Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/5606f77b8d0b02b2c41b293b948481/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv
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/8c/b86b4e9efe95c47d23943e876f257f/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/b5e5aa81766ed637c0fe06490d4bff/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/b86b4e9efe95c47d23943e876f257f/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/b5e5aa81766ed637c0fe06490d4bff/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.qK299E5g7p/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.qK299E5g7p/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.qK299E5g7p/1173_NMN_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_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.qK299E5g7p/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.qK299E5g7p/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fa
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.gtf
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.qK299E5g7p/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.qK299E5g7p/cytoBand.txt
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.bed
-parsing GTF file: /tmp/nxf.qK299E5g7p/1173_NMN_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.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.bed
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fa
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.qK299E5g7p/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.qK299E5g7p/fi_workdir --reads "/tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.qK299E5g7p/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.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 11:12:54 ..... started STAR run
Jun 08 11:12:54 ..... loading genome
Jun 08 11:14:37 ... generating Suffix Array index
Jun 08 11:18:30 ... completed Suffix Array index
Jun 08 11:18:31 ..... processing annotations GTF
Jun 08 11:18:31 ..... inserting junctions into the genome indices
Jun 08 11:19:32 ..... started mapping
Jun 08 11:58:52 ..... finished mapping
Jun 08 11:58:54 ..... started sorting BAM
Jun 08 11:58:55 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam
Execution Time = 46.05 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.qK299E5g7p/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.qK299E5g7p/fi_workdir --reads "/tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:59:09 : INFO : Done.
Execution Time = 0.20 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.qK299E5g7p/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.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.gtf
-parsing /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam
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[2580000] -done parsing /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 24,
'num genes matched < 2' => 17,
'low complexity anchor region' => 48,
'small anchor length' => 38,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 85,
'seq-similar region overlap' => 269,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 34,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 1,
'per_id < 96' => 9631,
'excessive soft clipping' => 14146,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 12,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 24,
' ** passed ** ' => 15919,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 2373,
'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 1
};
-writing fusion junction support info.
Execution Time = 1.35 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.qK299E5g7p/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.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[63000] -fusion SPANNING read extraction for scaff: GOLGA6L10--GOLGA2P6
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[29000] -fusion SPANNING read extraction for scaff: HIBADH--CPVL
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[94000] -fusion SPANNING read extraction for scaff: MARK2--PPM1D
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[60000] -fusion SPANNING read extraction for scaff: NELFB--TRAF2
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[266000] -fusion SPANNING read extraction for scaff: NFIB--AL035252.5
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[118000] -fusion SPANNING read extraction for scaff: NOLC1--PPRC1
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[30000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
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[28000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1
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[28000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
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[13000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC5
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[12000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC4
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[47000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA8
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB6
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[28000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA10
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[40000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC3
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[31000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA11
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[25000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB7
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA9
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[35000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA12
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[13000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5
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[12000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4
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[47000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6
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[28000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10
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[40000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3
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[31000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11
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[25000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9
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[34000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12
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[13000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5
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[12000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4
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[103000] -fusion SPANNING read extraction for scaff: VPS13A--PCSK5
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 121800,
'lacks exon overlap' => 7423
};
Execution Time = 2.90 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.qK299E5g7p/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.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_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.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -9363.085021
EM: Round [1] log likelihood: -9361.712357
EM: Round [2] log likelihood: -9360.559727
EM: Round [3] log likelihood: -9359.565190
EM: Round [4] log likelihood: -9358.691235
EM: Round [5] log likelihood: -9357.912432
EM: Round [6] log likelihood: -9357.210732
EM: Round [7] log likelihood: -9356.572897
EM: Round [8] log likelihood: -9355.988951
EM: Round [9] log likelihood: -9355.451206
EM: Round [10] log likelihood: -9354.953615
EM: Round [11] log likelihood: -9354.491335
EM: Round [12] log likelihood: -9354.060423
EM: Round [13] log likelihood: -9353.657613
EM: Round [14] log likelihood: -9353.280167
EM: Round [15] log likelihood: -9352.925750
EM: Round [16] log likelihood: -9352.592352
EM: Round [17] log likelihood: -9352.278220
EM: Round [18] log likelihood: -9351.981811
EM: Round [19] log likelihood: -9351.701755
EM: Round [20] log likelihood: -9351.436827
EM: Round [21] log likelihood: -9351.185921
EM: Round [22] log likelihood: -9350.948039
EM: Round [23] log likelihood: -9350.722273
EM: Round [24] log likelihood: -9350.507793
EM: Round [25] log likelihood: -9350.303842
EM: Round [26] log likelihood: -9350.109722
EM: Round [27] log likelihood: -9349.924795
EM: Round [28] log likelihood: -9349.748471
EM: Round [29] log likelihood: -9349.580208
EM: Round [30] log likelihood: -9349.419503
EM: Round [31] log likelihood: -9349.265892
EM: Round [32] log likelihood: -9349.118948
EM: Round [33] log likelihood: -9348.978273
EM: Round [34] log likelihood: -9348.843498
EM: Round [35] log likelihood: -9348.714283
EM: Round [36] log likelihood: -9348.590310
EM: Round [37] log likelihood: -9348.471285
EM: Round [38] log likelihood: -9348.356934
EM: Round [39] log likelihood: -9348.247002
EM: Round [40] log likelihood: -9348.141252
EM: Round [41] log likelihood: -9348.039462
EM: Round [42] log likelihood: -9347.941427
EM: Round [43] log likelihood: -9347.846952
EM: Round [44] log likelihood: -9347.755859
EM: Round [45] log likelihood: -9347.667977
EM: Round [46] log likelihood: -9347.583150
EM: Round [47] log likelihood: -9347.501229
EM: Round [48] log likelihood: -9347.422075
EM: Round [49] log likelihood: -9347.345558
EM: Round [50] log likelihood: -9347.271554
EM: Round [51] log likelihood: -9347.199949
EM: Round [52] log likelihood: -9347.130634
EM: Round [53] log likelihood: -9347.063507
EM: Round [54] log likelihood: -9346.998470
EM: Round [55] log likelihood: -9346.935433
EM: Round [56] log likelihood: -9346.874310
EM: Round [57] log likelihood: -9346.815018
EM: Round [58] log likelihood: -9346.757481
EM: Round [59] log likelihood: -9346.701626
EM: Round [60] log likelihood: -9346.647383
EM: Round [61] log likelihood: -9346.594687
EM: Round [62] log likelihood: -9346.543476
EM: Round [63] log likelihood: -9346.493689
EM: Round [64] log likelihood: -9346.445272
EM: Round [65] log likelihood: -9346.398171
EM: Round [66] log likelihood: -9346.352334
EM: Round [67] log likelihood: -9346.307714
EM: Round [68] log likelihood: -9346.264264
EM: Round [69] log likelihood: -9346.221940
EM: Round [70] log likelihood: -9346.180701
EM: Round [71] log likelihood: -9346.140506
EM: Round [72] log likelihood: -9346.101318
EM: Round [73] log likelihood: -9346.063100
EM: Round [74] log likelihood: -9346.025817
EM: Round [75] log likelihood: -9345.989436
EM: Round [76] log likelihood: -9345.953926
EM: Round [77] log likelihood: -9345.919256
EM: Round [78] log likelihood: -9345.885398
EM: Round [79] log likelihood: -9345.852323
EM: Round [80] log likelihood: -9345.820005
EM: Round [81] log likelihood: -9345.788418
EM: Round [82] log likelihood: -9345.757540
EM: Round [83] log likelihood: -9345.727345
EM: Round [84] log likelihood: -9345.697812
EM: Round [85] log likelihood: -9345.668920
EM: Round [86] log likelihood: -9345.640647
EM: Round [87] log likelihood: -9345.612975
EM: Round [88] log likelihood: -9345.585885
EM: Round [89] log likelihood: -9345.559358
EM: Round [90] log likelihood: -9345.533377
EM: Round [91] log likelihood: -9345.507926
EM: Round [92] log likelihood: -9345.482988
EM: Round [93] log likelihood: -9345.458549
EM: Round [94] log likelihood: -9345.434593
EM: Round [95] log likelihood: -9345.411106
EM: Round [96] log likelihood: -9345.388076
EM: Round [97] log likelihood: -9345.365487
EM: Round [98] log likelihood: -9345.343329
EM: Round [99] log likelihood: -9345.321589
EM: Round [100] log likelihood: -9345.300255
EM: Round [101] log likelihood: -9345.279316
EM: Round [102] log likelihood: -9345.258762
EM: Round [103] log likelihood: -9345.238582
EM: Round [104] log likelihood: -9345.218765
EM: Round [105] log likelihood: -9345.199303
EM: Round [106] log likelihood: -9345.180186
EM: Round [107] log likelihood: -9345.161405
EM: Round [108] log likelihood: -9345.142951
EM: Round [109] log likelihood: -9345.124817
EM: Round [110] log likelihood: -9345.106994
EM: Round [111] log likelihood: -9345.089474
EM: Round [112] log likelihood: -9345.072250
EM: Round [113] log likelihood: -9345.055315
EM: Round [114] log likelihood: -9345.038661
EM: Round [115] log likelihood: -9345.022283
EM: Round [116] log likelihood: -9345.006173
EM: Round [117] log likelihood: -9344.990325
EM: Round [118] log likelihood: -9344.974733
EM: Round [119] log likelihood: -9344.959391
EM: Round [120] log likelihood: -9344.944294
EM: Round [121] log likelihood: -9344.929436
EM: Round [122] log likelihood: -9344.914811
EM: Round [123] log likelihood: -9344.900416
EM: Round [124] log likelihood: -9344.886243
EM: Round [125] log likelihood: -9344.872289
EM: Round [126] log likelihood: -9344.858550
EM: Round [127] log likelihood: -9344.845019
EM: Round [128] log likelihood: -9344.831694
EM: Round [129] log likelihood: -9344.818569
EM: Round [130] log likelihood: -9344.805641
EM: Round [131] log likelihood: -9344.792905
EM: Round [132] log likelihood: -9344.780358
EM: Round [133] log likelihood: -9344.767996
EM: Round [134] log likelihood: -9344.755815
EM: Round [135] log likelihood: -9344.743811
EM: Round [136] log likelihood: -9344.731982
EM: Round [137] log likelihood: -9344.720323
EM: Round [138] log likelihood: -9344.708832
EM: Round [139] log likelihood: -9344.697504
EM: Round [140] log likelihood: -9344.686338
EM: Round [141] log likelihood: -9344.675330
EM: Round [142] log likelihood: -9344.664477
EM: Round [143] log likelihood: -9344.653775
EM: Round [144] log likelihood: -9344.643224
EM: Round [145] log likelihood: -9344.632819
EM: Round [146] log likelihood: -9344.622557
EM: Round [147] log likelihood: -9344.612438
EM: Round [148] log likelihood: -9344.602457
EM: Round [149] log likelihood: -9344.592612
EM: Round [150] log likelihood: -9344.582902
EM: Round [151] log likelihood: -9344.573323
EM: Round [152] log likelihood: -9344.563873
EM: Round [153] log likelihood: -9344.554551
EM: Round [154] log likelihood: -9344.545353
EM: Round [155] log likelihood: -9344.536278
EM: Round [156] log likelihood: -9344.527324
EM: Round [157] log likelihood: -9344.518489
EM: Round [158] log likelihood: -9344.509770
EM: Round [159] log likelihood: -9344.501166
EM: Round [160] log likelihood: -9344.492675
EM: Round [161] log likelihood: -9344.484295
EM: Round [162] log likelihood: -9344.476024
EM: Round [163] log likelihood: -9344.467861
EM: Round [164] log likelihood: -9344.459803
EM: Round [165] log likelihood: -9344.451849
EM: Round [166] log likelihood: -9344.443998
EM: Round [167] log likelihood: -9344.436247
EM: Round [168] log likelihood: -9344.428595
EM: Round [169] log likelihood: -9344.421041
EM: Round [170] log likelihood: -9344.413583
EM: Round [171] log likelihood: -9344.406219
EM: Round [172] log likelihood: -9344.398948
EM: Round [173] log likelihood: -9344.391769
EM: Round [174] log likelihood: -9344.384680
EM: Round [175] log likelihood: -9344.377680
EM: Round [176] log likelihood: -9344.370767
EM: Round [177] log likelihood: -9344.363941
EM: Round [178] log likelihood: -9344.357199
EM: Round [179] log likelihood: -9344.350541
EM: Round [180] log likelihood: -9344.343965
EM: Round [181] log likelihood: -9344.337470
EM: Round [182] log likelihood: -9344.331055
EM: Round [183] log likelihood: -9344.324719
EM: Round [184] log likelihood: -9344.318460
EM: Round [185] log likelihood: -9344.312278
EM: Round [186] log likelihood: -9344.306171
EM: Round [187] log likelihood: -9344.300138
EM: Round [188] log likelihood: -9344.294179
EM: Round [189] log likelihood: -9344.288291
EM: Round [190] log likelihood: -9344.282474
EM: Round [191] log likelihood: -9344.276727
EM: Round [192] log likelihood: -9344.271050
EM: Round [193] log likelihood: -9344.265440
EM: Round [194] log likelihood: -9344.259897
EM: Round [195] log likelihood: -9344.254421
EM: Round [196] log likelihood: -9344.249009
EM: Round [197] log likelihood: -9344.243662
EM: Round [198] log likelihood: -9344.238378
EM: Round [199] log likelihood: -9344.233156
EM: Round [200] log likelihood: -9344.227997
EM: Round [201] log likelihood: -9344.222897
EM: Round [202] log likelihood: -9344.217858
EM: Round [203] log likelihood: -9344.212878
EM: Round [204] log likelihood: -9344.207956
EM: Round [205] log likelihood: -9344.203091
EM: Round [206] log likelihood: -9344.198283
EM: Round [207] log likelihood: -9344.193531
EM: Round [208] log likelihood: -9344.188834
EM: Round [209] log likelihood: -9344.184192
EM: Round [210] log likelihood: -9344.179603
EM: Round [211] log likelihood: -9344.175067
EM: Round [212] log likelihood: -9344.170583
EM: Round [213] log likelihood: -9344.166151
EM: Round [214] log likelihood: -9344.161769
EM: Round [215] log likelihood: -9344.157438
EM: Round [216] log likelihood: -9344.153156
EM: Round [217] log likelihood: -9344.148922
EM: Round [218] log likelihood: -9344.144737
EM: Round [219] log likelihood: -9344.140600
EM: Round [220] log likelihood: -9344.136509
EM: Round [221] log likelihood: -9344.132465
EM: Round [222] log likelihood: -9344.128466
EM: Round [223] log likelihood: -9344.124512
EM: Round [224] log likelihood: -9344.120603
EM: Round [225] log likelihood: -9344.116737
EM: Round [226] log likelihood: -9344.112915
EM: Round [227] log likelihood: -9344.109136
EM: Round [228] log likelihood: -9344.105399
EM: Round [229] log likelihood: -9344.101703
EM: Round [230] log likelihood: -9344.098049
EM: Round [231] log likelihood: -9344.094435
EM: Round [232] log likelihood: -9344.090861
EM: Round [233] log likelihood: -9344.087327
EM: Round [234] log likelihood: -9344.083832
EM: Round [235] log likelihood: -9344.080375
EM: Round [236] log likelihood: -9344.076957
EM: Round [237] log likelihood: -9344.073576
EM: Round [238] log likelihood: -9344.070232
EM: Round [239] log likelihood: -9344.066925
EM: Round [240] log likelihood: -9344.063653
EM: Round [241] log likelihood: -9344.060418
EM: Round [242] log likelihood: -9344.057218
EM: Round [243] log likelihood: -9344.054052
EM: Round [244] log likelihood: -9344.050921
EM: Round [245] log likelihood: -9344.047824
EM: Round [246] log likelihood: -9344.044760
EM: Round [247] log likelihood: -9344.041730
EM: Round [248] log likelihood: -9344.038732
EM: Round [249] log likelihood: -9344.035766
EM: Round [250] log likelihood: -9344.032833
EM: Round [251] log likelihood: -9344.029930
EM: Round [252] log likelihood: -9344.027059
EM: Round [253] log likelihood: -9344.024219
EM: Round [254] log likelihood: -9344.021409
EM: Round [255] log likelihood: -9344.018628
EM: Round [256] log likelihood: -9344.015878
EM: Round [257] log likelihood: -9344.013156
EM: Round [258] log likelihood: -9344.010464
EM: Round [259] log likelihood: -9344.007800
EM: Round [260] log likelihood: -9344.005164
EM: Round [261] log likelihood: -9344.002556
EM: Round [262] log likelihood: -9343.999975
EM: Round [263] log likelihood: -9343.997422
EM: Round [264] log likelihood: -9343.994895
EM: Round [265] log likelihood: -9343.992395
EM: Round [266] log likelihood: -9343.989921
EM: Round [267] log likelihood: -9343.987473
EM: Round [268] log likelihood: -9343.985051
EM: Round [269] log likelihood: -9343.982654
EM: Round [270] log likelihood: -9343.980281
EM: Round [271] log likelihood: -9343.977934
EM: Round [272] log likelihood: -9343.975611
EM: Round [273] log likelihood: -9343.973311
EM: Round [274] log likelihood: -9343.971036
EM: Round [275] log likelihood: -9343.968784
EM: Round [276] log likelihood: -9343.966555
EM: Round [277] log likelihood: -9343.964349
EM: Round [278] log likelihood: -9343.962166
EM: Round [279] log likelihood: -9343.960005
EM: Round [280] log likelihood: -9343.957867
EM: Round [281] log likelihood: -9343.955750
EM: Round [282] log likelihood: -9343.953655
EM: Round [283] log likelihood: -9343.951581
EM: Round [284] log likelihood: -9343.949528
EM: Round [285] log likelihood: -9343.947497
EM: Round [286] log likelihood: -9343.945485
EM: Round [287] log likelihood: -9343.943495
EM: Round [288] log likelihood: -9343.941524
EM: Round [289] log likelihood: -9343.939573
EM: Round [290] log likelihood: -9343.937642
EM: Round [291] log likelihood: -9343.935731
EM: Round [292] log likelihood: -9343.933838
EM: Round [293] log likelihood: -9343.931965
EM: Round [294] log likelihood: -9343.930110
EM: Round [295] log likelihood: -9343.928274
EM: Round [296] log likelihood: -9343.926457
EM: Round [297] log likelihood: -9343.924657
EM: Round [298] log likelihood: -9343.922876
EM: Round [299] log likelihood: -9343.921112
EM: Round [300] log likelihood: -9343.919366
EM: Round [301] log likelihood: -9343.917637
EM: Round [302] log likelihood: -9343.915925
EM: Round [303] log likelihood: -9343.914230
EM: Round [304] log likelihood: -9343.912552
EM: Round [305] log likelihood: -9343.910890
EM: Round [306] log likelihood: -9343.909245
EM: Round [307] log likelihood: -9343.907616
EM: Round [308] log likelihood: -9343.906003
EM: Round [309] log likelihood: -9343.904406
EM: Round [310] log likelihood: -9343.902824
EM: Round [311] log likelihood: -9343.901258
EM: Round [312] log likelihood: -9343.899707
EM: Round [313] log likelihood: -9343.898171
EM: Round [314] log likelihood: -9343.896651
EM: Round [315] log likelihood: -9343.895145
EM: Round [316] log likelihood: -9343.893653
EM: Round [317] log likelihood: -9343.892176
EM: Round [318] log likelihood: -9343.890714
EM: Round [319] log likelihood: -9343.889265
EM: Round [320] log likelihood: -9343.887831
EM: Round [321] log likelihood: -9343.886410
EM: Round [322] log likelihood: -9343.885003
EM: Round [323] log likelihood: -9343.883610
EM: Round [324] log likelihood: -9343.882230
EM: Round [325] log likelihood: -9343.880863
EM: Round [326] log likelihood: -9343.879509
EM: Round [327] log likelihood: -9343.878168
EM: Round [328] log likelihood: -9343.876840
EM: Round [329] log likelihood: -9343.875525
EM: Round [330] log likelihood: -9343.874222
EM: Round [331] log likelihood: -9343.872932
EM: Round [332] log likelihood: -9343.871653
EM: Round [333] log likelihood: -9343.870387
EM: Round [334] log likelihood: -9343.869133
EM: Round [335] log likelihood: -9343.867891
EM: Round [336] log likelihood: -9343.866660
EM: Round [337] log likelihood: -9343.865441
EM: Round [338] log likelihood: -9343.864234
EM: Round [339] log likelihood: -9343.863038
EM: Round [340] log likelihood: -9343.861853
EM: Round [341] log likelihood: -9343.860679
EM: Round [342] log likelihood: -9343.859516
EM: Round [343] log likelihood: -9343.858364
EM: Round [344] log likelihood: -9343.857223
EM: Round [345] log likelihood: -9343.856093
EM: Round [346] log likelihood: -9343.854973
EM: Round [347] log likelihood: -9343.853863
EM: Round [348] log likelihood: -9343.852764
EM: Round [349] log likelihood: -9343.851674
EM: Round [350] log likelihood: -9343.850595
EM: Round [351] log likelihood: -9343.849526
EM: Round [352] log likelihood: -9343.848467
EM: Round [353] log likelihood: -9343.847418
EM: Round [354] log likelihood: -9343.846378
EM: Round [355] log likelihood: -9343.845348
EM: Round [356] log likelihood: -9343.844327
EM: Round [357] log likelihood: -9343.843315
EM: Round [358] log likelihood: -9343.842313
EM: Round [359] log likelihood: -9343.841320
EM: Round [360] log likelihood: -9343.840336
EM: Round [361] log likelihood: -9343.839361
EM: Round [362] log likelihood: -9343.838395
EM: Round [363] log likelihood: -9343.837438
EM: Round [364] log likelihood: -9343.836489
EM: Round [365] log likelihood: -9343.835549
EM: Round [366] log likelihood: -9343.834618
EM: Round [367] log likelihood: -9343.833695
EM: Round [368] log likelihood: -9343.832780
EM: Round [369] log likelihood: -9343.831874
EM: Round [370] log likelihood: -9343.830975
EM: Round [371] log likelihood: -9343.830085
EM: Round [372] log likelihood: -9343.829203
EM: Round [373] log likelihood: -9343.828329
EM: Round [374] log likelihood: -9343.827462
EM: Round [375] log likelihood: -9343.826603
EM: Round [376] log likelihood: -9343.825752
EM: Round [377] log likelihood: -9343.824909
EM: Round [378] log likelihood: -9343.824073
EM: Round [379] log likelihood: -9343.823245
EM: Round [380] log likelihood: -9343.822424
EM: Round [381] log likelihood: -9343.821610
EM: Round [382] log likelihood: -9343.820803
EM: Round [383] log likelihood: -9343.820004
EM: Round [384] log likelihood: -9343.819211
EM: Round [385] log likelihood: -9343.818426
EM: Round [386] log likelihood: -9343.817648
EM: Round [387] log likelihood: -9343.816876
EM: Round [388] log likelihood: -9343.816111
EM: Round [389] log likelihood: -9343.815353
EM: Round [390] log likelihood: -9343.814602
EM: Round [391] log likelihood: -9343.813857
EM: Round [392] log likelihood: -9343.813119
EM: Round [393] log likelihood: -9343.812387
EM: Round [394] log likelihood: -9343.811662
EM: Round [395] log likelihood: -9343.810942
EM: Round [396] log likelihood: -9343.810230
EM: Round [397] log likelihood: -9343.809523
EM: Round [398] log likelihood: -9343.808822
EM: Round [399] log likelihood: -9343.808128
EM: Round [400] log likelihood: -9343.807440
EM: Round [401] log likelihood: -9343.806757
EM: Round [402] log likelihood: -9343.806081
EM: Round [403] log likelihood: -9343.805410
EM: Round [404] log likelihood: -9343.804745
EM: Round [405] log likelihood: -9343.804086
EM: Round [406] log likelihood: -9343.803432
EM: Round [407] log likelihood: -9343.802785
EM: Round [408] log likelihood: -9343.802142
EM: Round [409] log likelihood: -9343.801505
EM: Round [410] log likelihood: -9343.800874
EM: Round [411] log likelihood: -9343.800248
EM: Round [412] log likelihood: -9343.799628
EM: Round [413] log likelihood: -9343.799012
EM: Round [414] log likelihood: -9343.798402
EM: Round [415] log likelihood: -9343.797797
EM: Round [416] log likelihood: -9343.797198
EM: Round [417] log likelihood: -9343.796603
EM: Round [418] log likelihood: -9343.796013
EM: Round [419] log likelihood: -9343.795429
EM: Round [420] log likelihood: -9343.794849
EM: Round [421] log likelihood: -9343.794274
EM: Round [422] log likelihood: -9343.793704
EM: Round [423] log likelihood: -9343.793139
EM: Round [424] log likelihood: -9343.792579
EM: Round [425] log likelihood: -9343.792023
EM: Round [426] log likelihood: -9343.791472
EM: Round [427] log likelihood: -9343.790926
EM: Round [428] log likelihood: -9343.790384
EM: Round [429] log likelihood: -9343.789847
EM: Round [430] log likelihood: -9343.789314
EM: Round [431] log likelihood: -9343.788786
EM: Round [432] log likelihood: -9343.788262
EM: Round [433] log likelihood: -9343.787743
EM: Round [434] log likelihood: -9343.787227
EM: Round [435] log likelihood: -9343.786716
EM: Round [436] log likelihood: -9343.786210
EM: Round [437] log likelihood: -9343.785707
EM: Round [438] log likelihood: -9343.785209
EM: Round [439] log likelihood: -9343.784715
EM: Round [440] log likelihood: -9343.784225
EM: Round [441] log likelihood: -9343.783739
EM: Round [442] log likelihood: -9343.783257
EM: Round [443] log likelihood: -9343.782779
EM: Round [444] log likelihood: -9343.782304
EM: Round [445] log likelihood: -9343.781834
EM: Round [446] log likelihood: -9343.781368
EM: Round [447] log likelihood: -9343.780905
EM: Round [448] log likelihood: -9343.780446
EM: Round [449] log likelihood: -9343.779991
EM: Round [450] log likelihood: -9343.779540
EM: Round [451] log likelihood: -9343.779092
EM: Round [452] log likelihood: -9343.778648
EM: Round [453] log likelihood: -9343.778208
EM: Round [454] log likelihood: -9343.777771
EM: Round [455] log likelihood: -9343.777338
EM: Round [456] log likelihood: -9343.776908
EM: Round [457] log likelihood: -9343.776482
EM: Round [458] log likelihood: -9343.776059
EM: Round [459] log likelihood: -9343.775640
EM: Round [460] log likelihood: -9343.775224
EM: Round [461] log likelihood: -9343.774812
EM: Round [462] log likelihood: -9343.774402
EM: Round [463] log likelihood: -9343.773996
EM: Round [464] log likelihood: -9343.773594
EM: Round [465] log likelihood: -9343.773194
EM: Round [466] log likelihood: -9343.772798
EM: Round [467] log likelihood: -9343.772405
EM: Round [468] log likelihood: -9343.772015
EM: Round [469] log likelihood: -9343.771628
EM: Round [470] log likelihood: -9343.771244
EM: Round [471] log likelihood: -9343.770864
EM: Round [472] log likelihood: -9343.770486
EM: Round [473] log likelihood: -9343.770111
EM: Round [474] log likelihood: -9343.769740
EM: Round [475] log likelihood: -9343.769371
EM: Round [476] log likelihood: -9343.769005
EM: Round [477] log likelihood: -9343.768643
EM: Round [478] log likelihood: -9343.768283
EM: Round [479] log likelihood: -9343.767925
EM: Round [480] log likelihood: -9343.767571
EM: Round [481] log likelihood: -9343.767220
EM: Round [482] log likelihood: -9343.766871
EM: Round [483] log likelihood: -9343.766525
EM: Round [484] log likelihood: -9343.766182
EM: Round [485] log likelihood: -9343.765841
EM: Round [486] log likelihood: -9343.765503
EM: Round [487] log likelihood: -9343.765168
EM: Round [488] log likelihood: -9343.764836
EM: Round [489] log likelihood: -9343.764506
EM: Round [490] log likelihood: -9343.764178
EM: Round [491] log likelihood: -9343.763854
EM: Round [492] log likelihood: -9343.763531
EM: Round [493] log likelihood: -9343.763211
EM: Round [494] log likelihood: -9343.762894
EM: Round [495] log likelihood: -9343.762579
EM: Round [496] log likelihood: -9343.762267
EM: Round [497] log likelihood: -9343.761957
EM: Round [498] log likelihood: -9343.761650
EM: Round [499] log likelihood: -9343.761345
EM: Round [500] log likelihood: -9343.761042
EM: Round [501] log likelihood: -9343.760741
EM: Round [502] log likelihood: -9343.760443
EM: Round [503] log likelihood: -9343.760148
EM: Round [504] log likelihood: -9343.759854
EM: Round [505] log likelihood: -9343.759563
EM: Round [506] log likelihood: -9343.759274
EM: Round [507] log likelihood: -9343.758987
EM: Round [508] log likelihood: -9343.758703
EM: Round [509] log likelihood: -9343.758420
EM: Round [510] log likelihood: -9343.758140
EM: Round [511] log likelihood: -9343.757862
EM: Round [512] log likelihood: -9343.757586
EM: Round [513] log likelihood: -9343.757312
EM: Round [514] log likelihood: -9343.757041
EM: Round [515] log likelihood: -9343.756771
EM: Round [516] log likelihood: -9343.756504
EM: Round [517] log likelihood: -9343.756238
EM: Round [518] log likelihood: -9343.755975
EM: Round [519] log likelihood: -9343.755713
EM: Round [520] log likelihood: -9343.755454
EM: Round [521] log likelihood: -9343.755196
EM: Round [522] log likelihood: -9343.754940
EM: Round [523] log likelihood: -9343.754687
EM: Round [524] log likelihood: -9343.754435
EM: Round [525] log likelihood: -9343.754185
EM: Round [526] log likelihood: -9343.753937
EM: Round [527] log likelihood: -9343.753691
EM: Round [528] log likelihood: -9343.753447
EM: Round [529] log likelihood: -9343.753205
EM: Round [530] log likelihood: -9343.752964
EM: Round [531] log likelihood: -9343.752726
EM: Round [532] log likelihood: -9343.752489
EM: Round [533] log likelihood: -9343.752254
EM: Round [534] log likelihood: -9343.752020
EM: Round [535] log likelihood: -9343.751789
EM: Round [536] log likelihood: -9343.751559
EM: Round [537] log likelihood: -9343.751331
EM: Round [538] log likelihood: -9343.751105
EM: Round [539] log likelihood: -9343.750880
EM: Round [540] log likelihood: -9343.750657
EM: Round [541] log likelihood: -9343.750435
EM: Round [542] log likelihood: -9343.750216
EM: Round [543] log likelihood: -9343.749998
EM: Round [544] log likelihood: -9343.749781
EM: Round [545] log likelihood: -9343.749566
EM: Round [546] log likelihood: -9343.749353
EM: Round [547] log likelihood: -9343.749141
EM: Round [548] log likelihood: -9343.748931
EM: Round [549] log likelihood: -9343.748723
EM: Round [550] log likelihood: -9343.748516
EM: Round [551] log likelihood: -9343.748310
EM: Round [552] log likelihood: -9343.748107
EM: Round [553] log likelihood: -9343.747904
EM: Round [554] log likelihood: -9343.747703
EM: Round [555] log likelihood: -9343.747504
EM: Round [556] log likelihood: -9343.747306
EM: Round [557] log likelihood: -9343.747109
EM: Round [558] log likelihood: -9343.746914
EM: Round [559] log likelihood: -9343.746721
EM: Round [560] log likelihood: -9343.746528
EM: Round [561] log likelihood: -9343.746338
EM: Round [562] log likelihood: -9343.746148
EM: Round [563] log likelihood: -9343.745960
EM: Round [564] log likelihood: -9343.745774
EM: Round [565] log likelihood: -9343.745588
EM: Round [566] log likelihood: -9343.745405
EM: Round [567] log likelihood: -9343.745222
EM: Round [568] log likelihood: -9343.745041
EM: Round [569] log likelihood: -9343.744861
EM: Round [570] log likelihood: -9343.744682
EM: Round [571] log likelihood: -9343.744505
EM: Round [572] log likelihood: -9343.744329
EM: Round [573] log likelihood: -9343.744154
EM: Round [574] log likelihood: -9343.743981
EM: Round [575] log likelihood: -9343.743809
EM: Round [576] log likelihood: -9343.743638
EM: Round [577] log likelihood: -9343.743468
EM: Round [578] log likelihood: -9343.743300
EM: Round [579] log likelihood: -9343.743133
EM: Round [580] log likelihood: -9343.742967
EM: Round [581] log likelihood: -9343.742802
EM: Round [582] log likelihood: -9343.742638
EM: Round [583] log likelihood: -9343.742476
EM: Round [584] log likelihood: -9343.742315
EM: Round [585] log likelihood: -9343.742155
EM: Round [586] log likelihood: -9343.741996
EM: Round [587] log likelihood: -9343.741838
EM: Round [588] log likelihood: -9343.741681
EM: Round [589] log likelihood: -9343.741526
EM: Round [590] log likelihood: -9343.741371
EM: Round [591] log likelihood: -9343.741218
EM: Round [592] log likelihood: -9343.741066
EM: Round [593] log likelihood: -9343.740915
EM: Round [594] log likelihood: -9343.740765
EM: Round [595] log likelihood: -9343.740616
EM: Round [596] log likelihood: -9343.740468
EM: Round [597] log likelihood: -9343.740321
EM: Round [598] log likelihood: -9343.740175
EM: Round [599] log likelihood: -9343.740031
EM: Round [600] log likelihood: -9343.739887
EM: Round [601] log likelihood: -9343.739744
EM: Round [602] log likelihood: -9343.739603
EM: Round [603] log likelihood: -9343.739462
EM: Round [604] log likelihood: -9343.739322
EM: Round [605] log likelihood: -9343.739184
EM: Round [606] log likelihood: -9343.739046
EM: Round [607] log likelihood: -9343.738909
EM: Round [608] log likelihood: -9343.738774
EM: Round [609] log likelihood: -9343.738639
EM: Round [610] log likelihood: -9343.738505
EM: Round [611] log likelihood: -9343.738372
EM: Round [612] log likelihood: -9343.738240
EM: Round [613] log likelihood: -9343.738110
EM: Round [614] log likelihood: -9343.737980
EM: Round [615] log likelihood: -9343.737850
EM: Round [616] log likelihood: -9343.737722
EM: Round [617] log likelihood: -9343.737595
EM: Round [618] log likelihood: -9343.737469
EM: Round [619] log likelihood: -9343.737343
EM: Round [620] log likelihood: -9343.737218
EM: Round [621] log likelihood: -9343.737095
EM: Round [622] log likelihood: -9343.736972
EM: Round [623] log likelihood: -9343.736850
EM: Round [624] log likelihood: -9343.736729
EM: Round [625] log likelihood: -9343.736608
EM: Round [626] log likelihood: -9343.736489
EM: Round [627] log likelihood: -9343.736370
EM: Round [628] log likelihood: -9343.736253
EM: Round [629] log likelihood: -9343.736136
EM: Round [630] log likelihood: -9343.736020
EM: Round [631] log likelihood: -9343.735904
EM: Round [632] log likelihood: -9343.735790
EM: Round [633] log likelihood: -9343.735676
EM: Round [634] log likelihood: -9343.735563
EM: Round [635] log likelihood: -9343.735451
EM: Round [636] log likelihood: -9343.735340
EM: Round [637] log likelihood: -9343.735229
EM: Round [638] log likelihood: -9343.735119
EM: Round [639] log likelihood: -9343.735010
EM: Round [640] log likelihood: -9343.734902
EM: Round [641] log likelihood: -9343.734795
EM: Round [642] log likelihood: -9343.734688
EM: Round [643] log likelihood: -9343.734582
EM: Round [644] log likelihood: -9343.734477
EM: Round [645] log likelihood: -9343.734372
EM: Round [646] log likelihood: -9343.734268
EM: Round [647] log likelihood: -9343.734165
EM: Round [648] log likelihood: -9343.734063
EM: Round [649] log likelihood: -9343.733961
EM: Round [650] log likelihood: -9343.733860
EM: Round [651] log likelihood: -9343.733760
EM: Round [652] log likelihood: -9343.733660
EM: Stopping iterations at round 652 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.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.qK299E5g7p/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.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_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.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_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.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.qK299E5g7p/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.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.qK299E5g7p/1173_NMN_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.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_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.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.qK299E5g7p/1173_NMN_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.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_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.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.qK299E5g7p/1173_NMN_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.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.qK299E5g7p/1173_NMN_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.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.qK299E5g7p/1173_NMN_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.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam into /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.qK299E5g7p/1173_NMN_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.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords > /tmp/nxf.qK299E5g7p/1173_NMN_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.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.64 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.qK299E5g7p/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.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.qK299E5g7p/1173_NMN_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.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.qK299E5g7p/1173_NMN_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.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.qK299E5g7p/1173_NMN_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.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.qK299E5g7p/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.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.qK299E5g7p/1173_NMN_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.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.qK299E5g7p/1173_NMN_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.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.qK299E5g7p/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.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_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.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.qK299E5g7p/1173_NMN_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.qK299E5g7p/fi_workdir/1173_NMN_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.qK299E5g7p/fi_workdir/1173_NMN_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.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.qK299E5g7p/1173_NMN_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.qK299E5g7p/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.qK299E5g7p/1173_NMN_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.qK299E5g7p/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.qK299E5g7p/ctat_genome_lib_build_dir
-done, see /tmp/nxf.qK299E5g7p/1173_NMN_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.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.qK299E5g7p/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -6830.284558
EM: Round [1] log likelihood: -6830.280231
EM: Round [2] log likelihood: -6830.280042
EM: Round [3] log likelihood: -6830.280034
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.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz: 267915314
Execution Time = 4.67 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.qK299E5g7p/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.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.qK299E5g7p/fi_workdir/microH.dat
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.qK299E5g7p/fi_workdir/microH.dat /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.qK299E5g7p/1173_NMN_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.qK299E5g7p/fi_workdir/microH.dat /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.qK299E5g7p/1173_NMN_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.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.qK299E5g7p --json_outfile /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_NMN_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.qK299E5g7p --json_outfile /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1
Running: touch /tmp/nxf.qK299E5g7p/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.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.qK299E5g7p/1173_NMN_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.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.qK299E5g7p/ctat_genome_lib_build_dir > /tmp/nxf.qK299E5g7p/1173_NMN_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.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.qK299E5g7p/ctat_genome_lib_build_dir > /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.qK299E5g7p/ctat_genome_lib_build_dir > /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000286472.1]
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 [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000241621.1]
WARNING, no entry stored in dbm for [ENSG00000241621.1]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000245248.8]
WARNING, no entry stored in dbm for [ENSG00000245248.8]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.qK299E5g7p/ctat_genome_lib_build_dir > /tmp/nxf.qK299E5g7p/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.qK299E5g7p/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory