File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/18ead07e6f265b2eaacbe3113a3fcd/.command.log
Size
65.8 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (tih_rna_sample_00711_B23MVV7LT4_1)
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/ae/326776efdb8d5bc33459641bfca857/tih_rna_sample_00711_B23MVV7LT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/18ead07e6f265b2eaacbe3113a3fcd/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/326776efdb8d5bc33459641bfca857/tih_rna_sample_00711_B23MVV7LT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/18ead07e6f265b2eaacbe3113a3fcd/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/df25eb442e30ebd3ef431ef9d81f64/tih_rna_sample_00711_B23MVV7LT4_1.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)

Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00711_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.p4ZFwUXnBn/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.p4ZFwUXnBn/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000 
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00711_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.p4ZFwUXnBn/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.p4ZFwUXnBn/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.fa /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.fa /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.gtf /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.gtf /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.gtf
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.fa /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.gtf > /tmp/nxf.p4ZFwUXnBn/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.fa /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.gtf > /tmp/nxf.p4ZFwUXnBn/cytoBand.txt
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.gtf > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.bed
-parsing GTF file: /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.gtf > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.bed
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.bed > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.bed > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/tih_rna_sample_00711_B23MVV7LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/tih_rna_sample_00711_B23MVV7LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/tih_rna_sample_00711_B23MVV7LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.p4ZFwUXnBn/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00711_B23MVV7LT4_1.star --out_dir /tmp/nxf.p4ZFwUXnBn/fi_workdir --reads "/tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.p4ZFwUXnBn/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.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 10:18:31 ..... started STAR run
Jun 08 10:18:31 ..... loading genome
Jun 08 10:20:12 ... generating Suffix Array index
Jun 08 10:23:53 ... completed Suffix Array index
Jun 08 10:23:53 ..... processing annotations GTF
Jun 08 10:23:54 ..... inserting junctions into the genome indices
Jun 08 10:24:54 ..... started mapping
Jun 08 11:21:41 ..... finished mapping
Jun 08 11:21:42 ..... started sorting BAM
Jun 08 11:21:43 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00711_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00711_B23MVV7LT4_1.star.sortedByCoord.out.bam
Execution Time = 63.21 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.p4ZFwUXnBn/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00711_B23MVV7LT4_1.star --out_dir /tmp/nxf.p4ZFwUXnBn/fi_workdir --reads "/tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
11:21:49 : INFO : Done.
Execution Time = 0.09 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.p4ZFwUXnBn/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.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam

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[1010000]   -done parsing /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 395,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 57,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 6,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 176,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 88,
          'exons hit < 2' => 7,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 28,
          'num genes matched < 2' => 636,
          'excessive soft clipping' => 4800,
          'per_id < 96' => 2549,
          ' ** passed ** ' => 4040,
          'small anchor length' => 24,
          'low complexity anchor region' => 1,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 8
        };
-writing fusion junction support info.
Execution Time = 0.55 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.p4ZFwUXnBn/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.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.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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[163000]   -fusion SPANNING read extraction for scaff: ARHGAP12--SVIL

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[38000]   -fusion SPANNING read extraction for scaff: ARHGAP12--AL353093.1

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[130000]   
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[133000]   
[134000]   
[135000]   
[136000]   
[137000]   
[138000]   -fusion SPANNING read extraction for scaff: ARHGEF35--GFM1

[1000]   
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[9000]   
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[14000]   
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[18000]   
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[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   -fusion SPANNING read extraction for scaff: ATG12--PGGT1B

[1000]   
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[4000]   
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[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   -fusion SPANNING read extraction for scaff: BMS1P7--AGAP14P

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   -fusion SPANNING read extraction for scaff: COX6CP1--COX6C

[1000]   
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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
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[11000]   
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[30000]   
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[66000]   
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[75000]   
[76000]   
[77000]   
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[79000]   
[80000]   
[81000]   
[82000]   
[83000]   
[84000]   
[85000]   
[86000]   
[87000]   
[88000]   
[89000]   
[90000]   
[91000]   
[92000]   
[93000]   
[94000]   
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[96000]   
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[99000]   
[100000]   
[101000]   
[102000]   
[103000]   
[104000]   
[105000]   
[106000]   
[107000]   
[108000]   
[109000]   -fusion SPANNING read extraction for scaff: CRYZL2P--SEC16B

[1000]   
[2000]   
[3000]   -fusion SPANNING read extraction for scaff: LRRC25--AP002414.4

[1000]   
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[6000]   
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[8000]   
[9000]   
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[14000]   
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[16000]   
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[20000]   
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[30000]   
[31000]   
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[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
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[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
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[50000]   
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[65000]   
[66000]   
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[75000]   
[76000]   
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[81000]   
[82000]   
[83000]   
[84000]   
[85000]   
[86000]   
[87000]   
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[91000]   
[92000]   
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[100000]   
[101000]   
[102000]   
[103000]   
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[110000]   
[111000]   
[112000]   
[113000]   
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[116000]   
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[118000]   
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[120000]   
[121000]   
[122000]   
[123000]   
[124000]   
[125000]   
[126000]   
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[128000]   
[129000]   
[130000]   
[131000]   
[132000]   
[133000]   
[134000]   
[135000]   
[136000]   
[137000]   -fusion SPANNING read extraction for scaff: NF1--GABBR2

[1000]   
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[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   -fusion SPANNING read extraction for scaff: PMS2P6--CCDC146

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[8000]   
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[20000]   
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[30000]   
[31000]   
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[33000]   
[34000]   
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[36000]   
[37000]   
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[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
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[50000]   
[51000]   
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[53000]   
[54000]   
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[57000]   
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[59000]   
[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   
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[79000]   
[80000]   
[81000]   
[82000]   
[83000]   
[84000]   
[85000]   
[86000]   
[87000]   
[88000]   
[89000]   
[90000]   
[91000]   -fusion SPANNING read extraction for scaff: SIRT2--NFKBIB

[1000]   
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[6000]   
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[8000]   
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[10000]   
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[13000]   
[14000]   
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[30000]   
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[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   -fusion SPANNING read extraction for scaff: SSBP4--AP002414.4

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[8000]   
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[40000]   
[41000]   
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[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
[66000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[8000]   
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[18000]   
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[20000]   
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[24000]   
[25000]   
[26000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[6000]   
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[8000]   
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[20000]   
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[25000]   
[26000]   
[27000]   -fusion SPANNING read extraction for scaff: TLK2--FAM157A

[1000]   
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[3000]   
[4000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

[1000]   
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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
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[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   -fusion SPANNING read extraction for scaff: UBXN6--AC011498.1
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 13756
        };
Execution Time = 1.54 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.p4ZFwUXnBn/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.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -6350.899182
EM: Round [1] log likelihood: -6348.871683
EM: Round [2] log likelihood: -6348.839084
EM: Round [3] log likelihood: -6348.830780
EM: Round [4] log likelihood: -6348.823669
EM: Round [5] log likelihood: -6348.816813
EM: Round [6] log likelihood: -6348.810121
EM: Round [7] log likelihood: -6348.803579
EM: Round [8] log likelihood: -6348.797179
EM: Round [9] log likelihood: -6348.790917
EM: Round [10] log likelihood: -6348.784790
EM: Round [11] log likelihood: -6348.778793
EM: Round [12] log likelihood: -6348.772923
EM: Round [13] log likelihood: -6348.767178
EM: Round [14] log likelihood: -6348.761553
EM: Round [15] log likelihood: -6348.756045
EM: Round [16] log likelihood: -6348.750651
EM: Round [17] log likelihood: -6348.745368
EM: Round [18] log likelihood: -6348.740194
EM: Round [19] log likelihood: -6348.735126
EM: Round [20] log likelihood: -6348.730160
EM: Round [21] log likelihood: -6348.725295
EM: Round [22] log likelihood: -6348.720528
EM: Round [23] log likelihood: -6348.715856
EM: Round [24] log likelihood: -6348.711277
EM: Round [25] log likelihood: -6348.706790
EM: Round [26] log likelihood: -6348.702390
EM: Round [27] log likelihood: -6348.698078
EM: Round [28] log likelihood: -6348.693849
EM: Round [29] log likelihood: -6348.689703
EM: Round [30] log likelihood: -6348.685638
EM: Round [31] log likelihood: -6348.681651
EM: Round [32] log likelihood: -6348.677741
EM: Round [33] log likelihood: -6348.673907
EM: Round [34] log likelihood: -6348.670145
EM: Round [35] log likelihood: -6348.666455
EM: Round [36] log likelihood: -6348.662835
EM: Round [37] log likelihood: -6348.659284
EM: Round [38] log likelihood: -6348.655799
EM: Round [39] log likelihood: -6348.652380
EM: Round [40] log likelihood: -6348.649025
EM: Round [41] log likelihood: -6348.645732
EM: Round [42] log likelihood: -6348.642501
EM: Round [43] log likelihood: -6348.639330
EM: Round [44] log likelihood: -6348.636217
EM: Round [45] log likelihood: -6348.633161
EM: Round [46] log likelihood: -6348.630162
EM: Round [47] log likelihood: -6348.627217
EM: Round [48] log likelihood: -6348.624326
EM: Round [49] log likelihood: -6348.621488
EM: Round [50] log likelihood: -6348.618702
EM: Round [51] log likelihood: -6348.615965
EM: Round [52] log likelihood: -6348.613279
EM: Round [53] log likelihood: -6348.610640
EM: Round [54] log likelihood: -6348.608049
EM: Round [55] log likelihood: -6348.605504
EM: Round [56] log likelihood: -6348.603005
EM: Round [57] log likelihood: -6348.600550
EM: Round [58] log likelihood: -6348.598139
EM: Round [59] log likelihood: -6348.595771
EM: Round [60] log likelihood: -6348.593445
EM: Round [61] log likelihood: -6348.591159
EM: Round [62] log likelihood: -6348.588914
EM: Round [63] log likelihood: -6348.586709
EM: Round [64] log likelihood: -6348.584542
EM: Round [65] log likelihood: -6348.582413
EM: Round [66] log likelihood: -6348.580321
EM: Round [67] log likelihood: -6348.578266
EM: Round [68] log likelihood: -6348.576246
EM: Round [69] log likelihood: -6348.574261
EM: Round [70] log likelihood: -6348.572311
EM: Round [71] log likelihood: -6348.570395
EM: Round [72] log likelihood: -6348.568511
EM: Round [73] log likelihood: -6348.566660
EM: Round [74] log likelihood: -6348.564841
EM: Round [75] log likelihood: -6348.563053
EM: Round [76] log likelihood: -6348.561296
EM: Round [77] log likelihood: -6348.559568
EM: Round [78] log likelihood: -6348.557870
EM: Round [79] log likelihood: -6348.556202
EM: Round [80] log likelihood: -6348.554561
EM: Round [81] log likelihood: -6348.552948
EM: Round [82] log likelihood: -6348.551363
EM: Round [83] log likelihood: -6348.549805
EM: Round [84] log likelihood: -6348.548273
EM: Round [85] log likelihood: -6348.546766
EM: Round [86] log likelihood: -6348.545286
EM: Round [87] log likelihood: -6348.543830
EM: Round [88] log likelihood: -6348.542398
EM: Round [89] log likelihood: -6348.540991
EM: Round [90] log likelihood: -6348.539607
EM: Round [91] log likelihood: -6348.538246
EM: Round [92] log likelihood: -6348.536908
EM: Round [93] log likelihood: -6348.535593
EM: Round [94] log likelihood: -6348.534299
EM: Round [95] log likelihood: -6348.533027
EM: Round [96] log likelihood: -6348.531776
EM: Round [97] log likelihood: -6348.530545
EM: Round [98] log likelihood: -6348.529336
EM: Round [99] log likelihood: -6348.528146
EM: Round [100] log likelihood: -6348.526976
EM: Round [101] log likelihood: -6348.525825
EM: Round [102] log likelihood: -6348.524693
EM: Round [103] log likelihood: -6348.523580
EM: Round [104] log likelihood: -6348.522485
EM: Round [105] log likelihood: -6348.521408
EM: Round [106] log likelihood: -6348.520349
EM: Round [107] log likelihood: -6348.519308
EM: Round [108] log likelihood: -6348.518283
EM: Round [109] log likelihood: -6348.517275
EM: Round [110] log likelihood: -6348.516284
EM: Round [111] log likelihood: -6348.515309
EM: Round [112] log likelihood: -6348.514350
EM: Round [113] log likelihood: -6348.513406
EM: Round [114] log likelihood: -6348.512478
EM: Round [115] log likelihood: -6348.511565
EM: Round [116] log likelihood: -6348.510667
EM: Round [117] log likelihood: -6348.509783
EM: Round [118] log likelihood: -6348.508914
EM: Round [119] log likelihood: -6348.508059
EM: Round [120] log likelihood: -6348.507218
EM: Round [121] log likelihood: -6348.506390
EM: Round [122] log likelihood: -6348.505576
EM: Round [123] log likelihood: -6348.504775
EM: Round [124] log likelihood: -6348.503987
EM: Round [125] log likelihood: -6348.503212
EM: Round [126] log likelihood: -6348.502449
EM: Round [127] log likelihood: -6348.501698
EM: Round [128] log likelihood: -6348.500960
EM: Round [129] log likelihood: -6348.500233
EM: Round [130] log likelihood: -6348.499519
EM: Round [131] log likelihood: -6348.498815
EM: Round [132] log likelihood: -6348.498123
EM: Round [133] log likelihood: -6348.497442
EM: Round [134] log likelihood: -6348.496772
EM: Round [135] log likelihood: -6348.496113
EM: Round [136] log likelihood: -6348.495464
EM: Round [137] log likelihood: -6348.494826
EM: Round [138] log likelihood: -6348.494198
EM: Round [139] log likelihood: -6348.493580
EM: Round [140] log likelihood: -6348.492972
EM: Round [141] log likelihood: -6348.492374
EM: Round [142] log likelihood: -6348.491785
EM: Round [143] log likelihood: -6348.491205
EM: Round [144] log likelihood: -6348.490635
EM: Round [145] log likelihood: -6348.490074
EM: Round [146] log likelihood: -6348.489522
EM: Round [147] log likelihood: -6348.488978
EM: Round [148] log likelihood: -6348.488443
EM: Round [149] log likelihood: -6348.487917
EM: Round [150] log likelihood: -6348.487399
EM: Round [151] log likelihood: -6348.486890
EM: Round [152] log likelihood: -6348.486388
EM: Round [153] log likelihood: -6348.485895
EM: Round [154] log likelihood: -6348.485409
EM: Round [155] log likelihood: -6348.484931
EM: Round [156] log likelihood: -6348.484460
EM: Round [157] log likelihood: -6348.483997
EM: Round [158] log likelihood: -6348.483542
EM: Round [159] log likelihood: -6348.483093
EM: Round [160] log likelihood: -6348.482652
EM: Round [161] log likelihood: -6348.482217
EM: Round [162] log likelihood: -6348.481790
EM: Round [163] log likelihood: -6348.481369
EM: Round [164] log likelihood: -6348.480955
EM: Round [165] log likelihood: -6348.480547
EM: Round [166] log likelihood: -6348.480146
EM: Round [167] log likelihood: -6348.479751
EM: Round [168] log likelihood: -6348.479363
EM: Round [169] log likelihood: -6348.478980
EM: Round [170] log likelihood: -6348.478604
EM: Round [171] log likelihood: -6348.478233
EM: Round [172] log likelihood: -6348.477869
EM: Round [173] log likelihood: -6348.477510
EM: Round [174] log likelihood: -6348.477156
EM: Round [175] log likelihood: -6348.476809
EM: Round [176] log likelihood: -6348.476466
EM: Round [177] log likelihood: -6348.476129
EM: Round [178] log likelihood: -6348.475798
EM: Round [179] log likelihood: -6348.475471
EM: Round [180] log likelihood: -6348.475150
EM: Round [181] log likelihood: -6348.474834
EM: Round [182] log likelihood: -6348.474523
EM: Round [183] log likelihood: -6348.474216
EM: Round [184] log likelihood: -6348.473915
EM: Round [185] log likelihood: -6348.473618
EM: Round [186] log likelihood: -6348.473326
EM: Round [187] log likelihood: -6348.473038
EM: Round [188] log likelihood: -6348.472755
EM: Round [189] log likelihood: -6348.472476
EM: Round [190] log likelihood: -6348.472202
EM: Round [191] log likelihood: -6348.471932
EM: Round [192] log likelihood: -6348.471666
EM: Round [193] log likelihood: -6348.471405
EM: Round [194] log likelihood: -6348.471147
EM: Round [195] log likelihood: -6348.470893
EM: Round [196] log likelihood: -6348.470644
EM: Round [197] log likelihood: -6348.470398
EM: Round [198] log likelihood: -6348.470156
EM: Round [199] log likelihood: -6348.469918
EM: Round [200] log likelihood: -6348.469684
EM: Round [201] log likelihood: -6348.469453
EM: Round [202] log likelihood: -6348.469226
EM: Round [203] log likelihood: -6348.469003
EM: Round [204] log likelihood: -6348.468783
EM: Round [205] log likelihood: -6348.468566
EM: Round [206] log likelihood: -6348.468353
EM: Round [207] log likelihood: -6348.468143
EM: Round [208] log likelihood: -6348.467937
EM: Round [209] log likelihood: -6348.467733
EM: Round [210] log likelihood: -6348.467533
EM: Round [211] log likelihood: -6348.467336
EM: Round [212] log likelihood: -6348.467142
EM: Round [213] log likelihood: -6348.466951
EM: Round [214] log likelihood: -6348.466763
EM: Round [215] log likelihood: -6348.466578
EM: Round [216] log likelihood: -6348.466395
EM: Round [217] log likelihood: -6348.466216
EM: Round [218] log likelihood: -6348.466039
EM: Round [219] log likelihood: -6348.465865
EM: Round [220] log likelihood: -6348.465694
EM: Round [221] log likelihood: -6348.465526
EM: Round [222] log likelihood: -6348.465360
EM: Round [223] log likelihood: -6348.465197
EM: Round [224] log likelihood: -6348.465036
EM: Round [225] log likelihood: -6348.464878
EM: Round [226] log likelihood: -6348.464722
EM: Round [227] log likelihood: -6348.464568
EM: Round [228] log likelihood: -6348.464417
EM: Round [229] log likelihood: -6348.464269
EM: Round [230] log likelihood: -6348.464122
EM: Round [231] log likelihood: -6348.463978
EM: Round [232] log likelihood: -6348.463837
EM: Round [233] log likelihood: -6348.463697
EM: Round [234] log likelihood: -6348.463559
EM: Round [235] log likelihood: -6348.463424
EM: Round [236] log likelihood: -6348.463291
EM: Round [237] log likelihood: -6348.463160
EM: Round [238] log likelihood: -6348.463031
EM: Round [239] log likelihood: -6348.462904
EM: Round [240] log likelihood: -6348.462778
EM: Round [241] log likelihood: -6348.462655
EM: Round [242] log likelihood: -6348.462534
EM: Round [243] log likelihood: -6348.462414
EM: Round [244] log likelihood: -6348.462297
EM: Round [245] log likelihood: -6348.462181
EM: Round [246] log likelihood: -6348.462067
EM: Round [247] log likelihood: -6348.461955
EM: Round [248] log likelihood: -6348.461844
EM: Round [249] log likelihood: -6348.461736
EM: Round [250] log likelihood: -6348.461629
EM: Round [251] log likelihood: -6348.461523
EM: Round [252] log likelihood: -6348.461420
EM: Round [253] log likelihood: -6348.461317
EM: Round [254] log likelihood: -6348.461217
EM: Round [255] log likelihood: -6348.461118
EM: Stopping iterations at round 255 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.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.p4ZFwUXnBn/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.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.p4ZFwUXnBn/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.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.junction_reads.bam
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/tih_rna_sample_00711_B23MVV7LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/tih_rna_sample_00711_B23MVV7LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/tih_rna_sample_00711_B23MVV7LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/tih_rna_sample_00711_B23MVV7LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.spanning_reads.bam || : 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.spanning_reads.bam || : 
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/tih_rna_sample_00711_B23MVV7LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/tih_rna_sample_00711_B23MVV7LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/tih_rna_sample_00711_B23MVV7LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/tih_rna_sample_00711_B23MVV7LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.25 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.p4ZFwUXnBn/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.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.igv.FusionJuncSpan
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.igv.Pfam.gff3 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.igv.Pfam.gff3 
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.p4ZFwUXnBn/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.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.igv.seqsimilar.gff3 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.p4ZFwUXnBn/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.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.fa > /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.fa > /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter  --genome_lib_dir ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 50 
CMD: cp /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.post_blast_and_promiscuity_filter
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.p4ZFwUXnBn/ctat_genome_lib_build_dir
-done, see /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.p4ZFwUXnBn/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -5449.205586
EM: Round [1] log likelihood: -5448.161578
EM: Round [2] log likelihood: -5448.156341
EM: Round [3] log likelihood: -5448.156261
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.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1_1.fastp.fastq.gz: 295812390
Execution Time = 5.79 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.fa --gtf /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.gtf  > /tmp/nxf.p4ZFwUXnBn/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.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.fa --gtf /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.gtf  > /tmp/nxf.p4ZFwUXnBn/fi_workdir/microH.dat
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.p4ZFwUXnBn/fi_workdir/microH.dat /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.p4ZFwUXnBn/fi_workdir/microH.dat /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.p4ZFwUXnBn --json_outfile /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00711_B23MVV7LT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.p4ZFwUXnBn --json_outfile /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00711_B23MVV7LT4_1
Running: touch /tmp/nxf.p4ZFwUXnBn/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.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00711_B23MVV7LT4_1 --html_output /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00711_B23MVV7LT4_1 --html_output /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.p4ZFwUXnBn/ctat_genome_lib_build_dir > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.p4ZFwUXnBn/ctat_genome_lib_build_dir > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.p4ZFwUXnBn/ctat_genome_lib_build_dir > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
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 [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 [ENSG00000280136.2]
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 [ENSG00000260318.1]
WARNING, no entry stored in dbm for [ENSG00000260318.1]
WARNING, no entry stored in dbm for [ENSG00000260318.1]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000279058.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000279058.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000279058.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000279058.2]
WARNING, no entry stored in dbm for [ENSG00000267011.5]
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]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.p4ZFwUXnBn/ctat_genome_lib_build_dir > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.p4ZFwUXnBn/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory