2026-06-08 08:39:28,922 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.j6ThnLCgnZ/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.j6ThnLCgnZ/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000
2026-06-08 08:39:35,990 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.j6ThnLCgnZ/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.j6ThnLCgnZ/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000
2026-06-08 08:39:35,990 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/fusion_contigs.ok
2026-06-08 08:39:35,992 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fa
2026-06-08 08:39:35,994 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fa
2026-06-08 08:39:35,994 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/cp_contigs_file_workdir
2026-06-08 08:39:35,996 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.gtf
2026-06-08 08:39:35,999 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.gtf
2026-06-08 08:39:35,999 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/cp_gtf_file_workdir.ok
2026-06-08 08:39:36,000 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.j6ThnLCgnZ/cytoBand.txt
2026-06-08 08:39:36,055 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.j6ThnLCgnZ/cytoBand.txt
2026-06-08 08:39:36,055 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/cytoband.ok
2026-06-08 08:39:36,057 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.bed
2026-06-08 08:39:36,188 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.bed
2026-06-08 08:39:36,188 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/merged_contig_gtf_to_bed.ok
2026-06-08 08:39:36,190 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
2026-06-08 08:39:36,192 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
2026-06-08 08:39:36,192 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.bed.bedsort.ok
2026-06-08 08:39:36,193 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
2026-06-08 08:39:36,200 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
2026-06-08 08:39:36,200 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.bed.bgzip.ok
2026-06-08 08:39:36,202 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
2026-06-08 08:39:36,207 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
2026-06-08 08:39:36,207 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.bed.tabix.ok
2026-06-08 08:39:36,208 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools faidx /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fa
2026-06-08 08:39:36,215 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fa
2026-06-08 08:39:36,215 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/merged_contig_fai.ok
2026-06-08 08:39:36,217 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.j6ThnLCgnZ/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_eu1-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.j6ThnLCgnZ/fi_workdir --reads "/tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
2026-06-08 09:15:28,101 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 35.86 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.j6ThnLCgnZ/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_eu1-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.j6ThnLCgnZ/fi_workdir --reads "/tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
2026-06-08 09:15:28,101 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/run_STAR.ok
2026-06-08 09:15:28,103 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --remove_dups
2026-06-08 09:15:40,403 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.20 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --remove_dups
2026-06-08 09:15:40,403 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/mark_dup_reads.ok
2026-06-08 09:15:40,405 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
2026-06-08 09:15:41,980 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
2026-06-08 09:15:41,980 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/mark_dups_reads.index.ok
2026-06-08 09:15:41,982 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
2026-06-08 09:17:21,920 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 1.67 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
2026-06-08 09:17:21,921 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok
2026-06-08 09:17:21,923 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
2026-06-08 09:22:21,933 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 5.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
2026-06-08 09:22:21,933 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok
2026-06-08 09:22:21,935 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary
2026-06-08 09:22:21,983 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary
2026-06-08 09:22:21,983 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/coalesce_junc_n_span.ok
2026-06-08 09:22:21,985 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
2026-06-08 09:22:22,026 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
2026-06-08 09:22:22,026 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/init_EM_adj_counts.ok
2026-06-08 09:22:22,028 INFO Pipeliner.Pipeliner.run_cmd at 21 :
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.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
2026-06-08 09:22:22,049 INFO Pipeliner.Pipeliner.run at 136 :
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.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
2026-06-08 09:22:22,049 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/filter_by_frag_threshs.ok
2026-06-08 09:22:22,050 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
2026-06-08 09:22:22,066 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
2026-06-08 09:22:22,066 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/prep_igv_extract_junc_reads.ok
2026-06-08 09:22:22,068 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam"
2026-06-08 09:22:22,245 INFO Pipeliner.Pipeliner.run at 136 :
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.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam"
2026-06-08 09:22:22,246 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/prep_igv_junc_reads_bam.ok
2026-06-08 09:22:22,248 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
2026-06-08 09:22:22,262 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
2026-06-08 09:22:22,262 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/samtools_idx_junc_reads_bam.ok
2026-06-08 09:22:22,264 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed
2026-06-08 09:22:22,576 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed
2026-06-08 09:22:22,576 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bam_to_bed.ok
2026-06-08 09:22:22,579 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
2026-06-08 09:22:22,587 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
2026-06-08 09:22:22,587 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bedsort.ok
2026-06-08 09:22:22,589 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
2026-06-08 09:22:22,608 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
2026-06-08 09:22:22,608 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bgzip.ok
2026-06-08 09:22:22,610 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
2026-06-08 09:22:22,619 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
2026-06-08 09:22:22,619 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.tabix.ok
2026-06-08 09:22:22,621 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
2026-06-08 09:22:22,635 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
2026-06-08 09:22:22,635 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/span_reads_acc.ok
2026-06-08 09:22:22,637 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools view -H /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
2026-06-08 09:22:22,642 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
2026-06-08 09:22:22,643 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/init_spanning_reads_bam.ok
2026-06-08 09:22:22,644 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || :
2026-06-08 09:22:22,681 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || :
2026-06-08 09:22:22,681 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/prep_spanning_reads.ok
2026-06-08 09:22:22,683 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
2026-06-08 09:22:22,688 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
2026-06-08 09:22:22,688 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/samtools_index_span_reads_bam.ok
2026-06-08 09:22:22,689 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed
2026-06-08 09:22:22,704 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed
2026-06-08 09:22:22,705 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bam_to_bed.ok
2026-06-08 09:22:22,707 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
2026-06-08 09:22:22,708 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
2026-06-08 09:22:22,709 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bedsort.ok
2026-06-08 09:22:22,710 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
2026-06-08 09:22:22,715 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
2026-06-08 09:22:22,715 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bgzip.ok
2026-06-08 09:22:22,717 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
2026-06-08 09:22:22,722 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
2026-06-08 09:22:22,722 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.tabix.ok
2026-06-08 09:22:22,724 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
2026-06-08 09:22:22,747 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
2026-06-08 09:22:22,747 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/cp_consol_bam.ok
2026-06-08 09:22:22,749 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
2026-06-08 09:22:24,308 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
2026-06-08 09:22:24,308 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/index_consol_bam.ok
2026-06-08 09:22:24,310 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000
2026-06-08 09:23:10,225 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.77 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000
2026-06-08 09:23:10,225 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/prep_igv_sam_frag_coordss.ok
2026-06-08 09:23:10,227 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan
2026-06-08 09:23:11,163 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan
2026-06-08 09:23:11,163 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/prep_igv_juncspan_fmt.ok
2026-06-08 09:23:11,165 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3
2026-06-08 09:23:11,274 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3
2026-06-08 09:23:11,274 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/prep_igv_pfam_gff3.ok
2026-06-08 09:23:11,276 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed
2026-06-08 09:23:11,345 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed
2026-06-08 09:23:11,345 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/prep_igv_pfam_bed.ok
2026-06-08 09:23:11,347 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3
2026-06-08 09:23:11,380 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3
2026-06-08 09:23:11,380 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/prep_igv_seqsim_gff3.ok
2026-06-08 09:23:11,382 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed
2026-06-08 09:23:11,403 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed
2026-06-08 09:23:11,403 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/prep_igv_seqsim_bed.ok
2026-06-08 09:23:11,405 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
2026-06-08 09:23:11,453 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
2026-06-08 09:23:11,453 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/add_splice_info.ok
2026-06-08 09:23:11,455 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
2026-06-08 09:23:11,609 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.j6ThnLCgnZ/fi_workdir/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
2026-06-08 09:23:11,609 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/blast_filter.ok
2026-06-08 09:23:11,611 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.j6ThnLCgnZ/ctat_genome_lib_build_dir
2026-06-08 09:23:11,631 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.j6ThnLCgnZ/ctat_genome_lib_build_dir
2026-06-08 09:23:11,631 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/annot_filter.ok
2026-06-08 09:23:11,633 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
2026-06-08 09:23:11,670 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
2026-06-08 09:23:11,670 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/EM_adj_counts.ok
2026-06-08 09:23:11,671 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
2026-06-08 09:25:30,028 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 2.31 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
2026-06-08 09:25:30,028 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/add_FFPM.ok
2026-06-08 09:25:30,031 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.j6ThnLCgnZ/fi_workdir/microH.dat
2026-06-08 09:25:30,197 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.j6ThnLCgnZ/fi_workdir/microH.dat
2026-06-08 09:25:30,198 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/microH.dat.ok
2026-06-08 09:25:30,200 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.j6ThnLCgnZ/fi_workdir/microH.dat /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
2026-06-08 09:25:30,247 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.j6ThnLCgnZ/fi_workdir/microH.dat /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
2026-06-08 09:25:30,247 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/append_microH_info.ok
2026-06-08 09:25:30,249 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
2026-06-08 09:25:30,252 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
2026-06-08 09:25:30,252 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/cp_final.ok
2026-06-08 09:25:30,253 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv
2026-06-08 09:25:30,268 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv
2026-06-08 09:25:30,268 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/final.abridged.ok
2026-06-08 09:25:30,270 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.j6ThnLCgnZ --json_outfile /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_eu1-T1-TRNA-1_B23MHV2LT4_1
2026-06-08 09:25:30,291 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.j6ThnLCgnZ --json_outfile /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_eu1-T1-TRNA-1_B23MHV2LT4_1
2026-06-08 09:25:30,291 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/create_fi_igvjs.ok
2026-06-08 09:25:30,292 INFO Pipeliner.Pipeliner.run_cmd at 21 :
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.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_eu1-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
2026-06-08 09:25:31,079 INFO Pipeliner.Pipeliner.run at 136 :
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.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_eu1-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
2026-06-08 09:25:31,079 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/fusion_reports_html.ok
2026-06-08 09:25:31,081 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.j6ThnLCgnZ/ctat_genome_lib_build_dir > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated
2026-06-08 09:25:31,107 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.j6ThnLCgnZ/ctat_genome_lib_build_dir > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated
2026-06-08 09:25:31,107 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/fusion_annotator.ok
2026-06-08 09:25:31,109 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.j6ThnLCgnZ/ctat_genome_lib_build_dir > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
2026-06-08 09:25:31,235 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.j6ThnLCgnZ/ctat_genome_lib_build_dir > /tmp/nxf.j6ThnLCgnZ/659_eu1-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
2026-06-08 09:25:31,235 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.j6ThnLCgnZ/chckpts_dir/fusion_coding_region_effect.ok