File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/440597ba7fc184f18662e7e3070c19/.command.log
Size
75.9 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (tih_rna_sample_00096_B23WHTKLT4_2)
Attempt

Content

View in new tab 
  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/a5/f9b3fda60f2b37d73df8d3b3845c20/tih_rna_sample_00096_B23WHTKLT4_2_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/440597ba7fc184f18662e7e3070c19/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/88709937ecf837e8f31a83cfd71f7e/tih_rna_sample_00096_B23WHTKLT4_2.fusionreport.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/440597ba7fc184f18662e7e3070c19/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/f9b3fda60f2b37d73df8d3b3845c20/tih_rna_sample_00096_B23WHTKLT4_2_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_00096_B23WHTKLT4_2.fusionreport.tsv --gtf /tmp/nxf.lxEUMOIMc1/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.lxEUMOIMc1/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2 --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_00096_B23WHTKLT4_2.fusionreport.tsv --gtf /tmp/nxf.lxEUMOIMc1/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.lxEUMOIMc1/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.fa /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.fa /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fa
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.gtf /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.gtf /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.gtf
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.fa /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.gtf > /tmp/nxf.lxEUMOIMc1/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.fa /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.gtf > /tmp/nxf.lxEUMOIMc1/cytoBand.txt
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.gtf > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.bed
-parsing GTF file: /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.gtf > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.bed
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.bed > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.bed > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.bed.sorted.bed
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/tih_rna_sample_00096_B23WHTKLT4_2.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.bed.sorted.bed
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/tih_rna_sample_00096_B23WHTKLT4_2.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.bed.sorted.bed.gz
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/tih_rna_sample_00096_B23WHTKLT4_2.bed.tabix.ok
Running: samtools faidx /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.fa
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.lxEUMOIMc1/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.gtf --CPU 8 --out_prefix tih_rna_sample_00096_B23WHTKLT4_2.star --out_dir /tmp/nxf.lxEUMOIMc1/fi_workdir --reads "/tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.lxEUMOIMc1/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.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 10:05:32 ..... started STAR run
Jun 08 10:05:32 ..... loading genome
Jun 08 10:07:11 ... generating Suffix Array index
Jun 08 10:10:59 ... completed Suffix Array index
Jun 08 10:10:59 ..... processing annotations GTF
Jun 08 10:10:59 ..... inserting junctions into the genome indices
Jun 08 10:12:00 ..... started mapping
Jun 08 11:07:18 ..... finished mapping
Jun 08 11:07:19 ..... started sorting BAM
Jun 08 11:07:20 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00096_B23WHTKLT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00096_B23WHTKLT4_2.star.sortedByCoord.out.bam
Execution Time = 61.86 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.lxEUMOIMc1/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.gtf --CPU 8 --out_prefix tih_rna_sample_00096_B23WHTKLT4_2.star --out_dir /tmp/nxf.lxEUMOIMc1/fi_workdir --reads "/tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2_2.fastp.fastq.gz"
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.sortedByCoord.out.bam   -o /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam   --remove_dups 
11:07:37 : INFO : Done.
Execution Time = 0.23 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.sortedByCoord.out.bam   -o /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.lxEUMOIMc1/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.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.gtf
-parsing /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam

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[2510000]   -done parsing /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2,
          'num genes matched < 2' => 83,
          'excessive soft clipping' => 14433,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 68,
          'seq-similar region overlap' => 156,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 349,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 6,
          ' ** passed ** ' => 6568,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 17,
          'small anchor length' => 27,
          'exons hit < 2' => 1,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 3,
          'low complexity anchor region' => 35,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 8,
          'per_id < 96' => 9328,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3
        };
-writing fusion junction support info.
Execution Time = 1.39 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.lxEUMOIMc1/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.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.
-fusion SPANNING read extraction for scaff: AC016629.1--RPL23AP53

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[8000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

[1000]   -fusion SPANNING read extraction for scaff: AC239859.5--AC013734.1

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[241000]   -fusion SPANNING read extraction for scaff: ARHGEF17--CCS

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[53000]   
[54000]   -fusion SPANNING read extraction for scaff: CCS--ACTN3

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[54000]   
[55000]   -fusion SPANNING read extraction for scaff: CHERP--OR2Z1

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[114000]   
[115000]   -fusion SPANNING read extraction for scaff: CTTN--SPCS2

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[77000]   -fusion SPANNING read extraction for scaff: FSIP1--AC013652.1

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[97000]   
[98000]   -fusion SPANNING read extraction for scaff: GRPEL2--HSPA9

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[254000]   -fusion SPANNING read extraction for scaff: KDM2A--AP000446.1

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[250000]   -fusion SPANNING read extraction for scaff: KDM4B--NFIC

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[167000]   
[168000]   -fusion SPANNING read extraction for scaff: NCOA6--AHCY

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[12000]   
[13000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1

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[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13

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[6000]   
[7000]   
[8000]   
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[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2

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[294000]   
[295000]   -fusion SPANNING read extraction for scaff: SEMA4B--EVL

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[79000]   
[80000]   
[81000]   -fusion SPANNING read extraction for scaff: SHANK2--DLG2

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[51000]   
[52000]   
[53000]   -fusion SPANNING read extraction for scaff: SSRP1--BDNF

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[84000]   
[85000]   -fusion SPANNING read extraction for scaff: ST3GAL1--NDRG1

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[127000]   
[128000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[46000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[7000]   
[8000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[32000]   
[33000]   -fusion SPANNING read extraction for scaff: TMEM138--AP001107.6

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[53000]   
[54000]   -fusion SPANNING read extraction for scaff: TSG101--CLPB

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[16000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[344000]   -fusion SPANNING read extraction for scaff: UVRAG--KDM2A
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 10668,
          'lacks exon overlap' => 55735
        };
Execution Time = 3.86 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.lxEUMOIMc1/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.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_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.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -9115.685203
EM: Round [1] log likelihood: -9106.411869
EM: Round [2] log likelihood: -9106.052890
EM: Round [3] log likelihood: -9105.762603
EM: Round [4] log likelihood: -9105.519288
EM: Round [5] log likelihood: -9105.314240
EM: Round [6] log likelihood: -9105.140687
EM: Round [7] log likelihood: -9104.993260
EM: Round [8] log likelihood: -9104.867651
EM: Round [9] log likelihood: -9104.760363
EM: Round [10] log likelihood: -9104.668530
EM: Round [11] log likelihood: -9104.589786
EM: Round [12] log likelihood: -9104.522162
EM: Round [13] log likelihood: -9104.464013
EM: Round [14] log likelihood: -9104.413957
EM: Round [15] log likelihood: -9104.370827
EM: Round [16] log likelihood: -9104.333635
EM: Round [17] log likelihood: -9104.301541
EM: Round [18] log likelihood: -9104.273831
EM: Round [19] log likelihood: -9104.249892
EM: Round [20] log likelihood: -9104.229203
EM: Round [21] log likelihood: -9104.211315
EM: Round [22] log likelihood: -9104.195845
EM: Round [23] log likelihood: -9104.182462
EM: Round [24] log likelihood: -9104.170881
EM: Round [25] log likelihood: -9104.160858
EM: Round [26] log likelihood: -9104.152182
EM: Round [27] log likelihood: -9104.144670
EM: Round [28] log likelihood: -9104.138165
EM: Round [29] log likelihood: -9104.132532
EM: Round [30] log likelihood: -9104.127653
EM: Round [31] log likelihood: -9104.123427
EM: Round [32] log likelihood: -9104.119766
EM: Round [33] log likelihood: -9104.116595
EM: Round [34] log likelihood: -9104.113847
EM: Round [35] log likelihood: -9104.111467
EM: Round [36] log likelihood: -9104.109405
EM: Round [37] log likelihood: -9104.107618
EM: Round [38] log likelihood: -9104.106069
EM: Round [39] log likelihood: -9104.104728
EM: Round [40] log likelihood: -9104.103565
EM: Round [41] log likelihood: -9104.102558
EM: Round [42] log likelihood: -9104.101685
EM: Round [43] log likelihood: -9104.100928
EM: Round [44] log likelihood: -9104.100273
EM: Round [45] log likelihood: -9104.099704
EM: Round [46] log likelihood: -9104.099212
EM: Round [47] log likelihood: -9104.098785
EM: Round [48] log likelihood: -9104.098416
EM: Round [49] log likelihood: -9104.098095
EM: Round [50] log likelihood: -9104.097817
EM: Round [51] log likelihood: -9104.097577
EM: Round [52] log likelihood: -9104.097368
EM: Round [53] log likelihood: -9104.097187
EM: Round [54] log likelihood: -9104.097031
EM: Round [55] log likelihood: -9104.096895
EM: Round [56] log likelihood: -9104.096777
EM: Round [57] log likelihood: -9104.096675
EM: Round [58] log likelihood: -9104.096587
EM: Stopping iterations at round 58 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.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.lxEUMOIMc1/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.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_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.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_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.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.lxEUMOIMc1/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.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_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.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.junction_reads.bam"
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.junction_reads.bam
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.junction_reads.bam > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_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.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.junction_reads.bam > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.junction_reads.bam.bed
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/tih_rna_sample_00096_B23WHTKLT4_2.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.junction_reads.bam.bed > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.junction_reads.bam.bed > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/tih_rna_sample_00096_B23WHTKLT4_2.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/tih_rna_sample_00096_B23WHTKLT4_2.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/tih_rna_sample_00096_B23WHTKLT4_2.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_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.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.spanning_reads.bam
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_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.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.spanning_reads.bam || : 
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.spanning_reads.bam
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.spanning_reads.bam > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_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.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.spanning_reads.bam > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.spanning_reads.bam.bed
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/tih_rna_sample_00096_B23WHTKLT4_2.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.spanning_reads.bam.bed > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.spanning_reads.bam.bed > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/tih_rna_sample_00096_B23WHTKLT4_2.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/tih_rna_sample_00096_B23WHTKLT4_2.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/tih_rna_sample_00096_B23WHTKLT4_2.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.consolidated.bam
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.consolidated.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.consolidated.bam
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.consolidated.bam into /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.consolidated.bam.read_coords

CMD: touch /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.consolidated.bam.read_coords > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.64 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.lxEUMOIMc1/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.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fusion_preds.coalesced.summary /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_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.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fusion_preds.coalesced.summary /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.igv.FusionJuncSpan
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_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.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.igv.Pfam.gff3 
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.igv.Pfam.gff3 > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.igv.Pfam.gff3 > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.igv.Pfam.bed
Running: touch /tmp/nxf.lxEUMOIMc1/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.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_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.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.igv.seqsimilar.bed
Running: touch /tmp/nxf.lxEUMOIMc1/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.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.fa > /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_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.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.fa > /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_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.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_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.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_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.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_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.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.lxEUMOIMc1/ctat_genome_lib_build_dir
-done, see /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_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.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.lxEUMOIMc1/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -8940.540134
EM: Round [1] log likelihood: -8934.700336
EM: Round [2] log likelihood: -8934.692570
EM: Round [3] log likelihood: -8934.692547
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2_1.fastp.fastq.gz: 295827505
Execution Time = 5.94 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.fa --gtf /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.gtf  > /tmp/nxf.lxEUMOIMc1/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.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.fa --gtf /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.gtf  > /tmp/nxf.lxEUMOIMc1/fi_workdir/microH.dat
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.lxEUMOIMc1/fi_workdir/microH.dat /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_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.lxEUMOIMc1/fi_workdir/microH.dat /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.lxEUMOIMc1 --json_outfile /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.fusion_inspector_web.json --file_prefix tih_rna_sample_00096_B23WHTKLT4_2
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.lxEUMOIMc1 --json_outfile /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.fusion_inspector_web.json --file_prefix tih_rna_sample_00096_B23WHTKLT4_2
Running: touch /tmp/nxf.lxEUMOIMc1/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.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00096_B23WHTKLT4_2 --html_output /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00096_B23WHTKLT4_2 --html_output /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.fusion_inspector_web.html
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.lxEUMOIMc1/ctat_genome_lib_build_dir > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.lxEUMOIMc1/ctat_genome_lib_build_dir > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.lxEUMOIMc1/ctat_genome_lib_build_dir > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000277702.1]
WARNING, no entry stored in dbm for [ENSG00000277146.1]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000255234.6]
WARNING, no entry stored in dbm for [ENSG00000255234.6]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000254756.1]
WARNING, no entry stored in dbm for [ENSG00000254756.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000269032.1]
WARNING, no entry stored in dbm for [ENSG00000223508.5]
WARNING, no entry stored in dbm for [ENSG00000269032.1]
WARNING, no entry stored in dbm for [ENSG00000223508.5]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.lxEUMOIMc1/ctat_genome_lib_build_dir > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.lxEUMOIMc1/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory