Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/dd2432a4a8b00129c1011fea41c7d2/659_b7Z-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/32e48b40e872483216ba363171bdb1/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/32e48b40e872483216ba363171bdb1/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/dd2432a4a8b00129c1011fea41c7d2/659_b7Z-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/653769f75e74b825b48f9c1b66148d/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)

Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.VFyNVpanxF/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.VFyNVpanxF/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000 
Done.
Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.VFyNVpanxF/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.VFyNVpanxF/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gtf
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.VFyNVpanxF/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.VFyNVpanxF/cytoBand.txt
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.bed
-parsing GTF file: /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.bed
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.VFyNVpanxF/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.VFyNVpanxF/fi_workdir --reads "/tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.VFyNVpanxF/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.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 09:58:29 ..... started STAR run
Jun 08 09:58:29 ..... loading genome
Jun 08 10:00:14 ... generating Suffix Array index
Jun 08 10:04:09 ... completed Suffix Array index
Jun 08 10:04:10 ..... processing annotations GTF
Jun 08 10:04:10 ..... inserting junctions into the genome indices
Jun 08 10:05:11 ..... started mapping
Jun 08 11:23:19 ..... finished mapping
Jun 08 11:23:20 ..... started sorting BAM
Jun 08 11:23:21 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
Execution Time = 84.88 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.VFyNVpanxF/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.VFyNVpanxF/fi_workdir --reads "/tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
11:23:27 : INFO : Done.
Execution Time = 0.09 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.VFyNVpanxF/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.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam

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[960000]   -done parsing /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'excessive soft clipping' => 5703,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 14,
          'exons hit < 2' => 5,
          'small anchor length' => 186,
          'seq-similar region overlap' => 319,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 64,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 12,
          'per_id < 96' => 4608,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 44,
          'low complexity anchor region' => 63,
          'num genes matched < 2' => 5,
          ' ** passed ** ' => 22685,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 6
        };
-writing fusion junction support info.
Execution Time = 0.54 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.VFyNVpanxF/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.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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-fusion SPANNING read extraction for scaff: CCDC169--SOHLH2

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[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
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[50000]   
[51000]   
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[53000]   
[54000]   
[55000]   
[56000]   
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[60000]   
[61000]   
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[64000]   
[65000]   
[66000]   
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[75000]   
[76000]   
[77000]   
[78000]   
[79000]   
[80000]   
[81000]   
[82000]   
[83000]   
[84000]   
[85000]   
[86000]   
[87000]   
[88000]   
[89000]   
[90000]   
[91000]   
[92000]   
[93000]   
[94000]   
[95000]   
[96000]   
[97000]   
[98000]   
[99000]   
[100000]   
[101000]   
[102000]   
[103000]   
[104000]   
[105000]   
[106000]   
[107000]   
[108000]   
[109000]   
[110000]   
[111000]   
[112000]   -fusion SPANNING read extraction for scaff: ETV6--FAR2

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: FBXO25--AC240565.1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   -fusion SPANNING read extraction for scaff: FSIP1--AC013652.1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   
[57000]   
[58000]   
[59000]   
[60000]   
[61000]   
[62000]   
[63000]   -fusion SPANNING read extraction for scaff: HGD--GTF2E1

[1000]   -fusion SPANNING read extraction for scaff: KLRC4--KLRK1

[1000]   
[2000]   
[3000]   -fusion SPANNING read extraction for scaff: LINC00993--PVT1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   -fusion SPANNING read extraction for scaff: RPF2--CDK19

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

[1000]   
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[4000]   
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[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
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[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   -fusion SPANNING read extraction for scaff: TLK2--LINC01347

[1000]   
[2000]   
[3000]   
[4000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 10589,
          'seq similar region alignment' => 31195
        };
Execution Time = 1.30 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.VFyNVpanxF/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.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_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.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -7868.240315
EM: Round [1] log likelihood: -7856.195531
EM: Round [2] log likelihood: -7853.026711
EM: Round [3] log likelihood: -7850.427076
EM: Round [4] log likelihood: -7848.257389
EM: Round [5] log likelihood: -7846.427775
EM: Round [6] log likelihood: -7844.871647
EM: Round [7] log likelihood: -7843.538416
EM: Round [8] log likelihood: -7842.388880
EM: Round [9] log likelihood: -7841.392166
EM: Round [10] log likelihood: -7840.523607
EM: Round [11] log likelihood: -7839.763257
EM: Round [12] log likelihood: -7839.094806
EM: Round [13] log likelihood: -7838.504793
EM: Round [14] log likelihood: -7837.982013
EM: Round [15] log likelihood: -7837.517071
EM: Round [16] log likelihood: -7837.102037
EM: Round [17] log likelihood: -7836.730188
EM: Round [18] log likelihood: -7836.395793
EM: Round [19] log likelihood: -7836.093949
EM: Round [20] log likelihood: -7835.820452
EM: Round [21] log likelihood: -7835.571683
EM: Round [22] log likelihood: -7835.344524
EM: Round [23] log likelihood: -7835.136281
EM: Round [24] log likelihood: -7834.944625
EM: Round [25] log likelihood: -7834.767539
EM: Round [26] log likelihood: -7834.603275
EM: Round [27] log likelihood: -7834.450315
EM: Round [28] log likelihood: -7834.307342
EM: Round [29] log likelihood: -7834.173212
EM: Round [30] log likelihood: -7834.046929
EM: Round [31] log likelihood: -7833.927627
EM: Round [32] log likelihood: -7833.814550
EM: Round [33] log likelihood: -7833.707040
EM: Round [34] log likelihood: -7833.604524
EM: Round [35] log likelihood: -7833.506500
EM: Round [36] log likelihood: -7833.412529
EM: Round [37] log likelihood: -7833.322228
EM: Round [38] log likelihood: -7833.235260
EM: Round [39] log likelihood: -7833.151329
EM: Round [40] log likelihood: -7833.070177
EM: Round [41] log likelihood: -7832.991574
EM: Round [42] log likelihood: -7832.915320
EM: Round [43] log likelihood: -7832.841235
EM: Round [44] log likelihood: -7832.769163
EM: Round [45] log likelihood: -7832.698963
EM: Round [46] log likelihood: -7832.630511
EM: Round [47] log likelihood: -7832.563695
EM: Round [48] log likelihood: -7832.498417
EM: Round [49] log likelihood: -7832.434587
EM: Round [50] log likelihood: -7832.372126
EM: Round [51] log likelihood: -7832.310961
EM: Round [52] log likelihood: -7832.251027
EM: Round [53] log likelihood: -7832.192266
EM: Round [54] log likelihood: -7832.134622
EM: Round [55] log likelihood: -7832.078048
EM: Round [56] log likelihood: -7832.022497
EM: Round [57] log likelihood: -7831.967930
EM: Round [58] log likelihood: -7831.914308
EM: Round [59] log likelihood: -7831.861595
EM: Round [60] log likelihood: -7831.809760
EM: Round [61] log likelihood: -7831.758772
EM: Round [62] log likelihood: -7831.708604
EM: Round [63] log likelihood: -7831.659227
EM: Round [64] log likelihood: -7831.610619
EM: Round [65] log likelihood: -7831.562756
EM: Round [66] log likelihood: -7831.515615
EM: Round [67] log likelihood: -7831.469177
EM: Round [68] log likelihood: -7831.423422
EM: Round [69] log likelihood: -7831.378332
EM: Round [70] log likelihood: -7831.333888
EM: Round [71] log likelihood: -7831.290075
EM: Round [72] log likelihood: -7831.246877
EM: Round [73] log likelihood: -7831.204278
EM: Round [74] log likelihood: -7831.162263
EM: Round [75] log likelihood: -7831.120820
EM: Round [76] log likelihood: -7831.079934
EM: Round [77] log likelihood: -7831.039594
EM: Round [78] log likelihood: -7830.999786
EM: Round [79] log likelihood: -7830.960499
EM: Round [80] log likelihood: -7830.921721
EM: Round [81] log likelihood: -7830.883442
EM: Round [82] log likelihood: -7830.845651
EM: Round [83] log likelihood: -7830.808338
EM: Round [84] log likelihood: -7830.771493
EM: Round [85] log likelihood: -7830.735107
EM: Round [86] log likelihood: -7830.699169
EM: Round [87] log likelihood: -7830.663673
EM: Round [88] log likelihood: -7830.628608
EM: Round [89] log likelihood: -7830.593966
EM: Round [90] log likelihood: -7830.559740
EM: Round [91] log likelihood: -7830.525921
EM: Round [92] log likelihood: -7830.492501
EM: Round [93] log likelihood: -7830.459474
EM: Round [94] log likelihood: -7830.426833
EM: Round [95] log likelihood: -7830.394569
EM: Round [96] log likelihood: -7830.362677
EM: Round [97] log likelihood: -7830.331149
EM: Round [98] log likelihood: -7830.299979
EM: Round [99] log likelihood: -7830.269162
EM: Round [100] log likelihood: -7830.238690
EM: Round [101] log likelihood: -7830.208558
EM: Round [102] log likelihood: -7830.178760
EM: Round [103] log likelihood: -7830.149291
EM: Round [104] log likelihood: -7830.120144
EM: Round [105] log likelihood: -7830.091315
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Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.VFyNVpanxF/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.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_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.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_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.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.VFyNVpanxF/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.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_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.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_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.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_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.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || : 
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_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.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.24 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.VFyNVpanxF/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.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_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.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_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.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.VFyNVpanxF/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.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_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.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.VFyNVpanxF/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.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_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.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_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.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_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.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_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.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_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.VFyNVpanxF/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.VFyNVpanxF/ctat_genome_lib_build_dir
-done, see /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_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.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.VFyNVpanxF/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -5480.708128
EM: Round [1] log likelihood: -5480.123038
EM: Round [2] log likelihood: -5480.121640
EM: Round [3] log likelihood: -5480.121632
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.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 296305715
Execution Time = 6.16 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gtf  > /tmp/nxf.VFyNVpanxF/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.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gtf  > /tmp/nxf.VFyNVpanxF/fi_workdir/microH.dat
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.VFyNVpanxF/fi_workdir/microH.dat /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_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.VFyNVpanxF/fi_workdir/microH.dat /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.VFyNVpanxF --json_outfile /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_b7Z-T1-TRNA-1_B23MHV2LT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.VFyNVpanxF --json_outfile /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_b7Z-T1-TRNA-1_B23MHV2LT4_1
Running: touch /tmp/nxf.VFyNVpanxF/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.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_b7Z-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_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.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_b7Z-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.VFyNVpanxF/ctat_genome_lib_build_dir > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.VFyNVpanxF/ctat_genome_lib_build_dir > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.VFyNVpanxF/ctat_genome_lib_build_dir > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000265018.6]
WARNING, no entry stored in dbm for [ENSG00000260261.2]
WARNING, no entry stored in dbm for [ENSG00000185485.14]
WARNING, no entry stored in dbm for [ENSG00000260261.2]
WARNING, no entry stored in dbm for [ENSG00000185485.14]
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 [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 [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 [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000226312.7]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.VFyNVpanxF/ctat_genome_lib_build_dir > /tmp/nxf.VFyNVpanxF/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.VFyNVpanxF/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory