.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (tih_rna_sample_00089_23H5VFLT4_s39)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/769f8aa83b47436208d94ea1f27306/.command.log
Size: 65.6 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (tih_rna_sample_00089_23H5VFLT4_s39)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/f3460ee2d245566975a8168415d31f/tih_rna_sample_00089_23H5VFLT4_s39_1.fastp.fastq.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/769f8aa83b47436208d94ea1f27306/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/769f8aa83b47436208d94ea1f27306/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/3743446bc20d01913bfdbb1758098e/tih_rna_sample_00089_23H5VFLT4_s39.fusionreport.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/f3460ee2d245566975a8168415d31f/tih_rna_sample_00089_23H5VFLT4_s39_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00089_23H5VFLT4_s39.fusionreport.tsv --gtf /tmp/nxf.0HSd2SUmKP/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.0HSd2SUmKP/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39 --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 tih_rna_sample_00089_23H5VFLT4_s39.fusionreport.tsv --gtf /tmp/nxf.0HSd2SUmKP/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.0HSd2SUmKP/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.fa /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.fa /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fa
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.gtf /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.gtf /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.gtf
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.fa /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.gtf > /tmp/nxf.0HSd2SUmKP/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.fa /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.gtf > /tmp/nxf.0HSd2SUmKP/cytoBand.txt
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.gtf > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.bed
-parsing GTF file: /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.gtf > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.bed
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.bed > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.bed > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.bed.sorted.bed
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/tih_rna_sample_00089_23H5VFLT4_s39.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.bed.sorted.bed
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/tih_rna_sample_00089_23H5VFLT4_s39.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.bed.sorted.bed.gz
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/tih_rna_sample_00089_23H5VFLT4_s39.bed.tabix.ok
Running: samtools faidx /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.fa
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.0HSd2SUmKP/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fa --max_mate_dist 100000 -G /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.gtf --CPU 8 --out_prefix tih_rna_sample_00089_23H5VFLT4_s39.star --out_dir /tmp/nxf.0HSd2SUmKP/fi_workdir --reads "/tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39_1.fastp.fastq.gz /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.0HSd2SUmKP/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.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39_1.fastp.fastq.gz /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 09:59:27 ..... started STAR run
Jun 08 09:59:27 ..... loading genome
Jun 08 10:01:09 ... generating Suffix Array index
Jun 08 10:04:56 ... completed Suffix Array index
Jun 08 10:04:56 ..... processing annotations GTF
Jun 08 10:04:57 ..... inserting junctions into the genome indices
Jun 08 10:05:58 ..... started mapping
Jun 08 11:05:11 ..... finished mapping
Jun 08 11:05:12 ..... started sorting BAM
Jun 08 11:05:13 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00089_23H5VFLT4_s39.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00089_23H5VFLT4_s39.star.sortedByCoord.out.bam
Execution Time = 65.80 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.0HSd2SUmKP/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fa --max_mate_dist 100000 -G /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.gtf --CPU 8 --out_prefix tih_rna_sample_00089_23H5VFLT4_s39.star --out_dir /tmp/nxf.0HSd2SUmKP/fi_workdir --reads "/tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39_1.fastp.fastq.gz /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39_2.fastp.fastq.gz"
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.sortedByCoord.out.bam   -o /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam   --remove_dups 
11:05:26 : INFO : Done.
Execution Time = 0.18 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.sortedByCoord.out.bam   -o /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.0HSd2SUmKP/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.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.gtf
-parsing /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam

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[1930000]   -done parsing /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'excessive soft clipping' => 13184,
          'small anchor length' => 49,
          'low complexity anchor region' => 16,
          'num genes matched < 2' => 11,
          'exons hit < 2' => 5,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 1030,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 12,
          'per_id < 96' => 7457,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 11,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 33,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 18,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 36,
          ' ** passed ** ' => 5730,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 16
        };
-writing fusion junction support info.
Execution Time = 1.07 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.0HSd2SUmKP/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.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

[1000]   -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L

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[89000]   -fusion SPANNING read extraction for scaff: ADNP--KATNBL1

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[159000]   -fusion SPANNING read extraction for scaff: ARAP1--FCHSD2

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[48000]   -fusion SPANNING read extraction for scaff: AVEN--NFATC2

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[91000]   
[92000]   -fusion SPANNING read extraction for scaff: CASZ1--UBE4B

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[83000]   
[84000]   -fusion SPANNING read extraction for scaff: CRYZL2P--SEC16B

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[41000]   
[42000]   -fusion SPANNING read extraction for scaff: FAM135A--AL080275.1

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[43000]   -fusion SPANNING read extraction for scaff: FAM135A--AL365226.1

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[7000]   -fusion SPANNING read extraction for scaff: FBXO25--AC240565.1

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[82000]   
[83000]   -fusion SPANNING read extraction for scaff: MAPK6--TRPM7

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[143000]   -fusion SPANNING read extraction for scaff: PIP5K1B--TJP2

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[52000]   -fusion SPANNING read extraction for scaff: PRELID3A--AFG3L2

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[26000]   -fusion SPANNING read extraction for scaff: PRSS27--TPSB2

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[70000]   -fusion SPANNING read extraction for scaff: PTPRK--RSPO3

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[57000]   -fusion SPANNING read extraction for scaff: RAI1--DRC3

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[86000]   
[87000]   -fusion SPANNING read extraction for scaff: ROCK1--AFG3L2

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[23000]   -fusion SPANNING read extraction for scaff: SAE1--AC011495.1

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[116000]   -fusion SPANNING read extraction for scaff: SF3B3--COG4

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[59000]   -fusion SPANNING read extraction for scaff: SIN3A--CORO2B

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[18000]   -fusion SPANNING read extraction for scaff: SPIRE1--GREB1L

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[72000]   
[73000]   -fusion SPANNING read extraction for scaff: SPRED1--ATP10A

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[65000]   
[66000]   
[67000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[40000]   
[41000]   
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[44000]   
[45000]   -fusion SPANNING read extraction for scaff: TAF4--UBE2Q2

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[17000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

[1000]   
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[4000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[30000]   
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[52000]   
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[55000]   
[56000]   -fusion SPANNING read extraction for scaff: TMEM87B--MERTK

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[53000]   
[54000]   
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[60000]   
[61000]   
[62000]   
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[64000]   
[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   
[75000]   -fusion SPANNING read extraction for scaff: TRPM7--TMOD3

[1000]   
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[20000]   
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[52000]   
[53000]   
[54000]   
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[60000]   
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[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   
[75000]   
[76000]   
[77000]   
[78000]   
[79000]   
[80000]   
[81000]   
[82000]   
[83000]   -fusion SPANNING read extraction for scaff: TRPM7--MAPK6

[1000]   
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[6000]   
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[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

[1000]   
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[6000]   
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[8000]   
[9000]   
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[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   -fusion SPANNING read extraction for scaff: VAPB--AURKA

[1000]   
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[6000]   
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[8000]   
[9000]   
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[30000]   
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[40000]   
[41000]   
[42000]   
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[44000]   
[45000]   
[46000]   
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[48000]   
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[50000]   
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[52000]   
[53000]   
[54000]   
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[56000]   
[57000]   
[58000]   
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[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   
[75000]   
[76000]   
[77000]   
[78000]   
[79000]   
[80000]   
[81000]   
[82000]   
[83000]   
[84000]   
[85000]   
[86000]   
[87000]   
[88000]   
[89000]   
[90000]   -fusion SPANNING read extraction for scaff: VWA8--ZNF346

[1000]   
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[9000]   
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[20000]   
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[25000]   
[26000]   
[27000]   
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[30000]   
[31000]   
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[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   
[57000]   
[58000]   
[59000]   
[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   
[75000]   
[76000]   
[77000]   
[78000]   
[79000]   
[80000]   
[81000]   
[82000]   -fusion SPANNING read extraction for scaff: WSB2--NOS1
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 36444
        };
Execution Time = 2.98 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.0HSd2SUmKP/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.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.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.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fusion_preds.coalesced.summary > /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -9227.192266
EM: Round [1] log likelihood: -9220.058251
EM: Round [2] log likelihood: -9220.032871
EM: Round [3] log likelihood: -9220.032021
EM: Round [4] log likelihood: -9220.031988
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.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fusion_preds.coalesced.summary > /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.0HSd2SUmKP/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.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.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.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.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.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.0HSd2SUmKP/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.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.fa -  | samtools sort -@ 8 - -o /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.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.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.fa -  | samtools sort -@ 8 - -o /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.junction_reads.bam"
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.junction_reads.bam
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.junction_reads.bam > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.junction_reads.bam > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.junction_reads.bam.bed
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/tih_rna_sample_00089_23H5VFLT4_s39.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.junction_reads.bam.bed > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.junction_reads.bam.bed > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/tih_rna_sample_00089_23H5VFLT4_s39.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/tih_rna_sample_00089_23H5VFLT4_s39.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/tih_rna_sample_00089_23H5VFLT4_s39.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.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.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.spanning_reads.bam
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.fa -  | samtools sort -@ 8 - -o /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.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.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.fa -  | samtools sort -@ 8 - -o /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.spanning_reads.bam || : 
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.spanning_reads.bam
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.spanning_reads.bam > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.spanning_reads.bam > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.spanning_reads.bam.bed
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/tih_rna_sample_00089_23H5VFLT4_s39.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.spanning_reads.bam.bed > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.spanning_reads.bam.bed > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/tih_rna_sample_00089_23H5VFLT4_s39.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/tih_rna_sample_00089_23H5VFLT4_s39.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/tih_rna_sample_00089_23H5VFLT4_s39.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.star.cSorted.dupsMarked.bam /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.consolidated.bam
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.consolidated.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.consolidated.bam
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.consolidated.bam into /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.consolidated.bam.read_coords

CMD: touch /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.consolidated.bam.read_coords > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.consolidated.bam.frag_coords > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.49 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.0HSd2SUmKP/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.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fusion_preds.coalesced.summary /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.consolidated.bam.frag_coords > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.igv.FusionJuncSpan
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fusion_preds.coalesced.summary /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.consolidated.bam.frag_coords > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.igv.FusionJuncSpan
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.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.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.igv.Pfam.gff3 
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.igv.Pfam.gff3 > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.igv.Pfam.gff3 > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.igv.Pfam.bed
Running: touch /tmp/nxf.0HSd2SUmKP/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.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.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.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.igv.seqsimilar.gff3 > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.igv.seqsimilar.gff3 > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.igv.seqsimilar.bed
Running: touch /tmp/nxf.0HSd2SUmKP/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.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.fa > /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.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.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.fa > /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39 --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.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.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.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.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.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.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.0HSd2SUmKP/fi_workdir/tih_rna_sample_00089_23H5VFLT4_s39.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.0HSd2SUmKP/ctat_genome_lib_build_dir
-done, see /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.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.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.0HSd2SUmKP/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -8960.516585
EM: Round [1] log likelihood: -8956.183808
EM: Round [2] log likelihood: -8956.159390
EM: Round [3] log likelihood: -8956.158540
EM: Round [4] log likelihood: -8956.158507
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.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39_1.fastp.fastq.gz /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39_1.fastp.fastq.gz: 296909533
Execution Time = 5.91 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39_1.fastp.fastq.gz /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.fa --gtf /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.gtf  > /tmp/nxf.0HSd2SUmKP/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.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.fa --gtf /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.gtf  > /tmp/nxf.0HSd2SUmKP/fi_workdir/microH.dat
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.0HSd2SUmKP/fi_workdir/microH.dat /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.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.0HSd2SUmKP/fi_workdir/microH.dat /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.0HSd2SUmKP --json_outfile /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.fusion_inspector_web.json --file_prefix tih_rna_sample_00089_23H5VFLT4_s39
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.0HSd2SUmKP --json_outfile /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.fusion_inspector_web.json --file_prefix tih_rna_sample_00089_23H5VFLT4_s39
Running: touch /tmp/nxf.0HSd2SUmKP/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.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00089_23H5VFLT4_s39 --html_output /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.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.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00089_23H5VFLT4_s39 --html_output /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.fusion_inspector_web.html
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.0HSd2SUmKP/ctat_genome_lib_build_dir > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.0HSd2SUmKP/ctat_genome_lib_build_dir > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.0HSd2SUmKP/ctat_genome_lib_build_dir > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
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 [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286065.2]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.0HSd2SUmKP/ctat_genome_lib_build_dir > /tmp/nxf.0HSd2SUmKP/tih_rna_sample_00089_23H5VFLT4_s39.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.0HSd2SUmKP/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory