Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/a37086b7056644892b15c7a927e2a1/tih_rna_sample_00462_B23WHTKLT4_2.fusionreport.tsv
  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/4c/cc26c6fb9bb769b1f132a278acb9a3/tih_rna_sample_00462_B23WHTKLT4_2_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/cdaa7ebb883db2b8fc35e559623a74/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/cc26c6fb9bb769b1f132a278acb9a3/tih_rna_sample_00462_B23WHTKLT4_2_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/cdaa7ebb883db2b8fc35e559623a74/.command.run
==> STAGING COMPLETE (6 inputs)

Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00462_B23WHTKLT4_2.fusionreport.tsv --gtf /tmp/nxf.WpLJscJaA8/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.WpLJscJaA8/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2 --shrink_introns --max_intron_length 1000 
Error, chr discrepancy in gtf info for chr5	ENSEMBL	exon	18236123	18236196	.	+	.	gene_id "SNORD81^ENSG00000212278.1"; transcript_id "ENST00000390976.1"; gene_type "snoRNA"; gene_name "SNORD81"; transcript_type "snoRNA"; transcript_name "SNORD81.3-201"; exon_number 1; exon_id "ENSE00001508760.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "SNORD81^ENSG00000212278.1"; orig_coord_info "chr5,18236123,18236196,+";
Error, chr discrepancy in gtf info for chr7	ENSEMBL	exon	137287687	137287762	.	+	.	gene_id "SNORD81^ENSG00000202023.1"; transcript_id "ENST00000365153.1"; gene_type "snoRNA"; gene_name "SNORD81"; transcript_type "snoRNA"; transcript_name "SNORD81.2-201"; exon_number 1; exon_id "ENSE00001439916.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "SNORD81^ENSG00000202023.1"; orig_coord_info "chr7,137287687,137287762,+";
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_00462_B23WHTKLT4_2.fusionreport.tsv --gtf /tmp/nxf.WpLJscJaA8/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.WpLJscJaA8/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.fa /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.fa /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fa
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.gtf /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.gtf /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.gtf
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.fa /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.gtf > /tmp/nxf.WpLJscJaA8/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.fa /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.gtf > /tmp/nxf.WpLJscJaA8/cytoBand.txt
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.gtf > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.bed
-parsing GTF file: /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.gtf > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.bed
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.bed > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.bed > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.bed.sorted.bed
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/tih_rna_sample_00462_B23WHTKLT4_2.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.bed.sorted.bed
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/tih_rna_sample_00462_B23WHTKLT4_2.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.bed.sorted.bed.gz
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/tih_rna_sample_00462_B23WHTKLT4_2.bed.tabix.ok
Running: samtools faidx /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.fa
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.WpLJscJaA8/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.gtf --CPU 8 --out_prefix tih_rna_sample_00462_B23WHTKLT4_2.star --out_dir /tmp/nxf.WpLJscJaA8/fi_workdir --reads "/tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.WpLJscJaA8/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.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 10:06:23 ..... started STAR run
Jun 08 10:06:23 ..... loading genome
Jun 08 10:08:04 ... generating Suffix Array index
Jun 08 10:11:52 ... completed Suffix Array index
Jun 08 10:11:52 ..... processing annotations GTF
Jun 08 10:11:53 ..... inserting junctions into the genome indices
Jun 08 10:12:54 ..... started mapping
Jun 08 11:12:48 ..... finished mapping
Jun 08 11:12:49 ..... started sorting BAM
Jun 08 11:12:53 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00462_B23WHTKLT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00462_B23WHTKLT4_2.star.sortedByCoord.out.bam
Execution Time = 66.62 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.WpLJscJaA8/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.gtf --CPU 8 --out_prefix tih_rna_sample_00462_B23WHTKLT4_2.star --out_dir /tmp/nxf.WpLJscJaA8/fi_workdir --reads "/tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2_2.fastp.fastq.gz"
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.sortedByCoord.out.bam   -o /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.cSorted.dupsMarked.bam   --remove_dups 
11:13:35 : INFO : Done.
Execution Time = 0.58 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.sortedByCoord.out.bam   -o /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.cSorted.dupsMarked.bam
Execution Time = 0.07 minutes. CMD: samtools index /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.WpLJscJaA8/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.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.gtf
-parsing /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.cSorted.dupsMarked.bam

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[6400000]   -done parsing /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          ' ** passed ** ' => 7973,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 64,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 24,
          'num genes matched < 2' => 11,
          'exons hit < 2' => 14,
          'per_id < 96' => 22030,
          'low complexity anchor region' => 5,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 6,
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 530,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 18,
          'small anchor length' => 41,
          'seq-similar region overlap' => 111,
          'excessive soft clipping' => 42739,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 24,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 26,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 568
        };
-writing fusion junction support info.
Execution Time = 3.74 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.WpLJscJaA8/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.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[28000]   -fusion SPANNING read extraction for scaff: AC004980.3--UPK3BL1

[1000]   -fusion SPANNING read extraction for scaff: AC015909.2--SGCA

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[14000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[1059000]   
[1060000]   -fusion SPANNING read extraction for scaff: ACTBP6--ACTB

[1000]   
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[31000]   
[32000]   -fusion SPANNING read extraction for scaff: ANKRD33B--SNORD81

[1000]   
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[31000]   
[32000]   -fusion SPANNING read extraction for scaff: ANKRD33B--RN7SL58P

[1000]   
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[550000]   
[551000]   -fusion SPANNING read extraction for scaff: CLTC--RPS6KB1

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[87000]   
[88000]   -fusion SPANNING read extraction for scaff: LGALS3--DLGAP5

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[247000]   
[248000]   
[249000]   
[250000]   -fusion SPANNING read extraction for scaff: MYO10--NSG2

[1000]   
[2000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13

[1000]   
[2000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1

[1000]   
[2000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC5

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA12

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
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[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   
[69000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA9

[1000]   
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[5000]   
[6000]   
[7000]   
[8000]   
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[254000]   
[255000]   
[256000]   
[257000]   
[258000]   
[259000]   
[260000]   
[261000]   -fusion SPANNING read extraction for scaff: SEMA5A--ADAMTS16

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
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[14000]   
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[20000]   
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[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
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[20000]   
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[30000]   
[31000]   
[32000]   
[33000]   -fusion SPANNING read extraction for scaff: SWAP70--ELAPOR2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
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[20000]   
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[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

[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]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   -fusion SPANNING read extraction for scaff: TMED7--TICAM2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
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[1813000]   -fusion SPANNING read extraction for scaff: TRIO--AC134878.2

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[1813000]   -fusion SPANNING read extraction for scaff: TRIO--DUX4L16

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[62000]   -fusion SPANNING read extraction for scaff: TRPC4AP--NDUFAF6

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

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[10000]   -fusion SPANNING read extraction for scaff: WARS2--RBM15-AS1
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 21883,
          'seq similar region alignment' => 19411
        };
Execution Time = 10.42 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.WpLJscJaA8/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.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -8288.862324
EM: Round [1] log likelihood: -8286.487352
EM: Round [2] log likelihood: -8285.600270
EM: Round [3] log likelihood: -8284.892557
EM: Round [4] log likelihood: -8284.322699
EM: Round [5] log likelihood: -8283.860246
EM: Round [6] log likelihood: -8283.482210
EM: Round [7] log likelihood: -8283.171039
EM: Round [8] log likelihood: -8282.913199
EM: Round [9] log likelihood: -8282.698167
EM: Round [10] log likelihood: -8282.517697
EM: Round [11] log likelihood: -8282.365282
EM: Round [12] log likelihood: -8282.235753
EM: Round [13] log likelihood: -8282.124979
EM: Round [14] log likelihood: -8282.029643
EM: Round [15] log likelihood: -8281.947064
EM: Round [16] log likelihood: -8281.875067
EM: Round [17] log likelihood: -8281.811881
EM: Round [18] log likelihood: -8281.756057
EM: Round [19] log likelihood: -8281.706404
EM: Round [20] log likelihood: -8281.661943
EM: Round [21] log likelihood: -8281.621863
EM: Round [22] log likelihood: -8281.585494
EM: Round [23] log likelihood: -8281.552279
EM: Round [24] log likelihood: -8281.521754
EM: Round [25] log likelihood: -8281.493533
EM: Round [26] log likelihood: -8281.467290
EM: Round [27] log likelihood: -8281.442756
EM: Round [28] log likelihood: -8281.419703
EM: Round [29] log likelihood: -8281.397938
EM: Round [30] log likelihood: -8281.377301
EM: Round [31] log likelihood: -8281.357655
EM: Round [32] log likelihood: -8281.338885
EM: Round [33] log likelihood: -8281.320892
EM: Round [34] log likelihood: -8281.303593
EM: Round [35] log likelihood: -8281.286917
EM: Round [36] log likelihood: -8281.270804
EM: Round [37] log likelihood: -8281.255201
EM: Round [38] log likelihood: -8281.240064
EM: Round [39] log likelihood: -8281.225353
EM: Round [40] log likelihood: -8281.211036
EM: Round [41] log likelihood: -8281.197083
EM: Round [42] log likelihood: -8281.183470
EM: Round [43] log likelihood: -8281.170173
EM: Round [44] log likelihood: -8281.157174
EM: Round [45] log likelihood: -8281.144456
EM: Round [46] log likelihood: -8281.132002
EM: Round [47] log likelihood: -8281.119800
EM: Round [48] log likelihood: -8281.107838
EM: Round [49] log likelihood: -8281.096104
EM: Round [50] log likelihood: -8281.084588
EM: Round [51] log likelihood: -8281.073282
EM: Round [52] log likelihood: -8281.062178
EM: Round [53] log likelihood: -8281.051267
EM: Round [54] log likelihood: -8281.040543
EM: Round [55] log likelihood: -8281.030000
EM: Round [56] log likelihood: -8281.019632
EM: Round [57] log likelihood: -8281.009432
EM: Round [58] log likelihood: -8280.999397
EM: Round [59] log likelihood: -8280.989521
EM: Round [60] log likelihood: -8280.979799
EM: Round [61] log likelihood: -8280.970228
EM: Round [62] log likelihood: -8280.960802
EM: Round [63] log likelihood: -8280.951519
EM: Round [64] log likelihood: -8280.942375
EM: Round [65] log likelihood: -8280.933365
EM: Round [66] log likelihood: -8280.924487
EM: Round [67] log likelihood: -8280.915738
EM: Round [68] log likelihood: -8280.907114
EM: Round [69] log likelihood: -8280.898613
EM: Round [70] log likelihood: -8280.890231
EM: Round [71] log likelihood: -8280.881966
EM: Round [72] log likelihood: -8280.873815
EM: Round [73] log likelihood: -8280.865776
EM: Round [74] log likelihood: -8280.857846
EM: Round [75] log likelihood: -8280.850023
EM: Round [76] log likelihood: -8280.842304
EM: Round [77] log likelihood: -8280.834688
EM: Round [78] log likelihood: -8280.827173
EM: Round [79] log likelihood: -8280.819755
EM: Round [80] log likelihood: -8280.812433
EM: Round [81] log likelihood: -8280.805206
EM: Round [82] log likelihood: -8280.798071
EM: Round [83] log likelihood: -8280.791026
EM: Round [84] log likelihood: -8280.784071
EM: Round [85] log likelihood: -8280.777202
EM: Round [86] log likelihood: -8280.770418
EM: Round [87] log likelihood: -8280.763718
EM: Round [88] log likelihood: -8280.757100
EM: Round [89] log likelihood: -8280.750563
EM: Round [90] log likelihood: -8280.744105
EM: Round [91] log likelihood: -8280.737724
EM: Round [92] log likelihood: -8280.731420
EM: Round [93] log likelihood: -8280.725190
EM: Round [94] log likelihood: -8280.719034
EM: Round [95] log likelihood: -8280.712950
EM: Round [96] log likelihood: -8280.706936
EM: Round [97] log likelihood: -8280.700993
EM: Round [98] log likelihood: -8280.695118
EM: Round [99] log likelihood: -8280.689310
EM: Round [100] log likelihood: -8280.683568
EM: Round [101] log likelihood: -8280.677891
EM: Round [102] log likelihood: -8280.672278
EM: Round [103] log likelihood: -8280.666727
EM: Round [104] log likelihood: -8280.661239
EM: Round [105] log likelihood: -8280.655811
EM: Round [106] log likelihood: -8280.650443
EM: Round [107] log likelihood: -8280.645133
EM: Round [108] log likelihood: -8280.639882
EM: Round [109] log likelihood: -8280.634687
EM: Round [110] log likelihood: -8280.629548
EM: Round [111] log likelihood: -8280.624464
EM: Round [112] log likelihood: -8280.619435
EM: Round [113] log likelihood: -8280.614459
EM: Round [114] log likelihood: -8280.609535
EM: Round [115] log likelihood: -8280.604664
EM: Round [116] log likelihood: -8280.599843
EM: Round [117] log likelihood: -8280.595072
EM: Round [118] log likelihood: -8280.590351
EM: Round [119] log likelihood: -8280.585678
EM: Round [120] log likelihood: -8280.581053
EM: Round [121] log likelihood: -8280.576476
EM: Round [122] log likelihood: -8280.571945
EM: Round [123] log likelihood: -8280.567460
EM: Round [124] log likelihood: -8280.563020
EM: Round [125] log likelihood: -8280.558625
EM: Round [126] log likelihood: -8280.554274
EM: Round [127] log likelihood: -8280.549965
EM: Round [128] log likelihood: -8280.545700
EM: Round [129] log likelihood: -8280.541477
EM: Round [130] log likelihood: -8280.537295
EM: Round [131] log likelihood: -8280.533154
EM: Round [132] log likelihood: -8280.529053
EM: Round [133] log likelihood: -8280.524992
EM: Round [134] log likelihood: -8280.520970
EM: Round [135] log likelihood: -8280.516987
EM: Round [136] log likelihood: -8280.513043
EM: Round [137] log likelihood: -8280.509135
EM: Round [138] log likelihood: -8280.505265
EM: Round [139] log likelihood: -8280.501432
EM: Round [140] log likelihood: -8280.497635
EM: Round [141] log likelihood: -8280.493873
EM: Round [142] log likelihood: -8280.490147
EM: Round [143] log likelihood: -8280.486456
EM: Round [144] log likelihood: -8280.482799
EM: Round [145] log likelihood: -8280.479175
EM: Round [146] log likelihood: -8280.475585
EM: Round [147] log likelihood: -8280.472029
EM: Round [148] log likelihood: -8280.468504
EM: Round [149] log likelihood: -8280.465012
EM: Round [150] log likelihood: -8280.461552
EM: Round [151] log likelihood: -8280.458123
EM: Round [152] log likelihood: -8280.454725
EM: Round [153] log likelihood: -8280.451358
EM: Round [154] log likelihood: -8280.448021
EM: Round [155] log likelihood: -8280.444714
EM: Round [156] log likelihood: -8280.441436
EM: Round [157] log likelihood: -8280.438187
EM: Round [158] log likelihood: -8280.434968
EM: Round [159] log likelihood: -8280.431776
EM: Round [160] log likelihood: -8280.428613
EM: Round [161] log likelihood: -8280.425477
EM: Round [162] log likelihood: -8280.422369
EM: Round [163] log likelihood: -8280.419288
EM: Round [164] log likelihood: -8280.416234
EM: Round [165] log likelihood: -8280.413207
EM: Round [166] log likelihood: -8280.410205
EM: Round [167] log likelihood: -8280.407229
EM: Round [168] log likelihood: -8280.404279
EM: Round [169] log likelihood: -8280.401354
EM: Round [170] log likelihood: -8280.398455
EM: Round [171] log likelihood: -8280.395579
EM: Round [172] log likelihood: -8280.392729
EM: Round [173] log likelihood: -8280.389902
EM: Round [174] log likelihood: -8280.387099
EM: Round [175] log likelihood: -8280.384320
EM: Round [176] log likelihood: -8280.381565
EM: Round [177] log likelihood: -8280.378832
EM: Round [178] log likelihood: -8280.376122
EM: Round [179] log likelihood: -8280.373435
EM: Round [180] log likelihood: -8280.370770
EM: Round [181] log likelihood: -8280.368127
EM: Round [182] log likelihood: -8280.365506
EM: Round [183] log likelihood: -8280.362906
EM: Round [184] log likelihood: -8280.360328
EM: Round [185] log likelihood: -8280.357771
EM: Round [186] log likelihood: -8280.355235
EM: Round [187] log likelihood: -8280.352720
EM: Round [188] log likelihood: -8280.350225
EM: Round [189] log likelihood: -8280.347750
EM: Round [190] log likelihood: -8280.345296
EM: Round [191] log likelihood: -8280.342861
EM: Round [192] log likelihood: -8280.340446
EM: Round [193] log likelihood: -8280.338050
EM: Round [194] log likelihood: -8280.335674
EM: Round [195] log likelihood: -8280.333316
EM: Round [196] log likelihood: -8280.330977
EM: Round [197] log likelihood: -8280.328657
EM: Round [198] log likelihood: -8280.326356
EM: Round [199] log likelihood: -8280.324072
EM: Round [200] log likelihood: -8280.321807
EM: Round [201] log likelihood: -8280.319559
EM: Round [202] log likelihood: -8280.317330
EM: Round [203] log likelihood: -8280.315117
EM: Round [204] log likelihood: -8280.312923
EM: Round [205] log likelihood: -8280.310745
EM: Round [206] log likelihood: -8280.308584
EM: Round [207] log likelihood: -8280.306440
EM: Round [208] log likelihood: -8280.304313
EM: Round [209] log likelihood: -8280.302202
EM: Round [210] log likelihood: -8280.300108
EM: Round [211] log likelihood: -8280.298030
EM: Round [212] log likelihood: -8280.295967
EM: Round [213] log likelihood: -8280.293921
EM: Round [214] log likelihood: -8280.291890
EM: Round [215] log likelihood: -8280.289875
EM: Round [216] log likelihood: -8280.287875
EM: Round [217] log likelihood: -8280.285891
EM: Round [218] log likelihood: -8280.283922
EM: Round [219] log likelihood: -8280.281967
EM: Round [220] log likelihood: -8280.280028
EM: Round [221] log likelihood: -8280.278103
EM: Round [222] log likelihood: -8280.276192
EM: Round [223] log likelihood: -8280.274296
EM: Round [224] log likelihood: -8280.272415
EM: Round [225] log likelihood: -8280.270547
EM: Round [226] log likelihood: -8280.268694
EM: Round [227] log likelihood: -8280.266854
EM: Round [228] log likelihood: -8280.265028
EM: Round [229] log likelihood: -8280.263216
EM: Round [230] log likelihood: -8280.261417
EM: Round [231] log likelihood: -8280.259632
EM: Round [232] log likelihood: -8280.257859
EM: Round [233] log likelihood: -8280.256100
EM: Round [234] log likelihood: -8280.254354
EM: Round [235] log likelihood: -8280.252621
EM: Round [236] log likelihood: -8280.250901
EM: Round [237] log likelihood: -8280.249193
EM: Round [238] log likelihood: -8280.247498
EM: Round [239] log likelihood: -8280.245815
EM: Round [240] log likelihood: -8280.244144
EM: Round [241] log likelihood: -8280.242486
EM: Round [242] log likelihood: -8280.240840
EM: Round [243] log likelihood: -8280.239206
EM: Round [244] log likelihood: -8280.237583
EM: Round [245] log likelihood: -8280.235973
EM: Round [246] log likelihood: -8280.234374
EM: Round [247] log likelihood: -8280.232786
EM: Round [248] log likelihood: -8280.231210
EM: Round [249] log likelihood: -8280.229646
EM: Round [250] log likelihood: -8280.228093
EM: Round [251] log likelihood: -8280.226550
EM: Round [252] log likelihood: -8280.225019
EM: Round [253] log likelihood: -8280.223499
EM: Round [254] log likelihood: -8280.221990
EM: Round [255] log likelihood: -8280.220492
EM: Round [256] log likelihood: -8280.219004
EM: Round [257] log likelihood: -8280.217527
EM: Round [258] log likelihood: -8280.216060
EM: Round [259] log likelihood: -8280.214604
EM: Round [260] log likelihood: -8280.213158
EM: Round [261] log likelihood: -8280.211723
EM: Round [262] log likelihood: -8280.210297
EM: Round [263] log likelihood: -8280.208882
EM: Round [264] log likelihood: -8280.207476
EM: Round [265] log likelihood: -8280.206081
EM: Round [266] log likelihood: -8280.204695
EM: Round [267] log likelihood: -8280.203319
EM: Round [268] log likelihood: -8280.201953
EM: Round [269] log likelihood: -8280.200596
EM: Round [270] log likelihood: -8280.199249
EM: Round [271] log likelihood: -8280.197911
EM: Round [272] log likelihood: -8280.196582
EM: Round [273] log likelihood: -8280.195263
EM: Round [274] log likelihood: -8280.193953
EM: Round [275] log likelihood: -8280.192652
EM: Round [276] log likelihood: -8280.191360
EM: Round [277] log likelihood: -8280.190077
EM: Round [278] log likelihood: -8280.188802
EM: Round [279] log likelihood: -8280.187537
EM: Round [280] log likelihood: -8280.186280
EM: Round [281] log likelihood: -8280.185032
EM: Round [282] log likelihood: -8280.183793
EM: Round [283] log likelihood: -8280.182562
EM: Round [284] log likelihood: -8280.181340
EM: Round [285] log likelihood: -8280.180126
EM: Round [286] log likelihood: -8280.178920
EM: Round [287] log likelihood: -8280.177723
EM: Round [288] log likelihood: -8280.176533
EM: Round [289] log likelihood: -8280.175352
EM: Round [290] log likelihood: -8280.174179
EM: Round [291] log likelihood: -8280.173014
EM: Round [292] log likelihood: -8280.171857
EM: Round [293] log likelihood: -8280.170708
EM: Round [294] log likelihood: -8280.169566
EM: Round [295] log likelihood: -8280.168432
EM: Round [296] log likelihood: -8280.167306
EM: Round [297] log likelihood: -8280.166188
EM: Round [298] log likelihood: -8280.165077
EM: Round [299] log likelihood: -8280.163974
EM: Round [300] log likelihood: -8280.162878
EM: Round [301] log likelihood: -8280.161789
EM: Round [302] log likelihood: -8280.160708
EM: Round [303] log likelihood: -8280.159634
EM: Round [304] log likelihood: -8280.158567
EM: Round [305] log likelihood: -8280.157507
EM: Round [306] log likelihood: -8280.156455
EM: Round [307] log likelihood: -8280.155409
EM: Round [308] log likelihood: -8280.154371
EM: Round [309] log likelihood: -8280.153339
EM: Round [310] log likelihood: -8280.152315
EM: Round [311] log likelihood: -8280.151297
EM: Round [312] log likelihood: -8280.150286
EM: Round [313] log likelihood: -8280.149281
EM: Round [314] log likelihood: -8280.148284
EM: Round [315] log likelihood: -8280.147293
EM: Round [316] log likelihood: -8280.146308
EM: Round [317] log likelihood: -8280.145330
EM: Round [318] log likelihood: -8280.144359
EM: Round [319] log likelihood: -8280.143394
EM: Round [320] log likelihood: -8280.142435
EM: Round [321] log likelihood: -8280.141483
EM: Round [322] log likelihood: -8280.140537
EM: Round [323] log likelihood: -8280.139597
EM: Round [324] log likelihood: -8280.138663
EM: Round [325] log likelihood: -8280.137736
EM: Round [326] log likelihood: -8280.136814
EM: Round [327] log likelihood: -8280.135899
EM: Round [328] log likelihood: -8280.134989
EM: Round [329] log likelihood: -8280.134086
EM: Round [330] log likelihood: -8280.133188
EM: Round [331] log likelihood: -8280.132297
EM: Round [332] log likelihood: -8280.131411
EM: Round [333] log likelihood: -8280.130531
EM: Round [334] log likelihood: -8280.129657
EM: Round [335] log likelihood: -8280.128788
EM: Round [336] log likelihood: -8280.127925
EM: Round [337] log likelihood: -8280.127068
EM: Round [338] log likelihood: -8280.126216
EM: Round [339] log likelihood: -8280.125370
EM: Round [340] log likelihood: -8280.124529
EM: Round [341] log likelihood: -8280.123694
EM: Round [342] log likelihood: -8280.122864
EM: Round [343] log likelihood: -8280.122039
EM: Round [344] log likelihood: -8280.121220
EM: Round [345] log likelihood: -8280.120406
EM: Round [346] log likelihood: -8280.119598
EM: Round [347] log likelihood: -8280.118794
EM: Round [348] log likelihood: -8280.117996
EM: Round [349] log likelihood: -8280.117203
EM: Round [350] log likelihood: -8280.116415
EM: Round [351] log likelihood: -8280.115632
EM: Round [352] log likelihood: -8280.114854
EM: Round [353] log likelihood: -8280.114081
EM: Round [354] log likelihood: -8280.113313
EM: Round [355] log likelihood: -8280.112550
EM: Round [356] log likelihood: -8280.111792
EM: Round [357] log likelihood: -8280.111039
EM: Round [358] log likelihood: -8280.110290
EM: Round [359] log likelihood: -8280.109547
EM: Round [360] log likelihood: -8280.108808
EM: Round [361] log likelihood: -8280.108074
EM: Round [362] log likelihood: -8280.107344
EM: Round [363] log likelihood: -8280.106619
EM: Round [364] log likelihood: -8280.105899
EM: Round [365] log likelihood: -8280.105183
EM: Round [366] log likelihood: -8280.104472
EM: Round [367] log likelihood: -8280.103766
EM: Round [368] log likelihood: -8280.103063
EM: Round [369] log likelihood: -8280.102366
EM: Round [370] log likelihood: -8280.101673
EM: Round [371] log likelihood: -8280.100984
EM: Round [372] log likelihood: -8280.100299
EM: Round [373] log likelihood: -8280.099619
EM: Round [374] log likelihood: -8280.098943
EM: Round [375] log likelihood: -8280.098272
EM: Round [376] log likelihood: -8280.097604
EM: Round [377] log likelihood: -8280.096941
EM: Round [378] log likelihood: -8280.096282
EM: Round [379] log likelihood: -8280.095627
EM: Round [380] log likelihood: -8280.094977
EM: Round [381] log likelihood: -8280.094330
EM: Round [382] log likelihood: -8280.093688
EM: Round [383] log likelihood: -8280.093049
EM: Round [384] log likelihood: -8280.092415
EM: Round [385] log likelihood: -8280.091784
EM: Round [386] log likelihood: -8280.091158
EM: Round [387] log likelihood: -8280.090535
EM: Round [388] log likelihood: -8280.089916
EM: Round [389] log likelihood: -8280.089302
EM: Round [390] log likelihood: -8280.088691
EM: Round [391] log likelihood: -8280.088083
EM: Round [392] log likelihood: -8280.087480
EM: Round [393] log likelihood: -8280.086881
EM: Round [394] log likelihood: -8280.086285
EM: Round [395] log likelihood: -8280.085693
EM: Round [396] log likelihood: -8280.085104
EM: Round [397] log likelihood: -8280.084519
EM: Round [398] log likelihood: -8280.083938
EM: Round [399] log likelihood: -8280.083361
EM: Round [400] log likelihood: -8280.082787
EM: Round [401] log likelihood: -8280.082217
EM: Round [402] log likelihood: -8280.081650
EM: Round [403] log likelihood: -8280.081087
EM: Round [404] log likelihood: -8280.080527
EM: Round [405] log likelihood: -8280.079970
EM: Round [406] log likelihood: -8280.079418
EM: Round [407] log likelihood: -8280.078868
EM: Round [408] log likelihood: -8280.078322
EM: Round [409] log likelihood: -8280.077780
EM: Round [410] log likelihood: -8280.077240
EM: Round [411] log likelihood: -8280.076704
EM: Round [412] log likelihood: -8280.076172
EM: Round [413] log likelihood: -8280.075642
EM: Round [414] log likelihood: -8280.075116
EM: Round [415] log likelihood: -8280.074593
EM: Round [416] log likelihood: -8280.074074
EM: Round [417] log likelihood: -8280.073557
EM: Round [418] log likelihood: -8280.073044
EM: Round [419] log likelihood: -8280.072534
EM: Round [420] log likelihood: -8280.072027
EM: Round [421] log likelihood: -8280.071523
EM: Round [422] log likelihood: -8280.071023
EM: Round [423] log likelihood: -8280.070525
EM: Round [424] log likelihood: -8280.070030
EM: Round [425] log likelihood: -8280.069539
EM: Round [426] log likelihood: -8280.069050
EM: Round [427] log likelihood: -8280.068565
EM: Round [428] log likelihood: -8280.068082
EM: Round [429] log likelihood: -8280.067603
EM: Round [430] log likelihood: -8280.067126
EM: Round [431] log likelihood: -8280.066652
EM: Round [432] log likelihood: -8280.066182
EM: Round [433] log likelihood: -8280.065714
EM: Round [434] log likelihood: -8280.065249
EM: Round [435] log likelihood: -8280.064786
EM: Round [436] log likelihood: -8280.064327
EM: Round [437] log likelihood: -8280.063870
EM: Round [438] log likelihood: -8280.063416
EM: Round [439] log likelihood: -8280.062965
EM: Round [440] log likelihood: -8280.062517
EM: Round [441] log likelihood: -8280.062071
EM: Round [442] log likelihood: -8280.061629
EM: Round [443] log likelihood: -8280.061188
EM: Round [444] log likelihood: -8280.060751
EM: Round [445] log likelihood: -8280.060316
EM: Round [446] log likelihood: -8280.059884
EM: Round [447] log likelihood: -8280.059454
EM: Round [448] log likelihood: -8280.059027
EM: Round [449] log likelihood: -8280.058603
EM: Round [450] log likelihood: -8280.058181
EM: Round [451] log likelihood: -8280.057762
EM: Round [452] log likelihood: -8280.057345
EM: Round [453] log likelihood: -8280.056931
EM: Round [454] log likelihood: -8280.056519
EM: Round [455] log likelihood: -8280.056110
EM: Round [456] log likelihood: -8280.055704
EM: Round [457] log likelihood: -8280.055299
EM: Round [458] log likelihood: -8280.054898
EM: Round [459] log likelihood: -8280.054498
EM: Round [460] log likelihood: -8280.054101
EM: Round [461] log likelihood: -8280.053707
EM: Round [462] log likelihood: -8280.053315
EM: Round [463] log likelihood: -8280.052925
EM: Round [464] log likelihood: -8280.052538
EM: Round [465] log likelihood: -8280.052152
EM: Round [466] log likelihood: -8280.051770
EM: Round [467] log likelihood: -8280.051389
EM: Round [468] log likelihood: -8280.051011
EM: Round [469] log likelihood: -8280.050635
EM: Round [470] log likelihood: -8280.050262
EM: Round [471] log likelihood: -8280.049890
EM: Round [472] log likelihood: -8280.049521
EM: Round [473] log likelihood: -8280.049154
EM: Round [474] log likelihood: -8280.048789
EM: Round [475] log likelihood: -8280.048427
EM: Round [476] log likelihood: -8280.048067
EM: Round [477] log likelihood: -8280.047708
EM: Round [478] log likelihood: -8280.047352
EM: Round [479] log likelihood: -8280.046999
EM: Round [480] log likelihood: -8280.046647
EM: Round [481] log likelihood: -8280.046297
EM: Round [482] log likelihood: -8280.045950
EM: Round [483] log likelihood: -8280.045604
EM: Round [484] log likelihood: -8280.045261
EM: Round [485] log likelihood: -8280.044919
EM: Round [486] log likelihood: -8280.044580
EM: Round [487] log likelihood: -8280.044243
EM: Round [488] log likelihood: -8280.043908
EM: Round [489] log likelihood: -8280.043574
EM: Round [490] log likelihood: -8280.043243
EM: Round [491] log likelihood: -8280.042914
EM: Round [492] log likelihood: -8280.042586
EM: Round [493] log likelihood: -8280.042261
EM: Round [494] log likelihood: -8280.041938
EM: Round [495] log likelihood: -8280.041616
EM: Round [496] log likelihood: -8280.041297
EM: Round [497] log likelihood: -8280.040979
EM: Round [498] log likelihood: -8280.040663
EM: Round [499] log likelihood: -8280.040349
EM: Round [500] log likelihood: -8280.040037
EM: Round [501] log likelihood: -8280.039727
EM: Round [502] log likelihood: -8280.039419
EM: Round [503] log likelihood: -8280.039113
EM: Round [504] log likelihood: -8280.038808
EM: Round [505] log likelihood: -8280.038505
EM: Round [506] log likelihood: -8280.038204
EM: Round [507] log likelihood: -8280.037905
EM: Round [508] log likelihood: -8280.037607
EM: Round [509] log likelihood: -8280.037312
EM: Round [510] log likelihood: -8280.037018
EM: Round [511] log likelihood: -8280.036726
EM: Round [512] log likelihood: -8280.036435
EM: Round [513] log likelihood: -8280.036146
EM: Round [514] log likelihood: -8280.035859
EM: Round [515] log likelihood: -8280.035574
EM: Round [516] log likelihood: -8280.035291
EM: Round [517] log likelihood: -8280.035009
EM: Round [518] log likelihood: -8280.034728
EM: Round [519] log likelihood: -8280.034450
EM: Round [520] log likelihood: -8280.034173
EM: Round [521] log likelihood: -8280.033897
EM: Round [522] log likelihood: -8280.033624
EM: Round [523] log likelihood: -8280.033352
EM: Round [524] log likelihood: -8280.033081
EM: Round [525] log likelihood: -8280.032812
EM: Round [526] log likelihood: -8280.032545
EM: Round [527] log likelihood: -8280.032280
EM: Round [528] log likelihood: -8280.032015
EM: Round [529] log likelihood: -8280.031753
EM: Round [530] log likelihood: -8280.031492
EM: Round [531] log likelihood: -8280.031232
EM: Round [532] log likelihood: -8280.030975
EM: Round [533] log likelihood: -8280.030718
EM: Round [534] log likelihood: -8280.030463
EM: Round [535] log likelihood: -8280.030210
EM: Round [536] log likelihood: -8280.029958
EM: Round [537] log likelihood: -8280.029708
EM: Round [538] log likelihood: -8280.029459
EM: Round [539] log likelihood: -8280.029211
EM: Round [540] log likelihood: -8280.028965
EM: Round [541] log likelihood: -8280.028721
EM: Round [542] log likelihood: -8280.028478
EM: Round [543] log likelihood: -8280.028236
EM: Round [544] log likelihood: -8280.027996
EM: Round [545] log likelihood: -8280.027757
EM: Round [546] log likelihood: -8280.027520
EM: Round [547] log likelihood: -8280.027284
EM: Round [548] log likelihood: -8280.027049
EM: Round [549] log likelihood: -8280.026816
EM: Round [550] log likelihood: -8280.026584
EM: Round [551] log likelihood: -8280.026353
EM: Round [552] log likelihood: -8280.026124
EM: Round [553] log likelihood: -8280.025896
EM: Round [554] log likelihood: -8280.025670
EM: Round [555] log likelihood: -8280.025445
EM: Round [556] log likelihood: -8280.025221
EM: Round [557] log likelihood: -8280.024998
EM: Round [558] log likelihood: -8280.024777
EM: Round [559] log likelihood: -8280.024557
EM: Round [560] log likelihood: -8280.024339
EM: Round [561] log likelihood: -8280.024121
EM: Round [562] log likelihood: -8280.023905
EM: Round [563] log likelihood: -8280.023690
EM: Round [564] log likelihood: -8280.023477
EM: Round [565] log likelihood: -8280.023265
EM: Round [566] log likelihood: -8280.023054
EM: Round [567] log likelihood: -8280.022844
EM: Round [568] log likelihood: -8280.022635
EM: Round [569] log likelihood: -8280.022428
EM: Round [570] log likelihood: -8280.022222
EM: Round [571] log likelihood: -8280.022017
EM: Round [572] log likelihood: -8280.021813
EM: Round [573] log likelihood: -8280.021610
EM: Round [574] log likelihood: -8280.021409
EM: Round [575] log likelihood: -8280.021209
EM: Round [576] log likelihood: -8280.021010
EM: Round [577] log likelihood: -8280.020812
EM: Round [578] log likelihood: -8280.020615
EM: Round [579] log likelihood: -8280.020420
EM: Round [580] log likelihood: -8280.020226
EM: Round [581] log likelihood: -8280.020032
EM: Round [582] log likelihood: -8280.019840
EM: Round [583] log likelihood: -8280.019649
EM: Round [584] log likelihood: -8280.019459
EM: Round [585] log likelihood: -8280.019270
EM: Round [586] log likelihood: -8280.019083
EM: Round [587] log likelihood: -8280.018896
EM: Round [588] log likelihood: -8280.018711
EM: Round [589] log likelihood: -8280.018526
EM: Round [590] log likelihood: -8280.018343
EM: Round [591] log likelihood: -8280.018161
EM: Round [592] log likelihood: -8280.017979
EM: Round [593] log likelihood: -8280.017799
EM: Round [594] log likelihood: -8280.017620
EM: Round [595] log likelihood: -8280.017442
EM: Round [596] log likelihood: -8280.017265
EM: Round [597] log likelihood: -8280.017089
EM: Round [598] log likelihood: -8280.016914
EM: Round [599] log likelihood: -8280.016740
EM: Round [600] log likelihood: -8280.016567
EM: Round [601] log likelihood: -8280.016395
EM: Round [602] log likelihood: -8280.016224
EM: Round [603] log likelihood: -8280.016055
EM: Round [604] log likelihood: -8280.015886
EM: Round [605] log likelihood: -8280.015718
EM: Round [606] log likelihood: -8280.015551
EM: Round [607] log likelihood: -8280.015385
EM: Round [608] log likelihood: -8280.015220
EM: Round [609] log likelihood: -8280.015056
EM: Round [610] log likelihood: -8280.014892
EM: Round [611] log likelihood: -8280.014730
EM: Round [612] log likelihood: -8280.014569
EM: Round [613] log likelihood: -8280.014409
EM: Round [614] log likelihood: -8280.014249
EM: Round [615] log likelihood: -8280.014091
EM: Round [616] log likelihood: -8280.013933
EM: Round [617] log likelihood: -8280.013777
EM: Round [618] log likelihood: -8280.013621
EM: Round [619] log likelihood: -8280.013466
EM: Round [620] log likelihood: -8280.013312
EM: Round [621] log likelihood: -8280.013159
EM: Round [622] log likelihood: -8280.013007
EM: Round [623] log likelihood: -8280.012856
EM: Round [624] log likelihood: -8280.012706
EM: Round [625] log likelihood: -8280.012556
EM: Round [626] log likelihood: -8280.012407
EM: Round [627] log likelihood: -8280.012260
EM: Round [628] log likelihood: -8280.012113
EM: Round [629] log likelihood: -8280.011967
EM: Round [630] log likelihood: -8280.011822
EM: Round [631] log likelihood: -8280.011677
EM: Round [632] log likelihood: -8280.011534
EM: Round [633] log likelihood: -8280.011391
EM: Round [634] log likelihood: -8280.011249
EM: Round [635] log likelihood: -8280.011108
EM: Round [636] log likelihood: -8280.010968
EM: Round [637] log likelihood: -8280.010828
EM: Round [638] log likelihood: -8280.010690
EM: Round [639] log likelihood: -8280.010552
EM: Round [640] log likelihood: -8280.010415
EM: Round [641] log likelihood: -8280.010279
EM: Round [642] log likelihood: -8280.010143
EM: Round [643] log likelihood: -8280.010009
EM: Round [644] log likelihood: -8280.009875
EM: Round [645] log likelihood: -8280.009742
EM: Round [646] log likelihood: -8280.009609
EM: Round [647] log likelihood: -8280.009478
EM: Round [648] log likelihood: -8280.009347
EM: Round [649] log likelihood: -8280.009217
EM: Round [650] log likelihood: -8280.009088
EM: Round [651] log likelihood: -8280.008959
EM: Round [652] log likelihood: -8280.008831
EM: Round [653] log likelihood: -8280.008704
EM: Round [654] log likelihood: -8280.008578
EM: Round [655] log likelihood: -8280.008452
EM: Round [656] log likelihood: -8280.008327
EM: Round [657] log likelihood: -8280.008203
EM: Round [658] log likelihood: -8280.008080
EM: Round [659] log likelihood: -8280.007957
EM: Round [660] log likelihood: -8280.007835
EM: Round [661] log likelihood: -8280.007714
EM: Round [662] log likelihood: -8280.007593
EM: Round [663] log likelihood: -8280.007473
EM: Round [664] log likelihood: -8280.007354
EM: Round [665] log likelihood: -8280.007235
EM: Round [666] log likelihood: -8280.007117
EM: Round [667] log likelihood: -8280.007000
EM: Round [668] log likelihood: -8280.006884
EM: Round [669] log likelihood: -8280.006768
EM: Round [670] log likelihood: -8280.006653
EM: Round [671] log likelihood: -8280.006538
EM: Round [672] log likelihood: -8280.006424
EM: Round [673] log likelihood: -8280.006311
EM: Round [674] log likelihood: -8280.006199
EM: Round [675] log likelihood: -8280.006087
EM: Round [676] log likelihood: -8280.005976
EM: Round [677] log likelihood: -8280.005865
EM: Round [678] log likelihood: -8280.005755
EM: Round [679] log likelihood: -8280.005646
EM: Round [680] log likelihood: -8280.005537
EM: Round [681] log likelihood: -8280.005429
EM: Round [682] log likelihood: -8280.005322
EM: Round [683] log likelihood: -8280.005215
EM: Round [684] log likelihood: -8280.005108
EM: Round [685] log likelihood: -8280.005003
EM: Round [686] log likelihood: -8280.004898
EM: Round [687] log likelihood: -8280.004793
EM: Round [688] log likelihood: -8280.004690
EM: Round [689] log likelihood: -8280.004587
EM: Round [690] log likelihood: -8280.004484
EM: Round [691] log likelihood: -8280.004382
EM: Round [692] log likelihood: -8280.004280
EM: Round [693] log likelihood: -8280.004180
EM: Round [694] log likelihood: -8280.004079
EM: Round [695] log likelihood: -8280.003980
EM: Stopping iterations at round 695 due to insufficient improvement in likelihood.
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.WpLJscJaA8/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.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.WpLJscJaA8/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.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.junction_reads.bam"
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.junction_reads.bam
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.junction_reads.bam > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.junction_reads.bam > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.junction_reads.bam.bed
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/tih_rna_sample_00462_B23WHTKLT4_2.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.junction_reads.bam.bed > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.junction_reads.bam.bed > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/tih_rna_sample_00462_B23WHTKLT4_2.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/tih_rna_sample_00462_B23WHTKLT4_2.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/tih_rna_sample_00462_B23WHTKLT4_2.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.spanning_reads.bam
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.spanning_reads.bam || : 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.spanning_reads.bam || : 
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.spanning_reads.bam
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.spanning_reads.bam > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.spanning_reads.bam > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.spanning_reads.bam.bed
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/tih_rna_sample_00462_B23WHTKLT4_2.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.spanning_reads.bam.bed > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.spanning_reads.bam.bed > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/tih_rna_sample_00462_B23WHTKLT4_2.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/tih_rna_sample_00462_B23WHTKLT4_2.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/tih_rna_sample_00462_B23WHTKLT4_2.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.consolidated.bam
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.consolidated.bam
Execution Time = 0.07 minutes. CMD: samtools index /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.consolidated.bam
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.consolidated.bam into /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.consolidated.bam.read_coords

CMD: touch /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.consolidated.bam.read_coords > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.consolidated.bam.frag_coords.coord_sorted
Execution Time = 1.65 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.WpLJscJaA8/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.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.igv.FusionJuncSpan
Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.igv.FusionJuncSpan
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.igv.Pfam.gff3 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.igv.Pfam.gff3 
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.igv.Pfam.gff3 > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.igv.Pfam.gff3 > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.igv.Pfam.bed
Running: touch /tmp/nxf.WpLJscJaA8/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.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.igv.seqsimilar.gff3 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.igv.seqsimilar.bed
Running: touch /tmp/nxf.WpLJscJaA8/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.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.fa > /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.fa > /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter  --genome_lib_dir ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 50 
CMD: cp /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.post_blast_and_promiscuity_filter
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.WpLJscJaA8/fi_workdir/tih_rna_sample_00462_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.WpLJscJaA8/ctat_genome_lib_build_dir
-done, see /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.WpLJscJaA8/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -6563.619101
EM: Round [1] log likelihood: -6563.450412
EM: Round [2] log likelihood: -6563.450029
EM: Round [3] log likelihood: -6563.450022
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.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2_1.fastp.fastq.gz: 296084088
Execution Time = 6.09 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.fa --gtf /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.gtf  > /tmp/nxf.WpLJscJaA8/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.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.fa --gtf /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.gtf  > /tmp/nxf.WpLJscJaA8/fi_workdir/microH.dat
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.WpLJscJaA8/fi_workdir/microH.dat /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.WpLJscJaA8/fi_workdir/microH.dat /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.WpLJscJaA8 --json_outfile /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.fusion_inspector_web.json --file_prefix tih_rna_sample_00462_B23WHTKLT4_2
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.WpLJscJaA8 --json_outfile /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.fusion_inspector_web.json --file_prefix tih_rna_sample_00462_B23WHTKLT4_2
Running: touch /tmp/nxf.WpLJscJaA8/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.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00462_B23WHTKLT4_2 --html_output /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00462_B23WHTKLT4_2 --html_output /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.fusion_inspector_web.html
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.WpLJscJaA8/ctat_genome_lib_build_dir > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.WpLJscJaA8/ctat_genome_lib_build_dir > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.WpLJscJaA8/ctat_genome_lib_build_dir > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000230305.2]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [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 [ENSG00000253730.1]
WARNING, no entry stored in dbm for [ENSG00000227963.1]
WARNING, no entry stored in dbm for [ENSG00000278212.2]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.WpLJscJaA8/ctat_genome_lib_build_dir > /tmp/nxf.WpLJscJaA8/tih_rna_sample_00462_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.WpLJscJaA8/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory