Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/cfb0cbf07fdb22704dd83d50aaf440/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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/9f/2f5f01907f54ef0ca6a3a2b88694e7/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/2f5f01907f54ef0ca6a3a2b88694e7/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/09ccc4496613519b4fb75dbd2aa5c6/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/cfb0cbf07fdb22704dd83d50aaf440/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.zW2b2UEleD/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.zW2b2UEleD/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.zW2b2UEleD/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.zW2b2UEleD/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.zW2b2UEleD/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.zW2b2UEleD/cytoBand.txt
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.bed
-parsing GTF file: /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.bed
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.zW2b2UEleD/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.zW2b2UEleD/fi_workdir --reads "/tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.zW2b2UEleD/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.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:52:52 ..... started STAR run
Jun 08 10:52:52 ..... loading genome
Jun 08 10:54:34 ... generating Suffix Array index
Jun 08 10:58:28 ... completed Suffix Array index
Jun 08 10:58:28 ..... processing annotations GTF
Jun 08 10:58:29 ..... inserting junctions into the genome indices
Jun 08 10:59:29 ..... started mapping
Jun 08 11:55:58 ..... finished mapping
Jun 08 11:56:00 ..... started sorting BAM
Jun 08 11:56:01 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam
Execution Time = 63.19 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.zW2b2UEleD/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.zW2b2UEleD/fi_workdir --reads "/tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:56:13 : INFO : Done.
Execution Time = 0.17 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.zW2b2UEleD/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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf
-parsing /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam
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[2000000] -done parsing /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 10 != num_counted_on_fusion_contigs 4 ' => 28,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 3,
'num_hits: 10 != num_counted_on_fusion_contigs 9 ' => 108,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 48,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 4,
'num_hits: 8 != num_counted_on_fusion_contigs 3 ' => 3,
'num_hits: 7 != num_counted_on_fusion_contigs 1 ' => 6,
'num_hits: 10 != num_counted_on_fusion_contigs 8 ' => 16,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 129,
'num_hits: 9 != num_counted_on_fusion_contigs 6 ' => 6,
'num_hits: 9 != num_counted_on_fusion_contigs 7 ' => 21,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 168,
'excessive soft clipping' => 10920,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 715,
'num_hits: 9 != num_counted_on_fusion_contigs 1 ' => 7,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 4,
'num_hits: 10 != num_counted_on_fusion_contigs 2 ' => 4,
'num_hits: 10 != num_counted_on_fusion_contigs 1 ' => 4,
'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 19,
'seq-similar region overlap' => 81,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
'num_hits: 10 != num_counted_on_fusion_contigs 3 ' => 3,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 21,
'num_hits: 9 != num_counted_on_fusion_contigs 8 ' => 120,
'small anchor length' => 285,
'num_hits: 8 != num_counted_on_fusion_contigs 1 ' => 5,
'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 120,
'num_hits: 9 != num_counted_on_fusion_contigs 3 ' => 6,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 31,
' ** passed ** ' => 10479,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 15,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 4,
'num genes matched < 2' => 19,
'num_hits: 7 != num_counted_on_fusion_contigs 6 ' => 78,
'per_id < 96' => 9526,
'num_hits: 9 != num_counted_on_fusion_contigs 4 ' => 20,
'num_hits: 8 != num_counted_on_fusion_contigs 7 ' => 56,
'num_hits: 10 != num_counted_on_fusion_contigs 5 ' => 10,
'exons hit < 2' => 10
};
-writing fusion junction support info.
Execution Time = 1.08 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.zW2b2UEleD/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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[37000] -fusion SPANNING read extraction for scaff: ACCS--DCDC1
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[572000] -fusion SPANNING read extraction for scaff: CCDC198--NPIPB12
[1000]
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[167000] -fusion SPANNING read extraction for scaff: FRG1--FAT1
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[14000] -fusion SPANNING read extraction for scaff: GDAP2--AC133865.1
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[14000] -fusion SPANNING read extraction for scaff: GDAP2--AC099786.3
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[111000] -fusion SPANNING read extraction for scaff: HK1--CAMK2G
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[60000] -fusion SPANNING read extraction for scaff: INPP5E--SMAD2
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[40000] -fusion SPANNING read extraction for scaff: PARVA--PRRT1B
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[13000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA8
[1000]
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[7000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC4
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[14000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA11
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[11000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB6
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[13000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA10
[1000]
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[8000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC5
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[12000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA9
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[15000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB7
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[17000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA12
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[59000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC3
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[13000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8
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[7000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4
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[14000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11
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[11000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6
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[13000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10
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[8000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5
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[12000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9
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[15000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7
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[17000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12
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[59000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3
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[13000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8
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[7000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4
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[14000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11
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[13000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10
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[8000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5
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[12000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA9
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[15000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7
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[17000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12
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[59000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3
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[14000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[13000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[8000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[12000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[15000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[17000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[59000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[135000] -fusion SPANNING read extraction for scaff: PRSS27--TPSB2
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[123000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
[1000]
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[13000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
[1000]
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[24000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 37644,
'lacks exon overlap' => 8697
};
Execution Time = 2.74 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.zW2b2UEleD/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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -4058.052681
EM: Round [1] log likelihood: -4057.025097
EM: Round [2] log likelihood: -4056.128091
EM: Round [3] log likelihood: -4055.311057
EM: Round [4] log likelihood: -4054.562860
EM: Round [5] log likelihood: -4053.874942
EM: Round [6] log likelihood: -4053.240511
EM: Round [7] log likelihood: -4052.654009
EM: Round [8] log likelihood: -4052.110747
EM: Round [9] log likelihood: -4051.606677
EM: Round [10] log likelihood: -4051.138235
EM: Round [11] log likelihood: -4050.702242
EM: Round [12] log likelihood: -4050.295839
EM: Round [13] log likelihood: -4049.916441
EM: Round [14] log likelihood: -4049.561707
EM: Round [15] log likelihood: -4049.229519
EM: Round [16] log likelihood: -4048.917954
EM: Round [17] log likelihood: -4048.625276
EM: Round [18] log likelihood: -4048.349915
EM: Round [19] log likelihood: -4048.090455
EM: Round [20] log likelihood: -4047.845620
EM: Round [21] log likelihood: -4047.614259
EM: Round [22] log likelihood: -4047.395335
EM: Round [23] log likelihood: -4047.187916
EM: Round [24] log likelihood: -4046.991160
EM: Round [25] log likelihood: -4046.804309
EM: Round [26] log likelihood: -4046.626679
EM: Round [27] log likelihood: -4046.457649
EM: Round [28] log likelihood: -4046.296659
EM: Round [29] log likelihood: -4046.143200
EM: Round [30] log likelihood: -4045.996808
EM: Round [31] log likelihood: -4045.857061
EM: Round [32] log likelihood: -4045.723572
EM: Round [33] log likelihood: -4045.595987
EM: Round [34] log likelihood: -4045.473980
EM: Round [35] log likelihood: -4045.357251
EM: Round [36] log likelihood: -4045.245523
EM: Round [37] log likelihood: -4045.138538
EM: Round [38] log likelihood: -4045.036056
EM: Round [39] log likelihood: -4044.937856
EM: Round [40] log likelihood: -4044.843729
EM: Round [41] log likelihood: -4044.753480
EM: Round [42] log likelihood: -4044.666927
EM: Round [43] log likelihood: -4044.583897
EM: Round [44] log likelihood: -4044.504229
EM: Round [45] log likelihood: -4044.427771
EM: Round [46] log likelihood: -4044.354377
EM: Round [47] log likelihood: -4044.283913
EM: Round [48] log likelihood: -4044.216247
EM: Round [49] log likelihood: -4044.151259
EM: Round [50] log likelihood: -4044.088831
EM: Round [51] log likelihood: -4044.028853
EM: Round [52] log likelihood: -4043.971220
EM: Round [53] log likelihood: -4043.915831
EM: Round [54] log likelihood: -4043.862592
EM: Round [55] log likelihood: -4043.811411
EM: Round [56] log likelihood: -4043.762202
EM: Round [57] log likelihood: -4043.714882
EM: Round [58] log likelihood: -4043.669373
EM: Round [59] log likelihood: -4043.625599
EM: Round [60] log likelihood: -4043.583488
EM: Round [61] log likelihood: -4043.542971
EM: Round [62] log likelihood: -4043.503984
EM: Round [63] log likelihood: -4043.466463
EM: Round [64] log likelihood: -4043.430348
EM: Round [65] log likelihood: -4043.395583
EM: Round [66] log likelihood: -4043.362112
EM: Round [67] log likelihood: -4043.329882
EM: Round [68] log likelihood: -4043.298845
EM: Round [69] log likelihood: -4043.268953
EM: Round [70] log likelihood: -4043.240158
EM: Round [71] log likelihood: -4043.212418
EM: Round [72] log likelihood: -4043.185690
EM: Round [73] log likelihood: -4043.159934
EM: Round [74] log likelihood: -4043.135112
EM: Round [75] log likelihood: -4043.111188
EM: Round [76] log likelihood: -4043.088125
EM: Round [77] log likelihood: -4043.065890
EM: Round [78] log likelihood: -4043.044451
EM: Round [79] log likelihood: -4043.023777
EM: Round [80] log likelihood: -4043.003839
EM: Round [81] log likelihood: -4042.984607
EM: Round [82] log likelihood: -4042.966054
EM: Round [83] log likelihood: -4042.948156
EM: Round [84] log likelihood: -4042.930886
EM: Round [85] log likelihood: -4042.914221
EM: Round [86] log likelihood: -4042.898138
EM: Round [87] log likelihood: -4042.882614
EM: Round [88] log likelihood: -4042.867630
EM: Round [89] log likelihood: -4042.853164
EM: Round [90] log likelihood: -4042.839197
EM: Round [91] log likelihood: -4042.825710
EM: Round [92] log likelihood: -4042.812687
EM: Round [93] log likelihood: -4042.800109
EM: Round [94] log likelihood: -4042.787960
EM: Round [95] log likelihood: -4042.776224
EM: Round [96] log likelihood: -4042.764887
EM: Round [97] log likelihood: -4042.753934
EM: Round [98] log likelihood: -4042.743350
EM: Round [99] log likelihood: -4042.733123
EM: Round [100] log likelihood: -4042.723240
EM: Round [101] log likelihood: -4042.713687
EM: Round [102] log likelihood: -4042.704454
EM: Round [103] log likelihood: -4042.695529
EM: Round [104] log likelihood: -4042.686901
EM: Round [105] log likelihood: -4042.678559
EM: Round [106] log likelihood: -4042.670493
EM: Round [107] log likelihood: -4042.662694
EM: Round [108] log likelihood: -4042.655153
EM: Round [109] log likelihood: -4042.647859
EM: Round [110] log likelihood: -4042.640804
EM: Round [111] log likelihood: -4042.633981
EM: Round [112] log likelihood: -4042.627381
EM: Round [113] log likelihood: -4042.620996
EM: Round [114] log likelihood: -4042.614820
EM: Round [115] log likelihood: -4042.608844
EM: Round [116] log likelihood: -4042.603061
EM: Round [117] log likelihood: -4042.597467
EM: Round [118] log likelihood: -4042.592052
EM: Round [119] log likelihood: -4042.586813
EM: Round [120] log likelihood: -4042.581742
EM: Round [121] log likelihood: -4042.576835
EM: Round [122] log likelihood: -4042.572085
EM: Round [123] log likelihood: -4042.567487
EM: Round [124] log likelihood: -4042.563036
EM: Round [125] log likelihood: -4042.558728
EM: Round [126] log likelihood: -4042.554556
EM: Round [127] log likelihood: -4042.550518
EM: Round [128] log likelihood: -4042.546608
EM: Round [129] log likelihood: -4042.542822
EM: Round [130] log likelihood: -4042.539157
EM: Round [131] log likelihood: -4042.535607
EM: Round [132] log likelihood: -4042.532169
EM: Round [133] log likelihood: -4042.528841
EM: Round [134] log likelihood: -4042.525617
EM: Round [135] log likelihood: -4042.522494
EM: Round [136] log likelihood: -4042.519470
EM: Round [137] log likelihood: -4042.516541
EM: Round [138] log likelihood: -4042.513703
EM: Round [139] log likelihood: -4042.510955
EM: Round [140] log likelihood: -4042.508293
EM: Round [141] log likelihood: -4042.505713
EM: Round [142] log likelihood: -4042.503215
EM: Round [143] log likelihood: -4042.500794
EM: Round [144] log likelihood: -4042.498449
EM: Round [145] log likelihood: -4042.496177
EM: Round [146] log likelihood: -4042.493975
EM: Round [147] log likelihood: -4042.491842
EM: Round [148] log likelihood: -4042.489775
EM: Round [149] log likelihood: -4042.487772
EM: Round [150] log likelihood: -4042.485831
EM: Round [151] log likelihood: -4042.483950
EM: Round [152] log likelihood: -4042.482127
EM: Round [153] log likelihood: -4042.480361
EM: Round [154] log likelihood: -4042.478649
EM: Round [155] log likelihood: -4042.476990
EM: Round [156] log likelihood: -4042.475382
EM: Round [157] log likelihood: -4042.473823
EM: Round [158] log likelihood: -4042.472313
EM: Round [159] log likelihood: -4042.470849
EM: Round [160] log likelihood: -4042.469429
EM: Round [161] log likelihood: -4042.468054
EM: Round [162] log likelihood: -4042.466720
EM: Round [163] log likelihood: -4042.465427
EM: Round [164] log likelihood: -4042.464174
EM: Round [165] log likelihood: -4042.462959
EM: Round [166] log likelihood: -4042.461782
EM: Round [167] log likelihood: -4042.460640
EM: Round [168] log likelihood: -4042.459533
EM: Round [169] log likelihood: -4042.458460
EM: Round [170] log likelihood: -4042.457419
EM: Round [171] log likelihood: -4042.456411
EM: Round [172] log likelihood: -4042.455433
EM: Round [173] log likelihood: -4042.454484
EM: Round [174] log likelihood: -4042.453565
EM: Round [175] log likelihood: -4042.452673
EM: Round [176] log likelihood: -4042.451809
EM: Round [177] log likelihood: -4042.450970
EM: Round [178] log likelihood: -4042.450158
EM: Round [179] log likelihood: -4042.449369
EM: Round [180] log likelihood: -4042.448605
EM: Round [181] log likelihood: -4042.447864
EM: Round [182] log likelihood: -4042.447145
EM: Round [183] log likelihood: -4042.446448
EM: Round [184] log likelihood: -4042.445772
EM: Round [185] log likelihood: -4042.445116
EM: Round [186] log likelihood: -4042.444480
EM: Round [187] log likelihood: -4042.443864
EM: Round [188] log likelihood: -4042.443266
EM: Round [189] log likelihood: -4042.442686
EM: Round [190] log likelihood: -4042.442123
EM: Round [191] log likelihood: -4042.441578
EM: Round [192] log likelihood: -4042.441048
EM: Round [193] log likelihood: -4042.440535
EM: Round [194] log likelihood: -4042.440037
EM: Round [195] log likelihood: -4042.439554
EM: Round [196] log likelihood: -4042.439086
EM: Round [197] log likelihood: -4042.438632
EM: Round [198] log likelihood: -4042.438191
EM: Round [199] log likelihood: -4042.437763
EM: Round [200] log likelihood: -4042.437349
EM: Round [201] log likelihood: -4042.436946
EM: Round [202] log likelihood: -4042.436556
EM: Round [203] log likelihood: -4042.436178
EM: Round [204] log likelihood: -4042.435810
EM: Round [205] log likelihood: -4042.435454
EM: Round [206] log likelihood: -4042.435109
EM: Round [207] log likelihood: -4042.434773
EM: Round [208] log likelihood: -4042.434448
EM: Round [209] log likelihood: -4042.434133
EM: Round [210] log likelihood: -4042.433826
EM: Round [211] log likelihood: -4042.433529
EM: Round [212] log likelihood: -4042.433241
EM: Round [213] log likelihood: -4042.432962
EM: Round [214] log likelihood: -4042.432691
EM: Round [215] log likelihood: -4042.432427
EM: Round [216] log likelihood: -4042.432172
EM: Round [217] log likelihood: -4042.431924
EM: Round [218] log likelihood: -4042.431684
EM: Round [219] log likelihood: -4042.431451
EM: Round [220] log likelihood: -4042.431225
EM: Round [221] log likelihood: -4042.431005
EM: Round [222] log likelihood: -4042.430792
EM: Round [223] log likelihood: -4042.430585
EM: Round [224] log likelihood: -4042.430385
EM: Round [225] log likelihood: -4042.430190
EM: Round [226] log likelihood: -4042.430001
EM: Round [227] log likelihood: -4042.429818
EM: Round [228] log likelihood: -4042.429640
EM: Round [229] log likelihood: -4042.429468
EM: Round [230] log likelihood: -4042.429300
EM: Round [231] log likelihood: -4042.429138
EM: Round [232] log likelihood: -4042.428980
EM: Round [233] log likelihood: -4042.428827
EM: Round [234] log likelihood: -4042.428679
EM: Round [235] log likelihood: -4042.428535
EM: Round [236] log likelihood: -4042.428395
EM: Round [237] log likelihood: -4042.428259
EM: Round [238] log likelihood: -4042.428128
EM: Round [239] log likelihood: -4042.428000
EM: Round [240] log likelihood: -4042.427876
EM: Round [241] log likelihood: -4042.427755
EM: Round [242] log likelihood: -4042.427639
EM: Round [243] log likelihood: -4042.427525
EM: Round [244] log likelihood: -4042.427415
EM: Round [245] log likelihood: -4042.427308
EM: Round [246] log likelihood: -4042.427205
EM: Round [247] log likelihood: -4042.427104
EM: Round [248] log likelihood: -4042.427007
EM: Stopping iterations at round 248 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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.zW2b2UEleD/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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.zW2b2UEleD/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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam into /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.55 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.zW2b2UEleD/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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.igv.FusionJuncSpan
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.zW2b2UEleD/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.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.zW2b2UEleD/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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.zW2b2UEleD/ctat_genome_lib_build_dir
-done, see /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.zW2b2UEleD/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -2875.390290
EM: Round [1] log likelihood: -2875.354583
EM: Round [2] log likelihood: -2875.354583
EM: Stopping iterations at round 2 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.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz: 294354607
Execution Time = 5.36 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.zW2b2UEleD/fi_workdir/microH.dat
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.zW2b2UEleD/fi_workdir/microH.dat
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.zW2b2UEleD/fi_workdir/microH.dat /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/fi_workdir/microH.dat /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.zW2b2UEleD --json_outfile /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.zW2b2UEleD --json_outfile /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1
Running: touch /tmp/nxf.zW2b2UEleD/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.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.01 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.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.zW2b2UEleD/ctat_genome_lib_build_dir > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.zW2b2UEleD/ctat_genome_lib_build_dir > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.zW2b2UEleD/ctat_genome_lib_build_dir > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.zW2b2UEleD/ctat_genome_lib_build_dir > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory