109950
EM: Round [203] log likelihood: -23941.109585
EM: Round [204] log likelihood: -23941.109223
EM: Round [205] log likelihood: -23941.108866
EM: Round [206] log likelihood: -23941.108513
EM: Round [207] log likelihood: -23941.108165
EM: Round [208] log likelihood: -23941.107821
EM: Round [209] log likelihood: -23941.107480
EM: Round [210] log likelihood: -23941.107145
EM: Round [211] log likelihood: -23941.106813
EM: Round [212] log likelihood: -23941.106485
EM: Round [213] log likelihood: -23941.106161
EM: Round [214] log likelihood: -23941.105841
EM: Round [215] log likelihood: -23941.105525
EM: Round [216] log likelihood: -23941.105212
EM: Round [217] log likelihood: -23941.104904
EM: Round [218] log likelihood: -23941.104599
EM: Round [219] log likelihood: -23941.104298
EM: Round [220] log likelihood: -23941.104000
EM: Round [221] log likelihood: -23941.103706
EM: Round [222] log likelihood: -23941.103416
EM: Round [223] log likelihood: -23941.103129
EM: Round [224] log likelihood: -23941.102846
EM: Round [225] log likelihood: -23941.102566
EM: Round [226] log likelihood: -23941.102289
EM: Round [227] log likelihood: -23941.102016
EM: Round [228] log likelihood: -23941.101746
EM: Round [229] log likelihood: -23941.101479
EM: Round [230] log likelihood: -23941.101215
EM: Round [231] log likelihood: -23941.100955
EM: Round [232] log likelihood: -23941.100697
EM: Round [233] log likelihood: -23941.100443
EM: Round [234] log likelihood: -23941.100192
EM: Round [235] log likelihood: -23941.099944
EM: Round [236] log likelihood: -23941.099699
EM: Round [237] log likelihood: -23941.099457
EM: Round [238] log likelihood: -23941.099217
EM: Round [239] log likelihood: -23941.098981
EM: Round [240] log likelihood: -23941.098747
EM: Round [241] log likelihood: -23941.098517
EM: Round [242] log likelihood: -23941.098289
EM: Round [243] log likelihood: -23941.098063
EM: Round [244] log likelihood: -23941.097841
EM: Round [245] log likelihood: -23941.097621
EM: Round [246] log likelihood: -23941.097404
EM: Round [247] log likelihood: -23941.097189
EM: Round [248] log likelihood: -23941.096977
EM: Round [249] log likelihood: -23941.096767
EM: Round [250] log likelihood: -23941.096560
EM: Round [251] log likelihood: -23941.096356
EM: Round [252] log likelihood: -23941.096154
EM: Round [253] log likelihood: -23941.095954
EM: Round [254] log likelihood: -23941.095756
EM: Round [255] log likelihood: -23941.095562
EM: Round [256] log likelihood: -23941.095369
EM: Round [257] log likelihood: -23941.095179
EM: Round [258] log likelihood: -23941.094991
EM: Round [259] log likelihood: -23941.094805
EM: Round [260] log likelihood: -23941.094621
EM: Round [261] log likelihood: -23941.094440
EM: Round [262] log likelihood: -23941.094261
EM: Round [263] log likelihood: -23941.094083
EM: Round [264] log likelihood: -23941.093908
EM: Round [265] log likelihood: -23941.093736
EM: Round [266] log likelihood: -23941.093565
EM: Round [267] log likelihood: -23941.093396
EM: Round [268] log likelihood: -23941.093229
EM: Round [269] log likelihood: -23941.093064
EM: Round [270] log likelihood: -23941.092902
EM: Round [271] log likelihood: -23941.092741
EM: Round [272] log likelihood: -23941.092582
EM: Round [273] log likelihood: -23941.092425
EM: Round [274] log likelihood: -23941.092270
EM: Round [275] log likelihood: -23941.092116
EM: Round [276] log likelihood: -23941.091965
EM: Round [277] log likelihood: -23941.091815
EM: Round [278] log likelihood: -23941.091667
EM: Round [279] log likelihood: -23941.091521
EM: Round [280] log likelihood: -23941.091376
EM: Round [281] log likelihood: -23941.091234
EM: Round [282] log likelihood: -23941.091093
EM: Round [283] log likelihood: -23941.090953
EM: Round [284] log likelihood: -23941.090816
EM: Round [285] log likelihood: -23941.090680
EM: Round [286] log likelihood: -23941.090545
EM: Round [287] log likelihood: -23941.090413
EM: Round [288] log likelihood: -23941.090281
EM: Round [289] log likelihood: -23941.090152
EM: Round [290] log likelihood: -23941.090024
EM: Round [291] log likelihood: -23941.089897
EM: Round [292] log likelihood: -23941.089772
EM: Round [293] log likelihood: -23941.089648
EM: Round [294] log likelihood: -23941.089526
EM: Round [295] log likelihood: -23941.089405
EM: Round [296] log likelihood: -23941.089286
EM: Round [297] log likelihood: -23941.089168
EM: Round [298] log likelihood: -23941.089052
EM: Round [299] log likelihood: -23941.088937
EM: Round [300] log likelihood: -23941.088823
EM: Round [301] log likelihood: -23941.088711
EM: Round [302] log likelihood: -23941.088600
EM: Round [303] log likelihood: -23941.088490
EM: Round [304] log likelihood: -23941.088382
EM: Round [305] log likelihood: -23941.088275
EM: Round [306] log likelihood: -23941.088169
EM: Round [307] log likelihood: -23941.088064
EM: Round [308] log likelihood: -23941.087961
EM: Round [309] log likelihood: -23941.087859
EM: Round [310] log likelihood: -23941.087758
EM: Round [311] log likelihood: -23941.087658
EM: Stopping iterations at round 311 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/init_EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/prep_igv_extract_junc_reads.ok
Running: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam || :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam
Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 1.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/prep_igv_sam_frag_coordss.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.igv.FusionJuncSpan
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.igv.Pfam.gff3
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/prep_igv_pfam_bed.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.igv.seqsimilar.gff3
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/prep_igv_seqsim_bed.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fa > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fa > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_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.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_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.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.3KRbpDehHe/ctat_genome_lib_build_dir
-done, see /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.3KRbpDehHe/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -20962.486294
EM: Round [1] log likelihood: -20961.615385
EM: Round [2] log likelihood: -20961.614366
EM: Round [3] log likelihood: -20961.614364
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1_1.fastp.fastq.gz: 295851949
Execution Time = 6.04 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fa --gtf /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.gtf > /tmp/nxf.3KRbpDehHe/fi_workdir/microH.dat
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fa --gtf /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.gtf > /tmp/nxf.3KRbpDehHe/fi_workdir/microH.dat
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.3KRbpDehHe/fi_workdir/microH.dat /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.3KRbpDehHe/fi_workdir/microH.dat /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.3KRbpDehHe --json_outfile /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00479_B23WHTKLT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.3KRbpDehHe --json_outfile /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00479_B23WHTKLT4_1
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/create_fi_igvjs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00479_B23WHTKLT4_1 --html_output /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.04 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00479_B23WHTKLT4_1 --html_output /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.3KRbpDehHe/ctat_genome_lib_build_dir > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.3KRbpDehHe/ctat_genome_lib_build_dir > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.3KRbpDehHe/ctat_genome_lib_build_dir > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000249383.2]
WARNING, no entry stored in dbm for [ENSG00000249383.2]
WARNING, no entry stored in dbm for [ENSG00000249383.2]
WARNING, no entry stored in dbm for [ENSG00000249383.2]
WARNING, no entry stored in dbm for [ENSG00000249383.2]
WARNING, no entry stored in dbm for [ENSG00000249383.2]
WARNING, no entry stored in dbm for [ENSG00000249383.2]
WARNING, no entry stored in dbm for [ENSG00000264515.6]
WARNING, no entry stored in dbm for [ENSG00000264515.6]
WARNING, no entry stored in dbm for [ENSG00000273068.1]
WARNING, no entry stored in dbm for [ENSG00000273068.1]
WARNING, no entry stored in dbm for [ENSG00000236137.1]
WARNING, no entry stored in dbm for [ENSG00000236137.1]
WARNING, no entry stored in dbm for [ENSG00000236137.1]
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 [ENSG00000232420.2]
WARNING, no entry stored in dbm for [ENSG00000232420.2]
WARNING, no entry stored in dbm for [ENSG00000232420.2]
WARNING, no entry stored in dbm for [ENSG00000232420.2]
WARNING, no entry stored in dbm for [ENSG00000232420.2]
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 [ENSG00000267122.1]
WARNING, no entry stored in dbm for [ENSG00000267122.1]
WARNING, no entry stored in dbm for [ENSG00000267122.1]
WARNING, no entry stored in dbm for [ENSG00000267122.1]
WARNING, no entry stored in dbm for [ENSG00000267122.1]
WARNING, no entry stored in dbm for [ENSG00000236828.1]
WARNING, no entry stored in dbm for [ENSG00000100058.12]
WARNING, no entry stored in dbm for [ENSG00000100058.12]
WARNING, no entry stored in dbm for [ENSG00000100058.12]
WARNING, no entry stored in dbm for [ENSG00000158483.17]
WARNING, no entry stored in dbm for [ENSG00000158483.17]
WARNING, no entry stored in dbm for [ENSG00000173209.23]
WARNING, no entry stored in dbm for [ENSG00000173209.23]
WARNING, no entry stored in dbm for [ENSG00000276538.1]
WARNING, no entry stored in dbm for [ENSG00000276538.1]
WARNING, no entry stored in dbm for [ENSG00000242759.8]
WARNING, no entry stored in dbm for [ENSG00000242759.8]
WARNING, no entry stored in dbm for [ENSG00000213753.11]
WARNING, no entry stored in dbm for [ENSG00000213753.11]
WARNING, no entry stored in dbm for [ENSG00000213753.11]
WARNING, no entry stored in dbm for [ENSG00000213753.11]
WARNING, no entry stored in dbm for [ENSG00000213753.11]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.3KRbpDehHe/ctat_genome_lib_build_dir > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory