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/83/0c870e2a2227a10d86d83776e1845b/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/0c870e2a2227a10d86d83776e1845b/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/44cfb09d6411ed48351ae95779688a/tih_rna_sample_00090_23H5VFLT4_s32.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/ce814f7e347982c60e35fde94dd387/tih_rna_sample_00090_23H5VFLT4_s32_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/ce814f7e347982c60e35fde94dd387/tih_rna_sample_00090_23H5VFLT4_s32_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00090_23H5VFLT4_s32.fusionreport.tsv --gtf /tmp/nxf.XV5eT4t5u0/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.XV5eT4t5u0/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00090_23H5VFLT4_s32.fusionreport.tsv --gtf /tmp/nxf.XV5eT4t5u0/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.XV5eT4t5u0/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.fa /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.fa /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fa
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.gtf /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.gtf /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.gtf
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.fa /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.gtf > /tmp/nxf.XV5eT4t5u0/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.fa /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.gtf > /tmp/nxf.XV5eT4t5u0/cytoBand.txt
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.gtf > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.bed
-parsing GTF file: /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.gtf > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.bed
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.bed > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.bed > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.bed.sorted.bed
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/tih_rna_sample_00090_23H5VFLT4_s32.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.bed.sorted.bed
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/tih_rna_sample_00090_23H5VFLT4_s32.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.bed.sorted.bed.gz
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/tih_rna_sample_00090_23H5VFLT4_s32.bed.tabix.ok
Running: samtools faidx /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.fa
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.XV5eT4t5u0/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fa --max_mate_dist 100000 -G /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.gtf --CPU 8 --out_prefix tih_rna_sample_00090_23H5VFLT4_s32.star --out_dir /tmp/nxf.XV5eT4t5u0/fi_workdir --reads "/tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32_1.fastp.fastq.gz /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.XV5eT4t5u0/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.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32_1.fastp.fastq.gz /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:01:53 ..... started STAR run
Jun 08 10:01:53 ..... loading genome
Jun 08 10:03:36 ... generating Suffix Array index
Jun 08 10:07:27 ... completed Suffix Array index
Jun 08 10:07:28 ..... processing annotations GTF
Jun 08 10:07:28 ..... inserting junctions into the genome indices
Jun 08 10:08:29 ..... started mapping
Jun 08 11:13:34 ..... finished mapping
Jun 08 11:13:37 ..... started sorting BAM
Jun 08 11:13:37 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00090_23H5VFLT4_s32.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00090_23H5VFLT4_s32.star.sortedByCoord.out.bam
Execution Time = 71.74 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.XV5eT4t5u0/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fa --max_mate_dist 100000 -G /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.gtf --CPU 8 --out_prefix tih_rna_sample_00090_23H5VFLT4_s32.star --out_dir /tmp/nxf.XV5eT4t5u0/fi_workdir --reads "/tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32_1.fastp.fastq.gz /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32_2.fastp.fastq.gz"
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.sortedByCoord.out.bam -o /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam --remove_dups
11:13:39 : INFO : Done.
Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.sortedByCoord.out.bam -o /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.XV5eT4t5u0/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.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.gtf
-parsing /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.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] -done parsing /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 12,
'excessive soft clipping' => 2690,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 6,
' ** passed ** ' => 1171,
'low complexity anchor region' => 2,
'seq-similar region overlap' => 36,
'small anchor length' => 22,
'per_id < 96' => 2261,
'num genes matched < 2' => 26,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 148
};
-writing fusion junction support info.
Execution Time = 0.18 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.XV5eT4t5u0/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.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
[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] -fusion SPANNING read extraction for scaff: ABHD12--NINL
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000]
[21000]
[22000]
[23000]
[24000]
[25000]
[26000]
[27000]
[28000]
[29000]
[30000]
[31000]
[32000]
[33000]
[34000]
[35000]
[36000]
[37000]
[38000]
[39000]
[40000]
[41000]
[42000]
[43000]
[44000]
[45000]
[46000]
[47000]
[48000]
[49000]
[50000]
[51000]
[52000]
[53000]
[54000]
[55000]
[56000]
[57000]
[58000]
[59000]
[60000]
[61000]
[62000]
[63000]
[64000]
[65000]
[66000]
[67000]
[68000]
[69000]
[70000]
[71000]
[72000]
[73000]
[74000]
[75000]
[76000]
[77000]
[78000]
[79000]
[80000]
[81000]
[82000]
[83000]
[84000]
[85000]
[86000]
[87000]
[88000]
[89000]
[90000]
[91000]
[92000]
[93000]
[94000]
[95000]
[96000]
[97000]
[98000]
[99000]
[100000]
[101000]
[102000]
[103000]
[104000]
[105000]
[106000]
[107000]
[108000]
[109000]
[110000]
[111000]
[112000]
[113000]
[114000]
[115000]
[116000]
[117000]
[118000]
[119000]
[120000]
[121000]
[122000]
[123000]
[124000]
[125000]
[126000]
[127000]
[128000]
[129000]
[130000]
[131000]
[132000]
[133000]
[134000]
[135000]
[136000]
[137000]
[138000]
[139000]
[140000]
[141000]
[142000]
[143000]
[144000]
[145000]
[146000]
[147000]
[148000]
[149000]
[150000]
[151000]
[152000]
[153000] -fusion SPANNING read extraction for scaff: CDH1--TANGO6
[1000]
[2000]
[3000]
[4000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
[1000]
[2000]
[3000]
[4000]
[5000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1
[1000]
[2000]
[3000]
[4000]
[5000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000]
[21000]
[22000]
[23000]
[24000] -fusion SPANNING read extraction for scaff: SH3YL1--FAM110C
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000] -fusion SPANNING read extraction for scaff: SH3YL1--AC079779.1
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000]
[21000]
[22000]
[23000]
[24000]
[25000]
[26000]
[27000]
[28000]
[29000]
[30000]
[31000]
[32000]
[33000]
[34000]
[35000]
[36000]
[37000]
[38000]
[39000]
[40000]
[41000]
[42000]
[43000]
[44000]
[45000]
[46000]
[47000]
[48000]
[49000]
[50000]
[51000]
[52000]
[53000]
[54000]
[55000]
[56000]
[57000]
[58000]
[59000]
[60000]
[61000]
[62000]
[63000]
[64000]
[65000]
[66000]
[67000]
[68000]
[69000]
[70000]
[71000]
[72000]
[73000]
[74000]
[75000] -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] -fusion SPANNING read extraction for scaff: SUMF1--AC087857.1
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 5117,
'lacks exon overlap' => 5000
};
Execution Time = 0.51 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.XV5eT4t5u0/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.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.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.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fusion_preds.coalesced.summary > /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -1155.104925
EM: Round [1] log likelihood: -1154.946850
EM: Round [2] log likelihood: -1154.808689
EM: Round [3] log likelihood: -1154.687378
EM: Round [4] log likelihood: -1154.580446
EM: Round [5] log likelihood: -1154.485872
EM: Round [6] log likelihood: -1154.401988
EM: Round [7] log likelihood: -1154.327399
EM: Round [8] log likelihood: -1154.260931
EM: Round [9] log likelihood: -1154.201586
EM: Round [10] log likelihood: -1154.148513
EM: Round [11] log likelihood: -1154.100978
EM: Round [12] log likelihood: -1154.058348
EM: Round [13] log likelihood: -1154.020073
EM: Round [14] log likelihood: -1153.985673
EM: Round [15] log likelihood: -1153.954726
EM: Round [16] log likelihood: -1153.926863
EM: Round [17] log likelihood: -1153.901759
EM: Round [18] log likelihood: -1153.879126
EM: Round [19] log likelihood: -1153.858708
EM: Round [20] log likelihood: -1153.840280
EM: Round [21] log likelihood: -1153.823638
EM: Round [22] log likelihood: -1153.808605
EM: Round [23] log likelihood: -1153.795018
EM: Round [24] log likelihood: -1153.782736
EM: Round [25] log likelihood: -1153.771628
EM: Round [26] log likelihood: -1153.761580
EM: Round [27] log likelihood: -1153.752489
EM: Round [28] log likelihood: -1153.744261
EM: Round [29] log likelihood: -1153.736813
EM: Round [30] log likelihood: -1153.730070
EM: Round [31] log likelihood: -1153.723964
EM: Round [32] log likelihood: -1153.718434
EM: Round [33] log likelihood: -1153.713425
EM: Round [34] log likelihood: -1153.708888
EM: Round [35] log likelihood: -1153.704777
EM: Round [36] log likelihood: -1153.701052
EM: Round [37] log likelihood: -1153.697676
EM: Round [38] log likelihood: -1153.694617
EM: Round [39] log likelihood: -1153.691845
EM: Round [40] log likelihood: -1153.689332
EM: Round [41] log likelihood: -1153.687054
EM: Round [42] log likelihood: -1153.684990
EM: Round [43] log likelihood: -1153.683118
EM: Round [44] log likelihood: -1153.681421
EM: Round [45] log likelihood: -1153.679883
EM: Round [46] log likelihood: -1153.678488
EM: Round [47] log likelihood: -1153.677223
EM: Round [48] log likelihood: -1153.676077
EM: Round [49] log likelihood: -1153.675037
EM: Round [50] log likelihood: -1153.674094
EM: Round [51] log likelihood: -1153.673240
EM: Round [52] log likelihood: -1153.672464
EM: Round [53] log likelihood: -1153.671761
EM: Round [54] log likelihood: -1153.671124
EM: Round [55] log likelihood: -1153.670546
EM: Round [56] log likelihood: -1153.670022
EM: Round [57] log likelihood: -1153.669546
EM: Round [58] log likelihood: -1153.669115
EM: Round [59] log likelihood: -1153.668724
EM: Round [60] log likelihood: -1153.668370
EM: Round [61] log likelihood: -1153.668048
EM: Round [62] log likelihood: -1153.667757
EM: Round [63] log likelihood: -1153.667492
EM: Round [64] log likelihood: -1153.667252
EM: Round [65] log likelihood: -1153.667035
EM: Round [66] log likelihood: -1153.666837
EM: Round [67] log likelihood: -1153.666659
EM: Round [68] log likelihood: -1153.666496
EM: Round [69] log likelihood: -1153.666349
EM: Round [70] log likelihood: -1153.666216
EM: Round [71] log likelihood: -1153.666095
EM: Round [72] log likelihood: -1153.665985
EM: Round [73] log likelihood: -1153.665885
EM: Stopping iterations at round 73 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.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fusion_preds.coalesced.summary > /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.XV5eT4t5u0/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.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.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.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.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.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.XV5eT4t5u0/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.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.fa - | samtools sort -@ 8 - -o /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.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.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.fa - | samtools sort -@ 8 - -o /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.junction_reads.bam"
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.junction_reads.bam
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.junction_reads.bam > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.junction_reads.bam > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.junction_reads.bam.bed
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/tih_rna_sample_00090_23H5VFLT4_s32.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.junction_reads.bam.bed > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.junction_reads.bam.bed > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/tih_rna_sample_00090_23H5VFLT4_s32.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/tih_rna_sample_00090_23H5VFLT4_s32.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/tih_rna_sample_00090_23H5VFLT4_s32.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.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.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.spanning_reads.bam
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.fa - | samtools sort -@ 8 - -o /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.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.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.fa - | samtools sort -@ 8 - -o /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.spanning_reads.bam || :
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.spanning_reads.bam
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.spanning_reads.bam > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.spanning_reads.bam > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.spanning_reads.bam.bed
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/tih_rna_sample_00090_23H5VFLT4_s32.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.spanning_reads.bam.bed > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.spanning_reads.bam.bed > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/tih_rna_sample_00090_23H5VFLT4_s32.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/tih_rna_sample_00090_23H5VFLT4_s32.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/tih_rna_sample_00090_23H5VFLT4_s32.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.star.cSorted.dupsMarked.bam /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.consolidated.bam
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.consolidated.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.consolidated.bam
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.consolidated.bam into /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.consolidated.bam.read_coords
CMD: touch /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.consolidated.bam.read_coords > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.consolidated.bam.frag_coords > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.09 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.XV5eT4t5u0/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.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fusion_preds.coalesced.summary /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.consolidated.bam.frag_coords > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.igv.FusionJuncSpan
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fusion_preds.coalesced.summary /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.consolidated.bam.frag_coords > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.igv.FusionJuncSpan
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.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.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.igv.Pfam.gff3
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.igv.Pfam.gff3 > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.igv.Pfam.gff3 > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.igv.Pfam.bed
Running: touch /tmp/nxf.XV5eT4t5u0/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.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.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.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.igv.seqsimilar.gff3
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.igv.seqsimilar.gff3 > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.igv.seqsimilar.gff3 > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.igv.seqsimilar.bed
Running: touch /tmp/nxf.XV5eT4t5u0/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.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.fa > /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.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.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.fa > /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32 --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.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.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.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.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.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.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.XV5eT4t5u0/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.XV5eT4t5u0/ctat_genome_lib_build_dir
-done, see /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.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.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.XV5eT4t5u0/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -1118.542712
EM: Round [1] log likelihood: -1118.542712
EM: Stopping iterations at round 1 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.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32_1.fastp.fastq.gz /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32_1.fastp.fastq.gz: 296131405
Execution Time = 5.49 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32_1.fastp.fastq.gz /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.fa --gtf /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.gtf > /tmp/nxf.XV5eT4t5u0/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.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.fa --gtf /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.gtf > /tmp/nxf.XV5eT4t5u0/fi_workdir/microH.dat
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.XV5eT4t5u0/fi_workdir/microH.dat /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.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.XV5eT4t5u0/fi_workdir/microH.dat /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.XV5eT4t5u0 --json_outfile /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.fusion_inspector_web.json --file_prefix tih_rna_sample_00090_23H5VFLT4_s32
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.XV5eT4t5u0 --json_outfile /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.fusion_inspector_web.json --file_prefix tih_rna_sample_00090_23H5VFLT4_s32
Running: touch /tmp/nxf.XV5eT4t5u0/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.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00090_23H5VFLT4_s32 --html_output /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.00 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.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00090_23H5VFLT4_s32 --html_output /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.fusion_inspector_web.html
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.XV5eT4t5u0/ctat_genome_lib_build_dir > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.XV5eT4t5u0/ctat_genome_lib_build_dir > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.XV5eT4t5u0/ctat_genome_lib_build_dir > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.XV5eT4t5u0/ctat_genome_lib_build_dir > /tmp/nxf.XV5eT4t5u0/tih_rna_sample_00090_23H5VFLT4_s32.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.XV5eT4t5u0/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory