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/db/5f8f1fa6f6349d23d679d0e69e25b6/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/5f8f1fa6f6349d23d679d0e69e25b6/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/8484a4abd3fff18b10ebb14514a352/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/8c5c614ebc4fb9b2d2925ad3c5d891/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/8484a4abd3fff18b10ebb14514a352/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusionreport.tsv --gtf /tmp/nxf.FBo812kcg8/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.FBo812kcg8/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusionreport.tsv --gtf /tmp/nxf.FBo812kcg8/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.FBo812kcg8/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf > /tmp/nxf.FBo812kcg8/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf > /tmp/nxf.FBo812kcg8/cytoBand.txt
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.bed
-parsing GTF file: /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.bed
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.bed > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.bed > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.FBo812kcg8/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star --out_dir /tmp/nxf.FBo812kcg8/fi_workdir --reads "/tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.FBo812kcg8/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.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:15:29 ..... started STAR run
Jun 08 10:15:29 ..... loading genome
Jun 08 10:17:14 ... generating Suffix Array index
Jun 08 10:21:05 ... completed Suffix Array index
Jun 08 10:21:05 ..... processing annotations GTF
Jun 08 10:21:06 ..... inserting junctions into the genome indices
Jun 08 10:22:07 ..... started mapping
Jun 08 11:49:11 ..... finished mapping
Jun 08 11:49:12 ..... started sorting BAM
Jun 08 11:49:13 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
Execution Time = 93.74 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.FBo812kcg8/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star --out_dir /tmp/nxf.FBo812kcg8/fi_workdir --reads "/tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:49:17 : INFO : Done.
Execution Time = 0.06 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.FBo812kcg8/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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf
-parsing /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam
[10000]
[20000]
[30000]
[40000]
[50000]
[60000]
[70000]
[80000]
[90000]
[100000]
[110000]
[120000]
[130000]
[140000]
[150000]
[160000]
[170000]
[180000]
[190000]
[200000]
[210000]
[220000]
[230000]
[240000]
[250000]
[260000]
[270000]
[280000]
[290000]
[300000]
[310000]
[320000]
[330000]
[340000]
[350000]
[360000]
[370000]
[380000]
[390000]
[400000]
[410000]
[420000]
[430000]
[440000]
[450000]
[460000]
[470000]
[480000]
[490000]
[500000]
[510000]
[520000]
[530000]
[540000]
[550000]
[560000]
[570000]
[580000]
[590000]
[600000]
[610000]
[620000]
[630000]
[640000] -done parsing /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'per_id < 96' => 1747,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 8,
' ** passed ** ' => 8697,
'num genes matched < 2' => 24,
'num_hits: 10 != num_counted_on_fusion_contigs 9 ' => 18,
'low complexity anchor region' => 7,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 3,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 17,
'small anchor length' => 36,
'exons hit < 2' => 4,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 4,
'seq-similar region overlap' => 350,
'excessive soft clipping' => 3440,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6
};
-writing fusion junction support info.
Execution Time = 0.33 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.FBo812kcg8/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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000] -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000] -fusion SPANNING read extraction for scaff: AC079781.4--ASNS
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1
[1000]
[2000]
[3000] -fusion SPANNING read extraction for scaff: KLRC4--KLRK1
[1000]
[2000]
[3000]
[4000] -fusion SPANNING read extraction for scaff: LHFPL5--CLPSL1
[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: PCDHA10--PCDHAC1
[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] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
[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] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13
[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: PCDHA6--PCDHAC1
[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: PCDHA6--PCDHAC2
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000]
[21000]
[22000]
[23000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13
[1000]
[2000]
[3000]
[4000]
[5000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7
[1000]
[2000]
[3000]
[4000]
[5000] -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]
[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] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12
[1000]
[2000]
[3000]
[4000]
[5000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
[1000]
[2000]
[3000]
[4000]
[5000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
[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] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000] -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]
[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] -fusion SPANNING read extraction for scaff: PDCL--RC3H2
[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] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
[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: 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]
[22000]
[23000]
[24000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 34002,
'lacks exon overlap' => 1963
};
Execution Time = 0.73 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.FBo812kcg8/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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -5646.071269
EM: Round [1] log likelihood: -5642.783408
EM: Round [2] log likelihood: -5641.809488
EM: Round [3] log likelihood: -5641.028046
EM: Round [4] log likelihood: -5640.379261
EM: Round [5] log likelihood: -5639.828661
EM: Round [6] log likelihood: -5639.353353
EM: Round [7] log likelihood: -5638.937372
EM: Round [8] log likelihood: -5638.569177
EM: Round [9] log likelihood: -5638.240193
EM: Round [10] log likelihood: -5637.943903
EM: Round [11] log likelihood: -5637.675257
EM: Round [12] log likelihood: -5637.430278
EM: Round [13] log likelihood: -5637.205783
EM: Round [14] log likelihood: -5636.999191
EM: Round [15] log likelihood: -5636.808379
EM: Round [16] log likelihood: -5636.631582
EM: Round [17] log likelihood: -5636.467315
EM: Round [18] log likelihood: -5636.314315
EM: Round [19] log likelihood: -5636.171500
EM: Round [20] log likelihood: -5636.037930
EM: Round [21] log likelihood: -5635.912789
EM: Round [22] log likelihood: -5635.795358
EM: Round [23] log likelihood: -5635.685001
EM: Round [24] log likelihood: -5635.581153
EM: Round [25] log likelihood: -5635.483310
EM: Round [26] log likelihood: -5635.391018
EM: Round [27] log likelihood: -5635.303869
EM: Round [28] log likelihood: -5635.221492
EM: Round [29] log likelihood: -5635.143552
EM: Round [30] log likelihood: -5635.069743
EM: Round [31] log likelihood: -5634.999786
EM: Round [32] log likelihood: -5634.933424
EM: Round [33] log likelihood: -5634.870423
EM: Round [34] log likelihood: -5634.810568
EM: Round [35] log likelihood: -5634.753658
EM: Round [36] log likelihood: -5634.699510
EM: Round [37] log likelihood: -5634.647955
EM: Round [38] log likelihood: -5634.598834
EM: Round [39] log likelihood: -5634.552002
EM: Round [40] log likelihood: -5634.507322
EM: Round [41] log likelihood: -5634.464668
EM: Round [42] log likelihood: -5634.423924
EM: Round [43] log likelihood: -5634.384978
EM: Round [44] log likelihood: -5634.347730
EM: Round [45] log likelihood: -5634.312082
EM: Round [46] log likelihood: -5634.277946
EM: Round [47] log likelihood: -5634.245239
EM: Round [48] log likelihood: -5634.213881
EM: Round [49] log likelihood: -5634.183799
EM: Round [50] log likelihood: -5634.154925
EM: Round [51] log likelihood: -5634.127194
EM: Round [52] log likelihood: -5634.100545
EM: Round [53] log likelihood: -5634.074922
EM: Round [54] log likelihood: -5634.050269
EM: Round [55] log likelihood: -5634.026538
EM: Round [56] log likelihood: -5634.003681
EM: Round [57] log likelihood: -5633.981653
EM: Round [58] log likelihood: -5633.960412
EM: Round [59] log likelihood: -5633.939918
EM: Round [60] log likelihood: -5633.920135
EM: Round [61] log likelihood: -5633.901026
EM: Round [62] log likelihood: -5633.882559
EM: Round [63] log likelihood: -5633.864703
EM: Round [64] log likelihood: -5633.847427
EM: Round [65] log likelihood: -5633.830704
EM: Round [66] log likelihood: -5633.814508
EM: Round [67] log likelihood: -5633.798813
EM: Round [68] log likelihood: -5633.783597
EM: Round [69] log likelihood: -5633.768837
EM: Round [70] log likelihood: -5633.754511
EM: Round [71] log likelihood: -5633.740600
EM: Round [72] log likelihood: -5633.727086
EM: Round [73] log likelihood: -5633.713950
EM: Round [74] log likelihood: -5633.701175
EM: Round [75] log likelihood: -5633.688747
EM: Round [76] log likelihood: -5633.676648
EM: Round [77] log likelihood: -5633.664866
EM: Round [78] log likelihood: -5633.653387
EM: Round [79] log likelihood: -5633.642197
EM: Round [80] log likelihood: -5633.631286
EM: Round [81] log likelihood: -5633.620640
EM: Round [82] log likelihood: -5633.610250
EM: Round [83] log likelihood: -5633.600104
EM: Round [84] log likelihood: -5633.590194
EM: Round [85] log likelihood: -5633.580509
EM: Round [86] log likelihood: -5633.571041
EM: Round [87] log likelihood: -5633.561781
EM: Round [88] log likelihood: -5633.552722
EM: Round [89] log likelihood: -5633.543855
EM: Round [90] log likelihood: -5633.535174
EM: Round [91] log likelihood: -5633.526672
EM: Round [92] log likelihood: -5633.518342
EM: Round [93] log likelihood: -5633.510177
EM: Round [94] log likelihood: -5633.502173
EM: Round [95] log likelihood: -5633.494323
EM: Round [96] log likelihood: -5633.486623
EM: Round [97] log likelihood: -5633.479066
EM: Round [98] log likelihood: -5633.471648
EM: Round [99] log likelihood: -5633.464365
EM: Round [100] log likelihood: -5633.457211
EM: Round [101] log likelihood: -5633.450184
EM: Round [102] log likelihood: -5633.443278
EM: Round [103] log likelihood: -5633.436491
EM: Round [104] log likelihood: -5633.429817
EM: Round [105] log likelihood: -5633.423255
EM: Round [106] log likelihood: -5633.416799
EM: Round [107] log likelihood: -5633.410448
EM: Round [108] log likelihood: -5633.404199
EM: Round [109] log likelihood: -5633.398047
EM: Round [110] log likelihood: -5633.391991
EM: Round [111] log likelihood: -5633.386028
EM: Round [112] log likelihood: -5633.380156
EM: Round [113] log likelihood: -5633.374371
EM: Round [114] log likelihood: -5633.368671
EM: Round [115] log likelihood: -5633.363055
EM: Round [116] log likelihood: -5633.357519
EM: Round [117] log likelihood: -5633.352063
EM: Round [118] log likelihood: -5633.346683
EM: Round [119] log likelihood: -5633.341379
EM: Round [120] log likelihood: -5633.336148
EM: Round [121] log likelihood: -5633.330988
EM: Round [122] log likelihood: -5633.325898
EM: Round [123] log likelihood: -5633.320876
EM: Round [124] log likelihood: -5633.315921
EM: Round [125] log likelihood: -5633.311030
EM: Round [126] log likelihood: -5633.306203
EM: Round [127] log likelihood: -5633.301439
EM: Round [128] log likelihood: -5633.296735
EM: Round [129] log likelihood: -5633.292090
EM: Round [130] log likelihood: -5633.287504
EM: Round [131] log likelihood: -5633.282975
EM: Round [132] log likelihood: -5633.278501
EM: Round [133] log likelihood: -5633.274083
EM: Round [134] log likelihood: -5633.269717
EM: Round [135] log likelihood: -5633.265405
EM: Round [136] log likelihood: -5633.261144
EM: Round [137] log likelihood: -5633.256933
EM: Round [138] log likelihood: -5633.252772
EM: Round [139] log likelihood: -5633.248659
EM: Round [140] log likelihood: -5633.244594
EM: Round [141] log likelihood: -5633.240576
EM: Round [142] log likelihood: -5633.236604
EM: Round [143] log likelihood: -5633.232677
EM: Round [144] log likelihood: -5633.228794
EM: Round [145] log likelihood: -5633.224954
EM: Round [146] log likelihood: -5633.221158
EM: Round [147] log likelihood: -5633.217403
EM: Round [148] log likelihood: -5633.213690
EM: Round [149] log likelihood: -5633.210018
EM: Round [150] log likelihood: -5633.206385
EM: Round [151] log likelihood: -5633.202792
EM: Round [152] log likelihood: -5633.199237
EM: Round [153] log likelihood: -5633.195721
EM: Round [154] log likelihood: -5633.192242
EM: Round [155] log likelihood: -5633.188799
EM: Round [156] log likelihood: -5633.185393
EM: Round [157] log likelihood: -5633.182023
EM: Round [158] log likelihood: -5633.178687
EM: Round [159] log likelihood: -5633.175387
EM: Round [160] log likelihood: -5633.172120
EM: Round [161] log likelihood: -5633.168887
EM: Round [162] log likelihood: -5633.165687
EM: Round [163] log likelihood: -5633.162519
EM: Round [164] log likelihood: -5633.159384
EM: Round [165] log likelihood: -5633.156280
EM: Round [166] log likelihood: -5633.153207
EM: Round [167] log likelihood: -5633.150165
EM: Round [168] log likelihood: -5633.147154
EM: Round [169] log likelihood: -5633.144172
EM: Round [170] log likelihood: -5633.141219
EM: Round [171] log likelihood: -5633.138296
EM: Round [172] log likelihood: -5633.135401
EM: Round [173] log likelihood: -5633.132535
EM: Round [174] log likelihood: -5633.129696
EM: Round [175] log likelihood: -5633.126884
EM: Round [176] log likelihood: -5633.124100
EM: Round [177] log likelihood: -5633.121343
EM: Round [178] log likelihood: -5633.118612
EM: Round [179] log likelihood: -5633.115907
EM: Round [180] log likelihood: -5633.113227
EM: Round [181] log likelihood: -5633.110573
EM: Round [182] log likelihood: -5633.107944
EM: Round [183] log likelihood: -5633.105340
EM: Round [184] log likelihood: -5633.102760
EM: Round [185] log likelihood: -5633.100204
EM: Round [186] log likelihood: -5633.097672
EM: Round [187] log likelihood: -5633.095163
EM: Round [188] log likelihood: -5633.092677
EM: Round [189] log likelihood: -5633.090214
EM: Round [190] log likelihood: -5633.087774
EM: Round [191] log likelihood: -5633.085356
EM: Round [192] log likelihood: -5633.082961
EM: Round [193] log likelihood: -5633.080586
EM: Round [194] log likelihood: -5633.078234
EM: Round [195] log likelihood: -5633.075902
EM: Round [196] log likelihood: -5633.073592
EM: Round [197] log likelihood: -5633.071302
EM: Round [198] log likelihood: -5633.069033
EM: Round [199] log likelihood: -5633.066784
EM: Round [200] log likelihood: -5633.064555
EM: Round [201] log likelihood: -5633.062345
EM: Round [202] log likelihood: -5633.060155
EM: Round [203] log likelihood: -5633.057985
EM: Round [204] log likelihood: -5633.055833
EM: Round [205] log likelihood: -5633.053700
EM: Round [206] log likelihood: -5633.051586
EM: Round [207] log likelihood: -5633.049490
EM: Round [208] log likelihood: -5633.047413
EM: Round [209] log likelihood: -5633.045353
EM: Round [210] log likelihood: -5633.043311
EM: Round [211] log likelihood: -5633.041287
EM: Round [212] log likelihood: -5633.039280
EM: Round [213] log likelihood: -5633.037290
EM: Round [214] log likelihood: -5633.035317
EM: Round [215] log likelihood: -5633.033361
EM: Round [216] log likelihood: -5633.031422
EM: Round [217] log likelihood: -5633.029498
EM: Round [218] log likelihood: -5633.027591
EM: Round [219] log likelihood: -5633.025700
EM: Round [220] log likelihood: -5633.023825
EM: Round [221] log likelihood: -5633.021966
EM: Round [222] log likelihood: -5633.020122
EM: Round [223] log likelihood: -5633.018293
EM: Round [224] log likelihood: -5633.016480
EM: Round [225] log likelihood: -5633.014682
EM: Round [226] log likelihood: -5633.012898
EM: Round [227] log likelihood: -5633.011129
EM: Round [228] log likelihood: -5633.009375
EM: Round [229] log likelihood: -5633.007634
EM: Round [230] log likelihood: -5633.005909
EM: Round [231] log likelihood: -5633.004197
EM: Round [232] log likelihood: -5633.002499
EM: Round [233] log likelihood: -5633.000815
EM: Round [234] log likelihood: -5632.999144
EM: Round [235] log likelihood: -5632.997487
EM: Round [236] log likelihood: -5632.995843
EM: Round [237] log likelihood: -5632.994212
EM: Round [238] log likelihood: -5632.992595
EM: Round [239] log likelihood: -5632.990990
EM: Round [240] log likelihood: -5632.989398
EM: Round [241] log likelihood: -5632.987819
EM: Round [242] log likelihood: -5632.986252
EM: Round [243] log likelihood: -5632.984697
EM: Round [244] log likelihood: -5632.983155
EM: Round [245] log likelihood: -5632.981625
EM: Round [246] log likelihood: -5632.980107
EM: Round [247] log likelihood: -5632.978600
EM: Round [248] log likelihood: -5632.977106
EM: Round [249] log likelihood: -5632.975623
EM: Round [250] log likelihood: -5632.974151
EM: Round [251] log likelihood: -5632.972691
EM: Round [252] log likelihood: -5632.971242
EM: Round [253] log likelihood: -5632.969805
EM: Round [254] log likelihood: -5632.968378
EM: Round [255] log likelihood: -5632.966962
EM: Round [256] log likelihood: -5632.965558
EM: Round [257] log likelihood: -5632.964163
EM: Round [258] log likelihood: -5632.962780
EM: Round [259] log likelihood: -5632.961407
EM: Round [260] log likelihood: -5632.960044
EM: Round [261] log likelihood: -5632.958692
EM: Round [262] log likelihood: -5632.957350
EM: Round [263] log likelihood: -5632.956017
EM: Round [264] log likelihood: -5632.954695
EM: Round [265] log likelihood: -5632.953383
EM: Round [266] log likelihood: -5632.952081
EM: Round [267] log likelihood: -5632.950788
EM: Round [268] log likelihood: -5632.949505
EM: Round [269] log likelihood: -5632.948231
EM: Round [270] log likelihood: -5632.946967
EM: Round [271] log likelihood: -5632.945712
EM: Round [272] log likelihood: -5632.944466
EM: Round [273] log likelihood: -5632.943230
EM: Round [274] log likelihood: -5632.942002
EM: Round [275] log likelihood: -5632.940784
EM: Round [276] log likelihood: -5632.939574
EM: Round [277] log likelihood: -5632.938373
EM: Round [278] log likelihood: -5632.937181
EM: Round [279] log likelihood: -5632.935997
EM: Round [280] log likelihood: -5632.934822
EM: Round [281] log likelihood: -5632.933656
EM: Round [282] log likelihood: -5632.932498
EM: Round [283] log likelihood: -5632.931348
EM: Round [284] log likelihood: -5632.930206
EM: Round [285] log likelihood: -5632.929073
EM: Round [286] log likelihood: -5632.927948
EM: Round [287] log likelihood: -5632.926830
EM: Round [288] log likelihood: -5632.925721
EM: Round [289] log likelihood: -5632.924619
EM: Round [290] log likelihood: -5632.923525
EM: Round [291] log likelihood: -5632.922439
EM: Round [292] log likelihood: -5632.921361
EM: Round [293] log likelihood: -5632.920290
EM: Round [294] log likelihood: -5632.919226
EM: Round [295] log likelihood: -5632.918170
EM: Round [296] log likelihood: -5632.917122
EM: Round [297] log likelihood: -5632.916080
EM: Round [298] log likelihood: -5632.915046
EM: Round [299] log likelihood: -5632.914019
EM: Round [300] log likelihood: -5632.912999
EM: Round [301] log likelihood: -5632.911986
EM: Round [302] log likelihood: -5632.910980
EM: Round [303] log likelihood: -5632.909981
EM: Round [304] log likelihood: -5632.908989
EM: Round [305] log likelihood: -5632.908004
EM: Round [306] log likelihood: -5632.907025
EM: Round [307] log likelihood: -5632.906053
EM: Round [308] log likelihood: -5632.905087
EM: Round [309] log likelihood: -5632.904129
EM: Round [310] log likelihood: -5632.903176
EM: Round [311] log likelihood: -5632.902230
EM: Round [312] log likelihood: -5632.901290
EM: Round [313] log likelihood: -5632.900357
EM: Round [314] log likelihood: -5632.899430
EM: Round [315] log likelihood: -5632.898509
EM: Round [316] log likelihood: -5632.897594
EM: Round [317] log likelihood: -5632.896686
EM: Round [318] log likelihood: -5632.895783
EM: Round [319] log likelihood: -5632.894886
EM: Round [320] log likelihood: -5632.893996
EM: Round [321] log likelihood: -5632.893111
EM: Round [322] log likelihood: -5632.892232
EM: Round [323] log likelihood: -5632.891358
EM: Round [324] log likelihood: -5632.890491
EM: Round [325] log likelihood: -5632.889629
EM: Round [326] log likelihood: -5632.888773
EM: Round [327] log likelihood: -5632.887922
EM: Round [328] log likelihood: -5632.887077
EM: Round [329] log likelihood: -5632.886237
EM: Round [330] log likelihood: -5632.885403
EM: Round [331] log likelihood: -5632.884574
EM: Round [332] log likelihood: -5632.883751
EM: Round [333] log likelihood: -5632.882933
EM: Round [334] log likelihood: -5632.882120
EM: Round [335] log likelihood: -5632.881312
EM: Round [336] log likelihood: -5632.880510
EM: Round [337] log likelihood: -5632.879712
EM: Round [338] log likelihood: -5632.878920
EM: Round [339] log likelihood: -5632.878133
EM: Round [340] log likelihood: -5632.877350
EM: Round [341] log likelihood: -5632.876573
EM: Round [342] log likelihood: -5632.875801
EM: Round [343] log likelihood: -5632.875033
EM: Round [344] log likelihood: -5632.874270
EM: Round [345] log likelihood: -5632.873512
EM: Round [346] log likelihood: -5632.872759
EM: Round [347] log likelihood: -5632.872011
EM: Round [348] log likelihood: -5632.871267
EM: Round [349] log likelihood: -5632.870528
EM: Round [350] log likelihood: -5632.869793
EM: Round [351] log likelihood: -5632.869063
EM: Round [352] log likelihood: -5632.868338
EM: Round [353] log likelihood: -5632.867617
EM: Round [354] log likelihood: -5632.866900
EM: Round [355] log likelihood: -5632.866188
EM: Round [356] log likelihood: -5632.865480
EM: Round [357] log likelihood: -5632.864777
EM: Round [358] log likelihood: -5632.864078
EM: Round [359] log likelihood: -5632.863383
EM: Round [360] log likelihood: -5632.862692
EM: Round [361] log likelihood: -5632.862006
EM: Round [362] log likelihood: -5632.861324
EM: Round [363] log likelihood: -5632.860646
EM: Round [364] log likelihood: -5632.859972
EM: Round [365] log likelihood: -5632.859302
EM: Round [366] log likelihood: -5632.858636
EM: Round [367] log likelihood: -5632.857974
EM: Round [368] log likelihood: -5632.857316
EM: Round [369] log likelihood: -5632.856662
EM: Round [370] log likelihood: -5632.856012
EM: Round [371] log likelihood: -5632.855366
EM: Round [372] log likelihood: -5632.854724
EM: Round [373] log likelihood: -5632.854086
EM: Round [374] log likelihood: -5632.853451
EM: Round [375] log likelihood: -5632.852820
EM: Round [376] log likelihood: -5632.852193
EM: Round [377] log likelihood: -5632.851569
EM: Round [378] log likelihood: -5632.850950
EM: Round [379] log likelihood: -5632.850334
EM: Round [380] log likelihood: -5632.849721
EM: Round [381] log likelihood: -5632.849112
EM: Round [382] log likelihood: -5632.848507
EM: Round [383] log likelihood: -5632.847905
EM: Round [384] log likelihood: -5632.847307
EM: Round [385] log likelihood: -5632.846712
EM: Round [386] log likelihood: -5632.846120
EM: Round [387] log likelihood: -5632.845533
EM: Round [388] log likelihood: -5632.844948
EM: Round [389] log likelihood: -5632.844367
EM: Round [390] log likelihood: -5632.843789
EM: Round [391] log likelihood: -5632.843215
EM: Round [392] log likelihood: -5632.842644
EM: Round [393] log likelihood: -5632.842076
EM: Round [394] log likelihood: -5632.841511
EM: Round [395] log likelihood: -5632.840950
EM: Round [396] log likelihood: -5632.840392
EM: Round [397] log likelihood: -5632.839837
EM: Round [398] log likelihood: -5632.839285
EM: Round [399] log likelihood: -5632.838736
EM: Round [400] log likelihood: -5632.838191
EM: Round [401] log likelihood: -5632.837648
EM: Round [402] log likelihood: -5632.837109
EM: Round [403] log likelihood: -5632.836572
EM: Round [404] log likelihood: -5632.836039
EM: Round [405] log likelihood: -5632.835509
EM: Round [406] log likelihood: -5632.834981
EM: Round [407] log likelihood: -5632.834457
EM: Round [408] log likelihood: -5632.833935
EM: Round [409] log likelihood: -5632.833417
EM: Round [410] log likelihood: -5632.832901
EM: Round [411] log likelihood: -5632.832388
EM: Round [412] log likelihood: -5632.831878
EM: Round [413] log likelihood: -5632.831371
EM: Round [414] log likelihood: -5632.830867
EM: Round [415] log likelihood: -5632.830365
EM: Round [416] log likelihood: -5632.829867
EM: Round [417] log likelihood: -5632.829371
EM: Round [418] log likelihood: -5632.828877
EM: Round [419] log likelihood: -5632.828387
EM: Round [420] log likelihood: -5632.827899
EM: Round [421] log likelihood: -5632.827414
EM: Round [422] log likelihood: -5632.826931
EM: Round [423] log likelihood: -5632.826451
EM: Round [424] log likelihood: -5632.825974
EM: Round [425] log likelihood: -5632.825500
EM: Round [426] log likelihood: -5632.825027
EM: Round [427] log likelihood: -5632.824558
EM: Round [428] log likelihood: -5632.824091
EM: Round [429] log likelihood: -5632.823627
EM: Round [430] log likelihood: -5632.823165
EM: Round [431] log likelihood: -5632.822705
EM: Round [432] log likelihood: -5632.822248
EM: Round [433] log likelihood: -5632.821794
EM: Round [434] log likelihood: -5632.821342
EM: Round [435] log likelihood: -5632.820892
EM: Round [436] log likelihood: -5632.820445
EM: Round [437] log likelihood: -5632.820000
EM: Round [438] log likelihood: -5632.819557
EM: Round [439] log likelihood: -5632.819117
EM: Round [440] log likelihood: -5632.818679
EM: Round [441] log likelihood: -5632.818244
EM: Round [442] log likelihood: -5632.817811
EM: Round [443] log likelihood: -5632.817380
EM: Round [444] log likelihood: -5632.816952
EM: Round [445] log likelihood: -5632.816525
EM: Round [446] log likelihood: -5632.816101
EM: Round [447] log likelihood: -5632.815679
EM: Round [448] log likelihood: -5632.815260
EM: Round [449] log likelihood: -5632.814842
EM: Round [450] log likelihood: -5632.814427
EM: Round [451] log likelihood: -5632.814014
EM: Round [452] log likelihood: -5632.813603
EM: Round [453] log likelihood: -5632.813195
EM: Round [454] log likelihood: -5632.812788
EM: Round [455] log likelihood: -5632.812384
EM: Round [456] log likelihood: -5632.811981
EM: Round [457] log likelihood: -5632.811581
EM: Round [458] log likelihood: -5632.811183
EM: Round [459] log likelihood: -5632.810787
EM: Round [460] log likelihood: -5632.810393
EM: Round [461] log likelihood: -5632.810001
EM: Round [462] log likelihood: -5632.809611
EM: Round [463] log likelihood: -5632.809223
EM: Round [464] log likelihood: -5632.808837
EM: Round [465] log likelihood: -5632.808453
EM: Round [466] log likelihood: -5632.808071
EM: Round [467] log likelihood: -5632.807690
EM: Round [468] log likelihood: -5632.807312
EM: Round [469] log likelihood: -5632.806936
EM: Round [470] log likelihood: -5632.806562
EM: Round [471] log likelihood: -5632.806189
EM: Round [472] log likelihood: -5632.805819
EM: Round [473] log likelihood: -5632.805450
EM: Round [474] log likelihood: -5632.805084
EM: Round [475] log likelihood: -5632.804719
EM: Round [476] log likelihood: -5632.804356
EM: Round [477] log likelihood: -5632.803994
EM: Round [478] log likelihood: -5632.803635
EM: Round [479] log likelihood: -5632.803278
EM: Round [480] log likelihood: -5632.802922
EM: Round [481] log likelihood: -5632.802568
EM: Round [482] log likelihood: -5632.802216
EM: Round [483] log likelihood: -5632.801865
EM: Round [484] log likelihood: -5632.801517
EM: Round [485] log likelihood: -5632.801170
EM: Round [486] log likelihood: -5632.800825
EM: Round [487] log likelihood: -5632.800481
EM: Round [488] log likelihood: -5632.800139
EM: Round [489] log likelihood: -5632.799799
EM: Round [490] log likelihood: -5632.799461
EM: Round [491] log likelihood: -5632.799124
EM: Round [492] log likelihood: -5632.798789
EM: Round [493] log likelihood: -5632.798456
EM: Round [494] log likelihood: -5632.798124
EM: Round [495] log likelihood: -5632.797794
EM: Round [496] log likelihood: -5632.797466
EM: Round [497] log likelihood: -5632.797139
EM: Round [498] log likelihood: -5632.796814
EM: Round [499] log likelihood: -5632.796490
EM: Round [500] log likelihood: -5632.796168
EM: Round [501] log likelihood: -5632.795848
EM: Round [502] log likelihood: -5632.795529
EM: Round [503] log likelihood: -5632.795212
EM: Round [504] log likelihood: -5632.794896
EM: Round [505] log likelihood: -5632.794582
EM: Round [506] log likelihood: -5632.794270
EM: Round [507] log likelihood: -5632.793958
EM: Round [508] log likelihood: -5632.793649
EM: Round [509] log likelihood: -5632.793341
EM: Round [510] log likelihood: -5632.793034
EM: Round [511] log likelihood: -5632.792729
EM: Round [512] log likelihood: -5632.792426
EM: Round [513] log likelihood: -5632.792123
EM: Round [514] log likelihood: -5632.791823
EM: Round [515] log likelihood: -5632.791524
EM: Round [516] log likelihood: -5632.791226
EM: Round [517] log likelihood: -5632.790929
EM: Round [518] log likelihood: -5632.790635
EM: Round [519] log likelihood: -5632.790341
EM: Round [520] log likelihood: -5632.790049
EM: Round [521] log likelihood: -5632.789758
EM: Round [522] log likelihood: -5632.789469
EM: Round [523] log likelihood: -5632.789181
EM: Round [524] log likelihood: -5632.788895
EM: Round [525] log likelihood: -5632.788610
EM: Round [526] log likelihood: -5632.788326
EM: Round [527] log likelihood: -5632.788044
EM: Round [528] log likelihood: -5632.787762
EM: Round [529] log likelihood: -5632.787483
EM: Round [530] log likelihood: -5632.787204
EM: Round [531] log likelihood: -5632.786927
EM: Round [532] log likelihood: -5632.786652
EM: Round [533] log likelihood: -5632.786377
EM: Round [534] log likelihood: -5632.786104
EM: Round [535] log likelihood: -5632.785832
EM: Round [536] log likelihood: -5632.785562
EM: Round [537] log likelihood: -5632.785292
EM: Round [538] log likelihood: -5632.785024
EM: Round [539] log likelihood: -5632.784758
EM: Round [540] log likelihood: -5632.784492
EM: Round [541] log likelihood: -5632.784228
EM: Round [542] log likelihood: -5632.783965
EM: Round [543] log likelihood: -5632.783703
EM: Round [544] log likelihood: -5632.783443
EM: Round [545] log likelihood: -5632.783184
EM: Round [546] log likelihood: -5632.782926
EM: Round [547] log likelihood: -5632.782669
EM: Round [548] log likelihood: -5632.782413
EM: Round [549] log likelihood: -5632.782159
EM: Round [550] log likelihood: -5632.781905
EM: Round [551] log likelihood: -5632.781653
EM: Round [552] log likelihood: -5632.781402
EM: Round [553] log likelihood: -5632.781153
EM: Round [554] log likelihood: -5632.780904
EM: Round [555] log likelihood: -5632.780657
EM: Round [556] log likelihood: -5632.780410
EM: Round [557] log likelihood: -5632.780165
EM: Round [558] log likelihood: -5632.779921
EM: Round [559] log likelihood: -5632.779678
EM: Round [560] log likelihood: -5632.779437
EM: Round [561] log likelihood: -5632.779196
EM: Round [562] log likelihood: -5632.778957
EM: Round [563] log likelihood: -5632.778718
EM: Round [564] log likelihood: -5632.778481
EM: Round [565] log likelihood: -5632.778245
EM: Round [566] log likelihood: -5632.778010
EM: Round [567] log likelihood: -5632.777776
EM: Round [568] log likelihood: -5632.777543
EM: Round [569] log likelihood: -5632.777311
EM: Round [570] log likelihood: -5632.777080
EM: Round [571] log likelihood: -5632.776850
EM: Round [572] log likelihood: -5632.776622
EM: Round [573] log likelihood: -5632.776394
EM: Round [574] log likelihood: -5632.776167
EM: Round [575] log likelihood: -5632.775942
EM: Round [576] log likelihood: -5632.775717
EM: Round [577] log likelihood: -5632.775494
EM: Round [578] log likelihood: -5632.775271
EM: Round [579] log likelihood: -5632.775050
EM: Round [580] log likelihood: -5632.774830
EM: Round [581] log likelihood: -5632.774610
EM: Round [582] log likelihood: -5632.774392
EM: Round [583] log likelihood: -5632.774174
EM: Round [584] log likelihood: -5632.773958
EM: Round [585] log likelihood: -5632.773742
EM: Round [586] log likelihood: -5632.773528
EM: Round [587] log likelihood: -5632.773314
EM: Round [588] log likelihood: -5632.773102
EM: Round [589] log likelihood: -5632.772890
EM: Round [590] log likelihood: -5632.772679
EM: Round [591] log likelihood: -5632.772470
EM: Round [592] log likelihood: -5632.772261
EM: Round [593] log likelihood: -5632.772053
EM: Round [594] log likelihood: -5632.771846
EM: Round [595] log likelihood: -5632.771640
EM: Round [596] log likelihood: -5632.771435
EM: Round [597] log likelihood: -5632.771231
EM: Round [598] log likelihood: -5632.771028
EM: Round [599] log likelihood: -5632.770826
EM: Round [600] log likelihood: -5632.770625
EM: Round [601] log likelihood: -5632.770424
EM: Round [602] log likelihood: -5632.770225
EM: Round [603] log likelihood: -5632.770026
EM: Round [604] log likelihood: -5632.769828
EM: Round [605] log likelihood: -5632.769631
EM: Round [606] log likelihood: -5632.769435
EM: Round [607] log likelihood: -5632.769240
EM: Round [608] log likelihood: -5632.769046
EM: Round [609] log likelihood: -5632.768853
EM: Round [610] log likelihood: -5632.768660
EM: Round [611] log likelihood: -5632.768469
EM: Round [612] log likelihood: -5632.768278
EM: Round [613] log likelihood: -5632.768088
EM: Round [614] log likelihood: -5632.767899
EM: Round [615] log likelihood: -5632.767711
EM: Round [616] log likelihood: -5632.767523
EM: Round [617] log likelihood: -5632.767337
EM: Round [618] log likelihood: -5632.767151
EM: Round [619] log likelihood: -5632.766966
EM: Round [620] log likelihood: -5632.766782
EM: Round [621] log likelihood: -5632.766599
EM: Round [622] log likelihood: -5632.766416
EM: Round [623] log likelihood: -5632.766234
EM: Round [624] log likelihood: -5632.766054
EM: Round [625] log likelihood: -5632.765874
EM: Round [626] log likelihood: -5632.765694
EM: Round [627] log likelihood: -5632.765516
EM: Round [628] log likelihood: -5632.765338
EM: Round [629] log likelihood: -5632.765161
EM: Round [630] log likelihood: -5632.764985
EM: Round [631] log likelihood: -5632.764810
EM: Round [632] log likelihood: -5632.764635
EM: Round [633] log likelihood: -5632.764461
EM: Round [634] log likelihood: -5632.764288
EM: Round [635] log likelihood: -5632.764116
EM: Round [636] log likelihood: -5632.763945
EM: Round [637] log likelihood: -5632.763774
EM: Round [638] log likelihood: -5632.763604
EM: Round [639] log likelihood: -5632.763434
EM: Round [640] log likelihood: -5632.763266
EM: Round [641] log likelihood: -5632.763098
EM: Round [642] log likelihood: -5632.762931
EM: Round [643] log likelihood: -5632.762765
EM: Round [644] log likelihood: -5632.762599
EM: Round [645] log likelihood: -5632.762434
EM: Round [646] log likelihood: -5632.762270
EM: Round [647] log likelihood: -5632.762107
EM: Round [648] log likelihood: -5632.761944
EM: Round [649] log likelihood: -5632.761782
EM: Round [650] log likelihood: -5632.761621
EM: Round [651] log likelihood: -5632.761460
EM: Round [652] log likelihood: -5632.761300
EM: Round [653] log likelihood: -5632.761141
EM: Round [654] log likelihood: -5632.760982
EM: Round [655] log likelihood: -5632.760825
EM: Round [656] log likelihood: -5632.760668
EM: Round [657] log likelihood: -5632.760511
EM: Round [658] log likelihood: -5632.760355
EM: Round [659] log likelihood: -5632.760200
EM: Round [660] log likelihood: -5632.760046
EM: Round [661] log likelihood: -5632.759892
EM: Round [662] log likelihood: -5632.759739
EM: Round [663] log likelihood: -5632.759587
EM: Round [664] log likelihood: -5632.759435
EM: Round [665] log likelihood: -5632.759284
EM: Round [666] log likelihood: -5632.759133
EM: Round [667] log likelihood: -5632.758983
EM: Round [668] log likelihood: -5632.758834
EM: Round [669] log likelihood: -5632.758686
EM: Round [670] log likelihood: -5632.758538
EM: Round [671] log likelihood: -5632.758391
EM: Round [672] log likelihood: -5632.758244
EM: Round [673] log likelihood: -5632.758098
EM: Round [674] log likelihood: -5632.757953
EM: Round [675] log likelihood: -5632.757808
EM: Round [676] log likelihood: -5632.757664
EM: Round [677] log likelihood: -5632.757521
EM: Round [678] log likelihood: -5632.757378
EM: Round [679] log likelihood: -5632.757236
EM: Round [680] log likelihood: -5632.757094
EM: Round [681] log likelihood: -5632.756953
EM: Round [682] log likelihood: -5632.756812
EM: Round [683] log likelihood: -5632.756673
EM: Round [684] log likelihood: -5632.756533
EM: Round [685] log likelihood: -5632.756395
EM: Round [686] log likelihood: -5632.756257
EM: Round [687] log likelihood: -5632.756119
EM: Round [688] log likelihood: -5632.755983
EM: Round [689] log likelihood: -5632.755846
EM: Round [690] log likelihood: -5632.755711
EM: Round [691] log likelihood: -5632.755576
EM: Round [692] log likelihood: -5632.755441
EM: Round [693] log likelihood: -5632.755307
EM: Round [694] log likelihood: -5632.755174
EM: Round [695] log likelihood: -5632.755041
EM: Round [696] log likelihood: -5632.754909
EM: Round [697] log likelihood: -5632.754777
EM: Round [698] log likelihood: -5632.754646
EM: Round [699] log likelihood: -5632.754516
EM: Round [700] log likelihood: -5632.754386
EM: Round [701] log likelihood: -5632.754256
EM: Round [702] log likelihood: -5632.754127
EM: Round [703] log likelihood: -5632.753999
EM: Round [704] log likelihood: -5632.753871
EM: Round [705] log likelihood: -5632.753744
EM: Round [706] log likelihood: -5632.753617
EM: Round [707] log likelihood: -5632.753491
EM: Round [708] log likelihood: -5632.753366
EM: Round [709] log likelihood: -5632.753241
EM: Round [710] log likelihood: -5632.753116
EM: Round [711] log likelihood: -5632.752992
EM: Round [712] log likelihood: -5632.752869
EM: Round [713] log likelihood: -5632.752746
EM: Round [714] log likelihood: -5632.752623
EM: Round [715] log likelihood: -5632.752501
EM: Round [716] log likelihood: -5632.752380
EM: Round [717] log likelihood: -5632.752259
EM: Round [718] log likelihood: -5632.752139
EM: Round [719] log likelihood: -5632.752019
EM: Round [720] log likelihood: -5632.751899
EM: Round [721] log likelihood: -5632.751781
EM: Round [722] log likelihood: -5632.751662
EM: Round [723] log likelihood: -5632.751544
EM: Round [724] log likelihood: -5632.751427
EM: Round [725] log likelihood: -5632.751310
EM: Round [726] log likelihood: -5632.751194
EM: Round [727] log likelihood: -5632.751078
EM: Round [728] log likelihood: -5632.750963
EM: Round [729] log likelihood: -5632.750848
EM: Round [730] log likelihood: -5632.750733
EM: Round [731] log likelihood: -5632.750619
EM: Round [732] log likelihood: -5632.750506
EM: Round [733] log likelihood: -5632.750393
EM: Round [734] log likelihood: -5632.750281
EM: Round [735] log likelihood: -5632.750169
EM: Round [736] log likelihood: -5632.750057
EM: Round [737] log likelihood: -5632.749946
EM: Round [738] log likelihood: -5632.749835
EM: Round [739] log likelihood: -5632.749725
EM: Round [740] log likelihood: -5632.749615
EM: Round [741] log likelihood: -5632.749506
EM: Round [742] log likelihood: -5632.749398
EM: Round [743] log likelihood: -5632.749289
EM: Round [744] log likelihood: -5632.749181
EM: Round [745] log likelihood: -5632.749074
EM: Round [746] log likelihood: -5632.748967
EM: Round [747] log likelihood: -5632.748861
EM: Round [748] log likelihood: -5632.748755
EM: Round [749] log likelihood: -5632.748649
EM: Round [750] log likelihood: -5632.748544
EM: Round [751] log likelihood: -5632.748439
EM: Round [752] log likelihood: -5632.748335
EM: Round [753] log likelihood: -5632.748231
EM: Round [754] log likelihood: -5632.748128
EM: Round [755] log likelihood: -5632.748025
EM: Round [756] log likelihood: -5632.747922
EM: Round [757] log likelihood: -5632.747820
EM: Round [758] log likelihood: -5632.747718
EM: Round [759] log likelihood: -5632.747617
EM: Round [760] log likelihood: -5632.747516
EM: Round [761] log likelihood: -5632.747416
EM: Round [762] log likelihood: -5632.747316
EM: Stopping iterations at round 762 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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.FBo812kcg8/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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.FBo812kcg8/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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam.bed > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam.bed > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam.bed > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam.bed > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam into /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam.read_coords > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.16 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.FBo812kcg8/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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.igv.Pfam.gff3 > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.igv.Pfam.gff3 > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.FBo812kcg8/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.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.FBo812kcg8/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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.FBo812kcg8/ctat_genome_lib_build_dir
-done, see /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.FBo812kcg8/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -4329.281678
EM: Round [1] log likelihood: -4329.012271
EM: Round [2] log likelihood: -4329.008266
EM: Round [3] log likelihood: -4329.004374
EM: Round [4] log likelihood: -4329.000513
EM: Round [5] log likelihood: -4328.996682
EM: Round [6] log likelihood: -4328.992880
EM: Round [7] log likelihood: -4328.989108
EM: Round [8] log likelihood: -4328.985366
EM: Round [9] log likelihood: -4328.981652
EM: Round [10] log likelihood: -4328.977966
EM: Round [11] log likelihood: -4328.974309
EM: Round [12] log likelihood: -4328.970680
EM: Round [13] log likelihood: -4328.967078
EM: Round [14] log likelihood: -4328.963503
EM: Round [15] log likelihood: -4328.959956
EM: Round [16] log likelihood: -4328.956435
EM: Round [17] log likelihood: -4328.952940
EM: Round [18] log likelihood: -4328.949471
EM: Round [19] log likelihood: -4328.946028
EM: Round [20] log likelihood: -4328.942611
EM: Round [21] log likelihood: -4328.939219
EM: Round [22] log likelihood: -4328.935852
EM: Round [23] log likelihood: -4328.932509
EM: Round [24] log likelihood: -4328.929191
EM: Round [25] log likelihood: -4328.925897
EM: Round [26] log likelihood: -4328.922627
EM: Round [27] log likelihood: -4328.919381
EM: Round [28] log likelihood: -4328.916158
EM: Round [29] log likelihood: -4328.912958
EM: Round [30] log likelihood: -4328.909781
EM: Round [31] log likelihood: -4328.906627
EM: Round [32] log likelihood: -4328.903495
EM: Round [33] log likelihood: -4328.900385
EM: Round [34] log likelihood: -4328.897298
EM: Round [35] log likelihood: -4328.894232
EM: Round [36] log likelihood: -4328.891188
EM: Round [37] log likelihood: -4328.888165
EM: Round [38] log likelihood: -4328.885163
EM: Round [39] log likelihood: -4328.882182
EM: Round [40] log likelihood: -4328.879222
EM: Round [41] log likelihood: -4328.876283
EM: Round [42] log likelihood: -4328.873363
EM: Round [43] log likelihood: -4328.870464
EM: Round [44] log likelihood: -4328.867585
EM: Round [45] log likelihood: -4328.864725
EM: Round [46] log likelihood: -4328.861885
EM: Round [47] log likelihood: -4328.859065
EM: Round [48] log likelihood: -4328.856263
EM: Round [49] log likelihood: -4328.853481
EM: Round [50] log likelihood: -4328.850717
EM: Round [51] log likelihood: -4328.847972
EM: Round [52] log likelihood: -4328.845245
EM: Round [53] log likelihood: -4328.842536
EM: Round [54] log likelihood: -4328.839846
EM: Round [55] log likelihood: -4328.837174
EM: Round [56] log likelihood: -4328.834519
EM: Round [57] log likelihood: -4328.831882
EM: Round [58] log likelihood: -4328.829262
EM: Round [59] log likelihood: -4328.826660
EM: Round [60] log likelihood: -4328.824074
EM: Round [61] log likelihood: -4328.821506
EM: Round [62] log likelihood: -4328.818954
EM: Round [63] log likelihood: -4328.816419
EM: Round [64] log likelihood: -4328.813901
EM: Round [65] log likelihood: -4328.811399
EM: Round [66] log likelihood: -4328.808913
EM: Round [67] log likelihood: -4328.806443
EM: Round [68] log likelihood: -4328.803989
EM: Round [69] log likelihood: -4328.801551
EM: Round [70] log likelihood: -4328.799129
EM: Round [71] log likelihood: -4328.796722
EM: Round [72] log likelihood: -4328.794330
EM: Round [73] log likelihood: -4328.791953
EM: Round [74] log likelihood: -4328.789592
EM: Round [75] log likelihood: -4328.787246
EM: Round [76] log likelihood: -4328.784914
EM: Round [77] log likelihood: -4328.782597
EM: Round [78] log likelihood: -4328.780295
EM: Round [79] log likelihood: -4328.778007
EM: Round [80] log likelihood: -4328.775734
EM: Round [81] log likelihood: -4328.773474
EM: Round [82] log likelihood: -4328.771229
EM: Round [83] log likelihood: -4328.768998
EM: Round [84] log likelihood: -4328.766781
EM: Round [85] log likelihood: -4328.764577
EM: Round [86] log likelihood: -4328.762387
EM: Round [87] log likelihood: -4328.760210
EM: Round [88] log likelihood: -4328.758047
EM: Round [89] log likelihood: -4328.755897
EM: Round [90] log likelihood: -4328.753761
EM: Round [91] log likelihood: -4328.751637
EM: Round [92] log likelihood: -4328.749526
EM: Round [93] log likelihood: -4328.747428
EM: Round [94] log likelihood: -4328.745343
EM: Round [95] log likelihood: -4328.743271
EM: Round [96] log likelihood: -4328.741211
EM: Round [97] log likelihood: -4328.739164
EM: Round [98] log likelihood: -4328.737128
EM: Round [99] log likelihood: -4328.735105
EM: Round [100] log likelihood: -4328.733095
EM: Round [101] log likelihood: -4328.731096
EM: Round [102] log likelihood: -4328.729109
EM: Round [103] log likelihood: -4328.727134
EM: Round [104] log likelihood: -4328.725171
EM: Round [105] log likelihood: -4328.723220
EM: Round [106] log likelihood: -4328.721280
EM: Round [107] log likelihood: -4328.719351
EM: Round [108] log likelihood: -4328.717434
EM: Round [109] log likelihood: -4328.715528
EM: Round [110] log likelihood: -4328.713634
EM: Round [111] log likelihood: -4328.711750
EM: Round [112] log likelihood: -4328.709878
EM: Round [113] log likelihood: -4328.708017
EM: Round [114] log likelihood: -4328.706166
EM: Round [115] log likelihood: -4328.704326
EM: Round [116] log likelihood: -4328.702497
EM: Round [117] log likelihood: -4328.700679
EM: Round [118] log likelihood: -4328.698871
EM: Round [119] log likelihood: -4328.697074
EM: Round [120] log likelihood: -4328.695287
EM: Round [121] log likelihood: -4328.693510
EM: Round [122] log likelihood: -4328.691743
EM: Round [123] log likelihood: -4328.689987
EM: Round [124] log likelihood: -4328.688241
EM: Round [125] log likelihood: -4328.686504
EM: Round [126] log likelihood: -4328.684778
EM: Round [127] log likelihood: -4328.683062
EM: Round [128] log likelihood: -4328.681355
EM: Round [129] log likelihood: -4328.679658
EM: Round [130] log likelihood: -4328.677970
EM: Round [131] log likelihood: -4328.676293
EM: Round [132] log likelihood: -4328.674624
EM: Round [133] log likelihood: -4328.672965
EM: Round [134] log likelihood: -4328.671316
EM: Round [135] log likelihood: -4328.669676
EM: Round [136] log likelihood: -4328.668045
EM: Round [137] log likelihood: -4328.666423
EM: Round [138] log likelihood: -4328.664810
EM: Round [139] log likelihood: -4328.663206
EM: Round [140] log likelihood: -4328.661611
EM: Round [141] log likelihood: -4328.660025
EM: Round [142] log likelihood: -4328.658448
EM: Round [143] log likelihood: -4328.656880
EM: Round [144] log likelihood: -4328.655320
EM: Round [145] log likelihood: -4328.653769
EM: Round [146] log likelihood: -4328.652227
EM: Round [147] log likelihood: -4328.650693
EM: Round [148] log likelihood: -4328.649168
EM: Round [149] log likelihood: -4328.647651
EM: Round [150] log likelihood: -4328.646142
EM: Round [151] log likelihood: -4328.644642
EM: Round [152] log likelihood: -4328.643150
EM: Round [153] log likelihood: -4328.641666
EM: Round [154] log likelihood: -4328.640190
EM: Round [155] log likelihood: -4328.638722
EM: Round [156] log likelihood: -4328.637262
EM: Round [157] log likelihood: -4328.635810
EM: Round [158] log likelihood: -4328.634366
EM: Round [159] log likelihood: -4328.632930
EM: Round [160] log likelihood: -4328.631502
EM: Round [161] log likelihood: -4328.630081
EM: Round [162] log likelihood: -4328.628668
EM: Round [163] log likelihood: -4328.627263
EM: Round [164] log likelihood: -4328.625865
EM: Round [165] log likelihood: -4328.624475
EM: Round [166] log likelihood: -4328.623092
EM: Round [167] log likelihood: -4328.621717
EM: Round [168] log likelihood: -4328.620349
EM: Round [169] log likelihood: -4328.618988
EM: Round [170] log likelihood: -4328.617635
EM: Round [171] log likelihood: -4328.616289
EM: Round [172] log likelihood: -4328.614950
EM: Round [173] log likelihood: -4328.613618
EM: Round [174] log likelihood: -4328.612293
EM: Round [175] log likelihood: -4328.610975
EM: Round [176] log likelihood: -4328.609664
EM: Round [177] log likelihood: -4328.608361
EM: Round [178] log likelihood: -4328.607064
EM: Round [179] log likelihood: -4328.605774
EM: Round [180] log likelihood: -4328.604490
EM: Round [181] log likelihood: -4328.603214
EM: Round [182] log likelihood: -4328.601944
EM: Round [183] log likelihood: -4328.600681
EM: Round [184] log likelihood: -4328.599424
EM: Round [185] log likelihood: -4328.598175
EM: Round [186] log likelihood: -4328.596931
EM: Round [187] log likelihood: -4328.595694
EM: Round [188] log likelihood: -4328.594464
EM: Round [189] log likelihood: -4328.593240
EM: Round [190] log likelihood: -4328.592022
EM: Round [191] log likelihood: -4328.590811
EM: Round [192] log likelihood: -4328.589606
EM: Round [193] log likelihood: -4328.588407
EM: Round [194] log likelihood: -4328.587215
EM: Round [195] log likelihood: -4328.586029
EM: Round [196] log likelihood: -4328.584848
EM: Round [197] log likelihood: -4328.583674
EM: Round [198] log likelihood: -4328.582506
EM: Round [199] log likelihood: -4328.581344
EM: Round [200] log likelihood: -4328.580188
EM: Round [201] log likelihood: -4328.579038
EM: Round [202] log likelihood: -4328.577894
EM: Round [203] log likelihood: -4328.576755
EM: Round [204] log likelihood: -4328.575623
EM: Round [205] log likelihood: -4328.574496
EM: Round [206] log likelihood: -4328.573375
EM: Round [207] log likelihood: -4328.572260
EM: Round [208] log likelihood: -4328.571151
EM: Round [209] log likelihood: -4328.570047
EM: Round [210] log likelihood: -4328.568949
EM: Round [211] log likelihood: -4328.567856
EM: Round [212] log likelihood: -4328.566769
EM: Round [213] log likelihood: -4328.565687
EM: Round [214] log likelihood: -4328.564611
EM: Round [215] log likelihood: -4328.563540
EM: Round [216] log likelihood: -4328.562475
EM: Round [217] log likelihood: -4328.561415
EM: Round [218] log likelihood: -4328.560361
EM: Round [219] log likelihood: -4328.559311
EM: Round [220] log likelihood: -4328.558267
EM: Round [221] log likelihood: -4328.557229
EM: Round [222] log likelihood: -4328.556195
EM: Round [223] log likelihood: -4328.555167
EM: Round [224] log likelihood: -4328.554144
EM: Round [225] log likelihood: -4328.553126
EM: Round [226] log likelihood: -4328.552113
EM: Round [227] log likelihood: -4328.551105
EM: Round [228] log likelihood: -4328.550102
EM: Round [229] log likelihood: -4328.549105
EM: Round [230] log likelihood: -4328.548112
EM: Round [231] log likelihood: -4328.547124
EM: Round [232] log likelihood: -4328.546141
EM: Round [233] log likelihood: -4328.545163
EM: Round [234] log likelihood: -4328.544190
EM: Round [235] log likelihood: -4328.543221
EM: Round [236] log likelihood: -4328.542258
EM: Round [237] log likelihood: -4328.541299
EM: Round [238] log likelihood: -4328.540345
EM: Round [239] log likelihood: -4328.539395
EM: Round [240] log likelihood: -4328.538451
EM: Round [241] log likelihood: -4328.537511
EM: Round [242] log likelihood: -4328.536575
EM: Round [243] log likelihood: -4328.535645
EM: Round [244] log likelihood: -4328.534718
EM: Round [245] log likelihood: -4328.533797
EM: Round [246] log likelihood: -4328.532880
EM: Round [247] log likelihood: -4328.531967
EM: Round [248] log likelihood: -4328.531059
EM: Round [249] log likelihood: -4328.530155
EM: Round [250] log likelihood: -4328.529256
EM: Round [251] log likelihood: -4328.528361
EM: Round [252] log likelihood: -4328.527470
EM: Round [253] log likelihood: -4328.526584
EM: Round [254] log likelihood: -4328.525702
EM: Round [255] log likelihood: -4328.524825
EM: Round [256] log likelihood: -4328.523951
EM: Round [257] log likelihood: -4328.523082
EM: Round [258] log likelihood: -4328.522217
EM: Round [259] log likelihood: -4328.521357
EM: Round [260] log likelihood: -4328.520500
EM: Round [261] log likelihood: -4328.519648
EM: Round [262] log likelihood: -4328.518800
EM: Round [263] log likelihood: -4328.517956
EM: Round [264] log likelihood: -4328.517116
EM: Round [265] log likelihood: -4328.516280
EM: Round [266] log likelihood: -4328.515448
EM: Round [267] log likelihood: -4328.514620
EM: Round [268] log likelihood: -4328.513796
EM: Round [269] log likelihood: -4328.512976
EM: Round [270] log likelihood: -4328.512160
EM: Round [271] log likelihood: -4328.511348
EM: Round [272] log likelihood: -4328.510540
EM: Round [273] log likelihood: -4328.509735
EM: Round [274] log likelihood: -4328.508935
EM: Round [275] log likelihood: -4328.508138
EM: Round [276] log likelihood: -4328.507345
EM: Round [277] log likelihood: -4328.506556
EM: Round [278] log likelihood: -4328.505771
EM: Round [279] log likelihood: -4328.504990
EM: Round [280] log likelihood: -4328.504212
EM: Round [281] log likelihood: -4328.503438
EM: Round [282] log likelihood: -4328.502667
EM: Round [283] log likelihood: -4328.501901
EM: Round [284] log likelihood: -4328.501138
EM: Round [285] log likelihood: -4328.500378
EM: Round [286] log likelihood: -4328.499622
EM: Round [287] log likelihood: -4328.498870
EM: Round [288] log likelihood: -4328.498121
EM: Round [289] log likelihood: -4328.497376
EM: Round [290] log likelihood: -4328.496634
EM: Round [291] log likelihood: -4328.495896
EM: Round [292] log likelihood: -4328.495162
EM: Round [293] log likelihood: -4328.494431
EM: Round [294] log likelihood: -4328.493703
EM: Round [295] log likelihood: -4328.492979
EM: Round [296] log likelihood: -4328.492258
EM: Round [297] log likelihood: -4328.491540
EM: Round [298] log likelihood: -4328.490826
EM: Round [299] log likelihood: -4328.490115
EM: Round [300] log likelihood: -4328.489408
EM: Round [301] log likelihood: -4328.488704
EM: Round [302] log likelihood: -4328.488003
EM: Round [303] log likelihood: -4328.487306
EM: Round [304] log likelihood: -4328.486612
EM: Round [305] log likelihood: -4328.485921
EM: Round [306] log likelihood: -4328.485233
EM: Round [307] log likelihood: -4328.484548
EM: Round [308] log likelihood: -4328.483867
EM: Round [309] log likelihood: -4328.483189
EM: Round [310] log likelihood: -4328.482514
EM: Round [311] log likelihood: -4328.481842
EM: Round [312] log likelihood: -4328.481173
EM: Round [313] log likelihood: -4328.480508
EM: Round [314] log likelihood: -4328.479845
EM: Round [315] log likelihood: -4328.479186
EM: Round [316] log likelihood: -4328.478530
EM: Round [317] log likelihood: -4328.477876
EM: Round [318] log likelihood: -4328.477226
EM: Round [319] log likelihood: -4328.476579
EM: Round [320] log likelihood: -4328.475935
EM: Round [321] log likelihood: -4328.475294
EM: Round [322] log likelihood: -4328.474655
EM: Round [323] log likelihood: -4328.474020
EM: Round [324] log likelihood: -4328.473388
EM: Round [325] log likelihood: -4328.472758
EM: Round [326] log likelihood: -4328.472132
EM: Round [327] log likelihood: -4328.471508
EM: Round [328] log likelihood: -4328.470887
EM: Round [329] log likelihood: -4328.470269
EM: Round [330] log likelihood: -4328.469654
EM: Round [331] log likelihood: -4328.469042
EM: Round [332] log likelihood: -4328.468433
EM: Round [333] log likelihood: -4328.467826
EM: Round [334] log likelihood: -4328.467222
EM: Round [335] log likelihood: -4328.466621
EM: Round [336] log likelihood: -4328.466023
EM: Round [337] log likelihood: -4328.465427
EM: Round [338] log likelihood: -4328.464834
EM: Round [339] log likelihood: -4328.464244
EM: Round [340] log likelihood: -4328.463657
EM: Round [341] log likelihood: -4328.463072
EM: Round [342] log likelihood: -4328.462490
EM: Round [343] log likelihood: -4328.461911
EM: Round [344] log likelihood: -4328.461334
EM: Round [345] log likelihood: -4328.460760
EM: Round [346] log likelihood: -4328.460188
EM: Round [347] log likelihood: -4328.459620
EM: Round [348] log likelihood: -4328.459053
EM: Round [349] log likelihood: -4328.458490
EM: Round [350] log likelihood: -4328.457929
EM: Round [351] log likelihood: -4328.457370
EM: Round [352] log likelihood: -4328.456814
EM: Round [353] log likelihood: -4328.456260
EM: Round [354] log likelihood: -4328.455709
EM: Round [355] log likelihood: -4328.455161
EM: Round [356] log likelihood: -4328.454615
EM: Round [357] log likelihood: -4328.454071
EM: Round [358] log likelihood: -4328.453530
EM: Round [359] log likelihood: -4328.452992
EM: Round [360] log likelihood: -4328.452456
EM: Round [361] log likelihood: -4328.451922
EM: Round [362] log likelihood: -4328.451391
EM: Round [363] log likelihood: -4328.450862
EM: Round [364] log likelihood: -4328.450335
EM: Round [365] log likelihood: -4328.449811
EM: Round [366] log likelihood: -4328.449289
EM: Round [367] log likelihood: -4328.448770
EM: Round [368] log likelihood: -4328.448253
EM: Round [369] log likelihood: -4328.447738
EM: Round [370] log likelihood: -4328.447225
EM: Round [371] log likelihood: -4328.446715
EM: Round [372] log likelihood: -4328.446208
EM: Round [373] log likelihood: -4328.445702
EM: Round [374] log likelihood: -4328.445199
EM: Round [375] log likelihood: -4328.444698
EM: Round [376] log likelihood: -4328.444199
EM: Round [377] log likelihood: -4328.443702
EM: Round [378] log likelihood: -4328.443208
EM: Round [379] log likelihood: -4328.442716
EM: Round [380] log likelihood: -4328.442226
EM: Round [381] log likelihood: -4328.441738
EM: Round [382] log likelihood: -4328.441253
EM: Round [383] log likelihood: -4328.440770
EM: Round [384] log likelihood: -4328.440288
EM: Round [385] log likelihood: -4328.439809
EM: Round [386] log likelihood: -4328.439333
EM: Round [387] log likelihood: -4328.438858
EM: Round [388] log likelihood: -4328.438385
EM: Round [389] log likelihood: -4328.437915
EM: Round [390] log likelihood: -4328.437446
EM: Round [391] log likelihood: -4328.436980
EM: Round [392] log likelihood: -4328.436516
EM: Round [393] log likelihood: -4328.436054
EM: Round [394] log likelihood: -4328.435593
EM: Round [395] log likelihood: -4328.435135
EM: Round [396] log likelihood: -4328.434679
EM: Round [397] log likelihood: -4328.434225
EM: Round [398] log likelihood: -4328.433773
EM: Round [399] log likelihood: -4328.433323
EM: Round [400] log likelihood: -4328.432875
EM: Round [401] log likelihood: -4328.432429
EM: Round [402] log likelihood: -4328.431985
EM: Round [403] log likelihood: -4328.431543
EM: Round [404] log likelihood: -4328.431103
EM: Round [405] log likelihood: -4328.430665
EM: Round [406] log likelihood: -4328.430229
EM: Round [407] log likelihood: -4328.429795
EM: Round [408] log likelihood: -4328.429362
EM: Round [409] log likelihood: -4328.428932
EM: Round [410] log likelihood: -4328.428503
EM: Round [411] log likelihood: -4328.428077
EM: Round [412] log likelihood: -4328.427652
EM: Round [413] log likelihood: -4328.427229
EM: Round [414] log likelihood: -4328.426808
EM: Round [415] log likelihood: -4328.426389
EM: Round [416] log likelihood: -4328.425972
EM: Round [417] log likelihood: -4328.425556
EM: Round [418] log likelihood: -4328.425143
EM: Round [419] log likelihood: -4328.424731
EM: Round [420] log likelihood: -4328.424321
EM: Round [421] log likelihood: -4328.423913
EM: Round [422] log likelihood: -4328.423506
EM: Round [423] log likelihood: -4328.423102
EM: Round [424] log likelihood: -4328.422699
EM: Round [425] log likelihood: -4328.422298
EM: Round [426] log likelihood: -4328.421898
EM: Round [427] log likelihood: -4328.421501
EM: Round [428] log likelihood: -4328.421105
EM: Round [429] log likelihood: -4328.420711
EM: Round [430] log likelihood: -4328.420319
EM: Round [431] log likelihood: -4328.419928
EM: Round [432] log likelihood: -4328.419539
EM: Round [433] log likelihood: -4328.419152
EM: Round [434] log likelihood: -4328.418767
EM: Round [435] log likelihood: -4328.418383
EM: Round [436] log likelihood: -4328.418001
EM: Round [437] log likelihood: -4328.417620
EM: Round [438] log likelihood: -4328.417241
EM: Round [439] log likelihood: -4328.416864
EM: Round [440] log likelihood: -4328.416489
EM: Round [441] log likelihood: -4328.416115
EM: Round [442] log likelihood: -4328.415743
EM: Round [443] log likelihood: -4328.415372
EM: Round [444] log likelihood: -4328.415003
EM: Round [445] log likelihood: -4328.414636
EM: Round [446] log likelihood: -4328.414270
EM: Round [447] log likelihood: -4328.413906
EM: Round [448] log likelihood: -4328.413543
EM: Round [449] log likelihood: -4328.413182
EM: Round [450] log likelihood: -4328.412823
EM: Round [451] log likelihood: -4328.412465
EM: Round [452] log likelihood: -4328.412108
EM: Round [453] log likelihood: -4328.411754
EM: Round [454] log likelihood: -4328.411400
EM: Round [455] log likelihood: -4328.411049
EM: Round [456] log likelihood: -4328.410699
EM: Round [457] log likelihood: -4328.410350
EM: Round [458] log likelihood: -4328.410003
EM: Round [459] log likelihood: -4328.409657
EM: Round [460] log likelihood: -4328.409313
EM: Round [461] log likelihood: -4328.408970
EM: Round [462] log likelihood: -4328.408629
EM: Round [463] log likelihood: -4328.408290
EM: Round [464] log likelihood: -4328.407951
EM: Round [465] log likelihood: -4328.407615
EM: Round [466] log likelihood: -4328.407279
EM: Round [467] log likelihood: -4328.406945
EM: Round [468] log likelihood: -4328.406613
EM: Round [469] log likelihood: -4328.406282
EM: Round [470] log likelihood: -4328.405953
EM: Round [471] log likelihood: -4328.405624
EM: Round [472] log likelihood: -4328.405298
EM: Round [473] log likelihood: -4328.404973
EM: Round [474] log likelihood: -4328.404649
EM: Round [475] log likelihood: -4328.404326
EM: Round [476] log likelihood: -4328.404005
EM: Round [477] log likelihood: -4328.403685
EM: Round [478] log likelihood: -4328.403367
EM: Round [479] log likelihood: -4328.403050
EM: Round [480] log likelihood: -4328.402735
EM: Round [481] log likelihood: -4328.402420
EM: Round [482] log likelihood: -4328.402108
EM: Round [483] log likelihood: -4328.401796
EM: Round [484] log likelihood: -4328.401486
EM: Round [485] log likelihood: -4328.401177
EM: Round [486] log likelihood: -4328.400869
EM: Round [487] log likelihood: -4328.400563
EM: Round [488] log likelihood: -4328.400258
EM: Round [489] log likelihood: -4328.399955
EM: Round [490] log likelihood: -4328.399653
EM: Round [491] log likelihood: -4328.399352
EM: Round [492] log likelihood: -4328.399052
EM: Round [493] log likelihood: -4328.398754
EM: Round [494] log likelihood: -4328.398456
EM: Round [495] log likelihood: -4328.398161
EM: Round [496] log likelihood: -4328.397866
EM: Round [497] log likelihood: -4328.397573
EM: Round [498] log likelihood: -4328.397281
EM: Round [499] log likelihood: -4328.396990
EM: Round [500] log likelihood: -4328.396700
EM: Round [501] log likelihood: -4328.396412
EM: Round [502] log likelihood: -4328.396125
EM: Round [503] log likelihood: -4328.395839
EM: Round [504] log likelihood: -4328.395555
EM: Round [505] log likelihood: -4328.395271
EM: Round [506] log likelihood: -4328.394989
EM: Round [507] log likelihood: -4328.394708
EM: Round [508] log likelihood: -4328.394428
EM: Round [509] log likelihood: -4328.394150
EM: Round [510] log likelihood: -4328.393872
EM: Round [511] log likelihood: -4328.393596
EM: Round [512] log likelihood: -4328.393321
EM: Round [513] log likelihood: -4328.393047
EM: Round [514] log likelihood: -4328.392774
EM: Round [515] log likelihood: -4328.392503
EM: Round [516] log likelihood: -4328.392232
EM: Round [517] log likelihood: -4328.391963
EM: Round [518] log likelihood: -4328.391695
EM: Round [519] log likelihood: -4328.391428
EM: Round [520] log likelihood: -4328.391162
EM: Round [521] log likelihood: -4328.390898
EM: Round [522] log likelihood: -4328.390634
EM: Round [523] log likelihood: -4328.390372
EM: Round [524] log likelihood: -4328.390111
EM: Round [525] log likelihood: -4328.389850
EM: Round [526] log likelihood: -4328.389591
EM: Round [527] log likelihood: -4328.389333
EM: Round [528] log likelihood: -4328.389076
EM: Round [529] log likelihood: -4328.388821
EM: Round [530] log likelihood: -4328.388566
EM: Round [531] log likelihood: -4328.388312
EM: Round [532] log likelihood: -4328.388060
EM: Round [533] log likelihood: -4328.387808
EM: Round [534] log likelihood: -4328.387558
EM: Round [535] log likelihood: -4328.387308
EM: Round [536] log likelihood: -4328.387060
EM: Round [537] log likelihood: -4328.386813
EM: Round [538] log likelihood: -4328.386567
EM: Round [539] log likelihood: -4328.386322
EM: Round [540] log likelihood: -4328.386078
EM: Round [541] log likelihood: -4328.385834
EM: Round [542] log likelihood: -4328.385592
EM: Round [543] log likelihood: -4328.385351
EM: Round [544] log likelihood: -4328.385111
EM: Round [545] log likelihood: -4328.384872
EM: Round [546] log likelihood: -4328.384634
EM: Round [547] log likelihood: -4328.384397
EM: Round [548] log likelihood: -4328.384162
EM: Round [549] log likelihood: -4328.383927
EM: Round [550] log likelihood: -4328.383693
EM: Round [551] log likelihood: -4328.383460
EM: Round [552] log likelihood: -4328.383228
EM: Round [553] log likelihood: -4328.382997
EM: Round [554] log likelihood: -4328.382767
EM: Round [555] log likelihood: -4328.382537
EM: Round [556] log likelihood: -4328.382309
EM: Round [557] log likelihood: -4328.382082
EM: Round [558] log likelihood: -4328.381856
EM: Round [559] log likelihood: -4328.381631
EM: Round [560] log likelihood: -4328.381407
EM: Round [561] log likelihood: -4328.381183
EM: Round [562] log likelihood: -4328.380961
EM: Round [563] log likelihood: -4328.380739
EM: Round [564] log likelihood: -4328.380519
EM: Round [565] log likelihood: -4328.380299
EM: Round [566] log likelihood: -4328.380081
EM: Round [567] log likelihood: -4328.379863
EM: Round [568] log likelihood: -4328.379646
EM: Round [569] log likelihood: -4328.379430
EM: Round [570] log likelihood: -4328.379215
EM: Round [571] log likelihood: -4328.379001
EM: Round [572] log likelihood: -4328.378788
EM: Round [573] log likelihood: -4328.378575
EM: Round [574] log likelihood: -4328.378364
EM: Round [575] log likelihood: -4328.378154
EM: Round [576] log likelihood: -4328.377944
EM: Round [577] log likelihood: -4328.377735
EM: Round [578] log likelihood: -4328.377527
EM: Round [579] log likelihood: -4328.377320
EM: Round [580] log likelihood: -4328.377114
EM: Round [581] log likelihood: -4328.376909
EM: Round [582] log likelihood: -4328.376704
EM: Round [583] log likelihood: -4328.376501
EM: Round [584] log likelihood: -4328.376298
EM: Round [585] log likelihood: -4328.376096
EM: Round [586] log likelihood: -4328.375895
EM: Round [587] log likelihood: -4328.375695
EM: Round [588] log likelihood: -4328.375496
EM: Round [589] log likelihood: -4328.375297
EM: Round [590] log likelihood: -4328.375100
EM: Round [591] log likelihood: -4328.374903
EM: Round [592] log likelihood: -4328.374707
EM: Round [593] log likelihood: -4328.374512
EM: Round [594] log likelihood: -4328.374317
EM: Round [595] log likelihood: -4328.374124
EM: Round [596] log likelihood: -4328.373931
EM: Round [597] log likelihood: -4328.373739
EM: Round [598] log likelihood: -4328.373548
EM: Round [599] log likelihood: -4328.373358
EM: Round [600] log likelihood: -4328.373168
EM: Round [601] log likelihood: -4328.372979
EM: Round [602] log likelihood: -4328.372791
EM: Round [603] log likelihood: -4328.372604
EM: Round [604] log likelihood: -4328.372418
EM: Round [605] log likelihood: -4328.372232
EM: Round [606] log likelihood: -4328.372047
EM: Round [607] log likelihood: -4328.371863
EM: Round [608] log likelihood: -4328.371680
EM: Round [609] log likelihood: -4328.371498
EM: Round [610] log likelihood: -4328.371316
EM: Round [611] log likelihood: -4328.371135
EM: Round [612] log likelihood: -4328.370955
EM: Round [613] log likelihood: -4328.370775
EM: Round [614] log likelihood: -4328.370596
EM: Round [615] log likelihood: -4328.370418
EM: Round [616] log likelihood: -4328.370241
EM: Round [617] log likelihood: -4328.370065
EM: Round [618] log likelihood: -4328.369889
EM: Round [619] log likelihood: -4328.369714
EM: Round [620] log likelihood: -4328.369539
EM: Round [621] log likelihood: -4328.369366
EM: Round [622] log likelihood: -4328.369193
EM: Round [623] log likelihood: -4328.369021
EM: Round [624] log likelihood: -4328.368849
EM: Round [625] log likelihood: -4328.368679
EM: Round [626] log likelihood: -4328.368509
EM: Round [627] log likelihood: -4328.368339
EM: Round [628] log likelihood: -4328.368171
EM: Round [629] log likelihood: -4328.368003
EM: Round [630] log likelihood: -4328.367836
EM: Round [631] log likelihood: -4328.367669
EM: Round [632] log likelihood: -4328.367503
EM: Round [633] log likelihood: -4328.367338
EM: Round [634] log likelihood: -4328.367174
EM: Round [635] log likelihood: -4328.367010
EM: Round [636] log likelihood: -4328.366847
EM: Round [637] log likelihood: -4328.366685
EM: Round [638] log likelihood: -4328.366523
EM: Round [639] log likelihood: -4328.366362
EM: Round [640] log likelihood: -4328.366202
EM: Round [641] log likelihood: -4328.366042
EM: Round [642] log likelihood: -4328.365883
EM: Round [643] log likelihood: -4328.365724
EM: Round [644] log likelihood: -4328.365567
EM: Round [645] log likelihood: -4328.365410
EM: Round [646] log likelihood: -4328.365253
EM: Round [647] log likelihood: -4328.365097
EM: Round [648] log likelihood: -4328.364942
EM: Round [649] log likelihood: -4328.364788
EM: Round [650] log likelihood: -4328.364634
EM: Round [651] log likelihood: -4328.364481
EM: Round [652] log likelihood: -4328.364328
EM: Round [653] log likelihood: -4328.364176
EM: Round [654] log likelihood: -4328.364025
EM: Round [655] log likelihood: -4328.363874
EM: Round [656] log likelihood: -4328.363724
EM: Round [657] log likelihood: -4328.363575
EM: Round [658] log likelihood: -4328.363426
EM: Round [659] log likelihood: -4328.363278
EM: Round [660] log likelihood: -4328.363130
EM: Round [661] log likelihood: -4328.362983
EM: Round [662] log likelihood: -4328.362837
EM: Round [663] log likelihood: -4328.362691
EM: Round [664] log likelihood: -4328.362546
EM: Round [665] log likelihood: -4328.362401
EM: Round [666] log likelihood: -4328.362257
EM: Round [667] log likelihood: -4328.362114
EM: Round [668] log likelihood: -4328.361971
EM: Round [669] log likelihood: -4328.361829
EM: Round [670] log likelihood: -4328.361688
EM: Round [671] log likelihood: -4328.361547
EM: Round [672] log likelihood: -4328.361406
EM: Round [673] log likelihood: -4328.361266
EM: Round [674] log likelihood: -4328.361127
EM: Round [675] log likelihood: -4328.360988
EM: Round [676] log likelihood: -4328.360850
EM: Round [677] log likelihood: -4328.360713
EM: Round [678] log likelihood: -4328.360576
EM: Round [679] log likelihood: -4328.360439
EM: Round [680] log likelihood: -4328.360303
EM: Round [681] log likelihood: -4328.360168
EM: Round [682] log likelihood: -4328.360033
EM: Round [683] log likelihood: -4328.359899
EM: Round [684] log likelihood: -4328.359766
EM: Round [685] log likelihood: -4328.359633
EM: Round [686] log likelihood: -4328.359500
EM: Round [687] log likelihood: -4328.359368
EM: Round [688] log likelihood: -4328.359237
EM: Round [689] log likelihood: -4328.359106
EM: Round [690] log likelihood: -4328.358975
EM: Round [691] log likelihood: -4328.358846
EM: Round [692] log likelihood: -4328.358716
EM: Round [693] log likelihood: -4328.358588
EM: Round [694] log likelihood: -4328.358459
EM: Round [695] log likelihood: -4328.358332
EM: Round [696] log likelihood: -4328.358205
EM: Round [697] log likelihood: -4328.358078
EM: Round [698] log likelihood: -4328.357952
EM: Round [699] log likelihood: -4328.357826
EM: Round [700] log likelihood: -4328.357701
EM: Round [701] log likelihood: -4328.357577
EM: Round [702] log likelihood: -4328.357453
EM: Round [703] log likelihood: -4328.357329
EM: Round [704] log likelihood: -4328.357206
EM: Round [705] log likelihood: -4328.357083
EM: Round [706] log likelihood: -4328.356961
EM: Round [707] log likelihood: -4328.356840
EM: Round [708] log likelihood: -4328.356719
EM: Round [709] log likelihood: -4328.356598
EM: Round [710] log likelihood: -4328.356478
EM: Round [711] log likelihood: -4328.356359
EM: Round [712] log likelihood: -4328.356240
EM: Round [713] log likelihood: -4328.356121
EM: Round [714] log likelihood: -4328.356003
EM: Round [715] log likelihood: -4328.355886
EM: Round [716] log likelihood: -4328.355769
EM: Round [717] log likelihood: -4328.355652
EM: Round [718] log likelihood: -4328.355536
EM: Round [719] log likelihood: -4328.355420
EM: Round [720] log likelihood: -4328.355305
EM: Round [721] log likelihood: -4328.355190
EM: Round [722] log likelihood: -4328.355076
EM: Round [723] log likelihood: -4328.354962
EM: Round [724] log likelihood: -4328.354849
EM: Round [725] log likelihood: -4328.354736
EM: Round [726] log likelihood: -4328.354624
EM: Round [727] log likelihood: -4328.354512
EM: Round [728] log likelihood: -4328.354400
EM: Round [729] log likelihood: -4328.354290
EM: Round [730] log likelihood: -4328.354179
EM: Round [731] log likelihood: -4328.354069
EM: Round [732] log likelihood: -4328.353959
EM: Round [733] log likelihood: -4328.353850
EM: Round [734] log likelihood: -4328.353741
EM: Round [735] log likelihood: -4328.353633
EM: Round [736] log likelihood: -4328.353525
EM: Round [737] log likelihood: -4328.353418
EM: Round [738] log likelihood: -4328.353311
EM: Round [739] log likelihood: -4328.353204
EM: Round [740] log likelihood: -4328.353098
EM: Round [741] log likelihood: -4328.352993
EM: Round [742] log likelihood: -4328.352887
EM: Round [743] log likelihood: -4328.352783
EM: Round [744] log likelihood: -4328.352678
EM: Round [745] log likelihood: -4328.352574
EM: Round [746] log likelihood: -4328.352471
EM: Round [747] log likelihood: -4328.352368
EM: Round [748] log likelihood: -4328.352265
EM: Round [749] log likelihood: -4328.352163
EM: Round [750] log likelihood: -4328.352061
EM: Round [751] log likelihood: -4328.351960
EM: Round [752] log likelihood: -4328.351859
EM: Round [753] log likelihood: -4328.351758
EM: Round [754] log likelihood: -4328.351658
EM: Round [755] log likelihood: -4328.351558
EM: Stopping iterations at round 755 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.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1_1.fastp.fastq.gz: 267401418
Execution Time = 5.33 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa --gtf /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf > /tmp/nxf.FBo812kcg8/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.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa --gtf /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf > /tmp/nxf.FBo812kcg8/fi_workdir/microH.dat
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.FBo812kcg8/fi_workdir/microH.dat /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/fi_workdir/microH.dat /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.FBo812kcg8 --json_outfile /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-1ffee4-R1_A23WJ53LT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.FBo812kcg8 --json_outfile /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-1ffee4-R1_A23WJ53LT4_1
Running: touch /tmp/nxf.FBo812kcg8/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.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-1ffee4-R1_A23WJ53LT4_1 --html_output /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-1ffee4-R1_A23WJ53LT4_1 --html_output /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.FBo812kcg8/ctat_genome_lib_build_dir > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.FBo812kcg8/ctat_genome_lib_build_dir > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.FBo812kcg8/ctat_genome_lib_build_dir > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000284627.1]
WARNING, no entry stored in dbm for [ENSG00000284627.1]
WARNING, no entry stored in dbm for [ENSG00000284627.1]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000214837.8]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286065.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
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]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.FBo812kcg8/ctat_genome_lib_build_dir > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory