Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/da3803aafa772993448b27fe5e3e08/.command.sh
  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/c3/f256390537d79a60618c58b7233b7d/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/f256390537d79a60618c58b7233b7d/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/da3803aafa772993448b27fe5e3e08/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/0b0ed93894ad7f613e4816cbd7faf8/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)

Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv --gtf /tmp/nxf.hiYgVpGOtI/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.hiYgVpGOtI/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2 --shrink_introns --max_intron_length 1000 
Done.
Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv --gtf /tmp/nxf.hiYgVpGOtI/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.hiYgVpGOtI/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fa
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.gtf /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.gtf /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.gtf
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.hiYgVpGOtI/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.hiYgVpGOtI/cytoBand.txt
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.bed
-parsing GTF file: /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.bed
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.bed > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.bed > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed.gz
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.bed.tabix.ok
Running: samtools faidx /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fa
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.hiYgVpGOtI/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.gtf --CPU 8 --out_prefix 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star --out_dir /tmp/nxf.hiYgVpGOtI/fi_workdir --reads "/tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.hiYgVpGOtI/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.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 09:01:43 ..... started STAR run
Jun 08 09:01:43 ..... loading genome
Jun 08 09:03:32 ... generating Suffix Array index
Jun 08 09:08:07 ... completed Suffix Array index
Jun 08 09:08:08 ..... processing annotations GTF
Jun 08 09:08:08 ..... inserting junctions into the genome indices
Jun 08 09:09:09 ..... started mapping
Jun 08 09:41:36 ..... finished mapping
Jun 08 09:41:38 ..... started sorting BAM
Jun 08 09:41:38 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam
Execution Time = 39.93 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.hiYgVpGOtI/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.gtf --CPU 8 --out_prefix 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star --out_dir /tmp/nxf.hiYgVpGOtI/fi_workdir --reads "/tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz"
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam   -o /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam   --remove_dups 
09:41:44 : INFO : Done.
Execution Time = 0.08 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam   -o /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.hiYgVpGOtI/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.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.gtf
-parsing /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam

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[1070000]   -done parsing /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 10,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 4,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 96,
          'low complexity anchor region' => 9,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 8,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6,
          'excessive soft clipping' => 7052,
          'num genes matched < 2' => 10,
          'per_id < 96' => 3824,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 37,
          'small anchor length' => 11,
          ' ** passed ** ' => 5202
        };
-writing fusion junction support info.
Execution Time = 0.60 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.hiYgVpGOtI/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.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[15000]   -fusion SPANNING read extraction for scaff: AP1M2--ZFR2

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[46000]   -fusion SPANNING read extraction for scaff: MAN2B1--CACNA1A

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[81000]   -fusion SPANNING read extraction for scaff: MAN2B1--CCDC130

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[18000]   -fusion SPANNING read extraction for scaff: MON1B--AC106733.1

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[441000]   
[442000]   -fusion SPANNING read extraction for scaff: MYB--ADGRB3

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[8000]   
[9000]   
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[14000]   
[15000]   -fusion SPANNING read extraction for scaff: MYO18B--IGL-@-ext

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[41000]   -fusion SPANNING read extraction for scaff: NPHP3--ACAD11

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[21000]   
[22000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13

[1000]   
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[21000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1

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[19000]   
[20000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2

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[218000]   -fusion SPANNING read extraction for scaff: SREBF2--NCLN

[1000]   
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[8000]   
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[26000]   -fusion SPANNING read extraction for scaff: TLK2--AL669831.1

[1000]   
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[11000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 3605,
          'lacks exon overlap' => 2047
        };
Execution Time = 1.54 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.hiYgVpGOtI/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.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.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.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -3959.824592
EM: Round [1] log likelihood: -3959.810359
EM: Round [2] log likelihood: -3959.808341
EM: Round [3] log likelihood: -3959.808055
EM: Round [4] log likelihood: -3959.808014
EM: Stopping iterations at round 4 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.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.hiYgVpGOtI/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.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.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.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.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.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.hiYgVpGOtI/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.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.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.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam"
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.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.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.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.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam || : 
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam into /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords

CMD: touch /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.28 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.hiYgVpGOtI/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.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.igv.FusionJuncSpan
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.igv.FusionJuncSpan
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.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.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.bed
Running: touch /tmp/nxf.hiYgVpGOtI/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.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.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.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.bed
Running: touch /tmp/nxf.hiYgVpGOtI/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.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fa > /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.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.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fa > /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2 --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.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter  --genome_lib_dir ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 50 
CMD: cp /tmp/nxf.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.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.hiYgVpGOtI/fi_workdir/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.hiYgVpGOtI/ctat_genome_lib_build_dir
-done, see /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.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.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.hiYgVpGOtI/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -3784.659825
EM: Round [1] log likelihood: -3784.645592
EM: Round [2] log likelihood: -3784.643574
EM: Round [3] log likelihood: -3784.643288
EM: Round [4] log likelihood: -3784.643247
EM: Stopping iterations at round 4 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.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz: 172844936
Execution Time = 3.06 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fa --gtf /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.gtf  > /tmp/nxf.hiYgVpGOtI/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.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fa --gtf /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.gtf  > /tmp/nxf.hiYgVpGOtI/fi_workdir/microH.dat
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.hiYgVpGOtI/fi_workdir/microH.dat /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.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.hiYgVpGOtI/fi_workdir/microH.dat /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.hiYgVpGOtI --json_outfile /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --file_prefix 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.hiYgVpGOtI --json_outfile /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --file_prefix 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2
Running: touch /tmp/nxf.hiYgVpGOtI/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.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --input_file_prefix 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2 --html_output /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.02 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.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --input_file_prefix 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2 --html_output /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.html
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.hiYgVpGOtI/ctat_genome_lib_build_dir > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.hiYgVpGOtI/ctat_genome_lib_build_dir > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.hiYgVpGOtI/ctat_genome_lib_build_dir > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000228327.3]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [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.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.hiYgVpGOtI/ctat_genome_lib_build_dir > /tmp/nxf.hiYgVpGOtI/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.hiYgVpGOtI/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory