2026-06-08 10:46:39,211 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.D0FM3SWIx1/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.D0FM3SWIx1/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1 --shrink_introns --max_intron_length 1000
2026-06-08 10:46:46,904 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.D0FM3SWIx1/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.D0FM3SWIx1/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1 --shrink_introns --max_intron_length 1000
2026-06-08 10:46:46,904 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/fusion_contigs.ok
2026-06-08 10:46:46,906 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fa
2026-06-08 10:46:46,909 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fa
2026-06-08 10:46:46,909 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/cp_contigs_file_workdir
2026-06-08 10:46:46,911 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.gtf
2026-06-08 10:46:46,914 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.gtf
2026-06-08 10:46:46,914 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/cp_gtf_file_workdir.ok
2026-06-08 10:46:46,915 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.D0FM3SWIx1/cytoBand.txt
2026-06-08 10:46:47,060 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.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.D0FM3SWIx1/cytoBand.txt
2026-06-08 10:46:47,060 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/cytoband.ok
2026-06-08 10:46:47,062 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.bed
2026-06-08 10:46:47,233 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.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.bed
2026-06-08 10:46:47,233 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/merged_contig_gtf_to_bed.ok
2026-06-08 10:46:47,235 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
2026-06-08 10:46:47,237 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
2026-06-08 10:46:47,237 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.bed.bedsort.ok
2026-06-08 10:46:47,238 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
2026-06-08 10:46:47,248 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
2026-06-08 10:46:47,248 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.bed.bgzip.ok
2026-06-08 10:46:47,250 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz
2026-06-08 10:46:47,255 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz
2026-06-08 10:46:47,256 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.bed.tabix.ok
2026-06-08 10:46:47,257 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools faidx /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fa
2026-06-08 10:46:47,271 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fa
2026-06-08 10:46:47,271 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/merged_contig_fai.ok
2026-06-08 10:46:47,272 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.D0FM3SWIx1/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.D0FM3SWIx1/fi_workdir --reads "/tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz"
2026-06-08 11:41:44,568 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 54.95 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.D0FM3SWIx1/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.D0FM3SWIx1/fi_workdir --reads "/tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz"
2026-06-08 11:41:44,568 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/run_STAR.ok
2026-06-08 11:41:44,570 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --remove_dups
2026-06-08 11:43:56,056 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 2.19 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --remove_dups
2026-06-08 11:43:56,056 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/mark_dup_reads.ok
2026-06-08 11:43:56,059 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam
2026-06-08 11:44:12,580 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.28 minutes. CMD: samtools index /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam
2026-06-08 11:44:12,580 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/mark_dups_reads.index.ok
2026-06-08 11:44:12,582 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.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
2026-06-08 12:00:42,684 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 16.50 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
2026-06-08 12:00:42,684 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok
2026-06-08 12:00:42,687 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.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
2026-06-08 12:41:42,979 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 41.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
2026-06-08 12:41:42,979 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok
2026-06-08 12:41:42,981 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary
2026-06-08 12:41:43,080 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.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary
2026-06-08 12:41:43,080 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/coalesce_junc_n_span.ok
2026-06-08 12:41:43,082 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj
2026-06-08 12:41:43,137 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.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj
2026-06-08 12:41:43,137 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/init_EM_adj_counts.ok
2026-06-08 12:41:43,139 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.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
2026-06-08 12:41:43,164 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.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
2026-06-08 12:41:43,164 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/filter_by_frag_threshs.ok
2026-06-08 12:41:43,165 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
2026-06-08 12:41:43,183 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
2026-06-08 12:41:43,183 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/prep_igv_extract_junc_reads.ok
2026-06-08 12:41:43,184 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.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam"
2026-06-08 12:41:43,276 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.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam"
2026-06-08 12:41:43,277 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/prep_igv_junc_reads_bam.ok
2026-06-08 12:41:43,279 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam
2026-06-08 12:41:43,289 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam
2026-06-08 12:41:43,289 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/samtools_idx_junc_reads_bam.ok
2026-06-08 12:41:43,291 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed
2026-06-08 12:41:43,444 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.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed
2026-06-08 12:41:43,444 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bam_to_bed.ok
2026-06-08 12:41:43,446 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
2026-06-08 12:41:43,451 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
2026-06-08 12:41:43,451 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bedsort.ok
2026-06-08 12:41:43,453 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
2026-06-08 12:41:43,467 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
2026-06-08 12:41:43,467 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bgzip.ok
2026-06-08 12:41:43,469 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz
2026-06-08 12:41:43,476 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz
2026-06-08 12:41:43,476 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.tabix.ok
2026-06-08 12:41:43,478 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
2026-06-08 12:41:43,495 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
2026-06-08 12:41:43,495 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/span_reads_acc.ok
2026-06-08 12:41:43,497 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools view -H /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
2026-06-08 12:41:43,502 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
2026-06-08 12:41:43,502 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/init_spanning_reads_bam.ok
2026-06-08 12:41:43,504 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam || :
2026-06-08 12:41:43,542 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.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam || :
2026-06-08 12:41:43,542 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/prep_spanning_reads.ok
2026-06-08 12:41:43,544 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
2026-06-08 12:41:43,549 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
2026-06-08 12:41:43,549 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/samtools_index_span_reads_bam.ok
2026-06-08 12:41:43,551 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed
2026-06-08 12:41:43,566 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.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed
2026-06-08 12:41:43,566 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bam_to_bed.ok
2026-06-08 12:41:43,567 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
2026-06-08 12:41:43,569 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
2026-06-08 12:41:43,569 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bedsort.ok
2026-06-08 12:41:43,571 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
2026-06-08 12:41:43,577 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
2026-06-08 12:41:43,577 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bgzip.ok
2026-06-08 12:41:43,579 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz
2026-06-08 12:41:43,583 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz
2026-06-08 12:41:43,583 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.tabix.ok
2026-06-08 12:41:43,585 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
2026-06-08 12:41:43,828 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
2026-06-08 12:41:43,828 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/cp_consol_bam.ok
2026-06-08 12:41:43,830 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
2026-06-08 12:42:00,301 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.27 minutes. CMD: samtools index /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
2026-06-08 12:42:00,301 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/index_consol_bam.ok
2026-06-08 12:42:00,303 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000
2026-06-08 12:50:21,519 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 8.35 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000
2026-06-08 12:50:21,519 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/prep_igv_sam_frag_coordss.ok
2026-06-08 12:50:21,521 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.igv.FusionJuncSpan
2026-06-08 12:50:30,522 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.15 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.igv.FusionJuncSpan
2026-06-08 12:50:30,522 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/prep_igv_juncspan_fmt.ok
2026-06-08 12:50:30,524 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3
2026-06-08 12:50:30,619 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.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3
2026-06-08 12:50:30,619 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/prep_igv_pfam_gff3.ok
2026-06-08 12:50:30,621 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed
2026-06-08 12:50:30,668 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.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed
2026-06-08 12:50:30,668 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/prep_igv_pfam_bed.ok
2026-06-08 12:50:30,670 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.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3
2026-06-08 12:50:30,708 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.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3
2026-06-08 12:50:30,708 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/prep_igv_seqsim_gff3.ok
2026-06-08 12:50:30,710 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed
2026-06-08 12:50:30,732 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.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed
2026-06-08 12:50:30,733 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/prep_igv_seqsim_bed.ok
2026-06-08 12:50:30,734 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.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
2026-06-08 12:50:30,864 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.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
2026-06-08 12:50:30,864 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/add_splice_info.ok
2026-06-08 12:50:30,866 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.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
2026-06-08 12:50:31,018 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.D0FM3SWIx1/fi_workdir/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
2026-06-08 12:50:31,018 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/blast_filter.ok
2026-06-08 12:50:31,020 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.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.D0FM3SWIx1/ctat_genome_lib_build_dir
2026-06-08 12:50:31,041 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.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.D0FM3SWIx1/ctat_genome_lib_build_dir
2026-06-08 12:50:31,041 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/annot_filter.ok
2026-06-08 12:50:31,043 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
2026-06-08 12:50:31,070 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.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
2026-06-08 12:50:31,070 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/EM_adj_counts.ok
2026-06-08 12:50:31,072 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
2026-06-08 12:55:41,299 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 5.17 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
2026-06-08 12:55:41,300 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/add_FFPM.ok
2026-06-08 12:55:41,302 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.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.D0FM3SWIx1/fi_workdir/microH.dat
2026-06-08 12:55:42,414 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.D0FM3SWIx1/fi_workdir/microH.dat
2026-06-08 12:55:42,414 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/microH.dat.ok
2026-06-08 12:55:42,416 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.D0FM3SWIx1/fi_workdir/microH.dat /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
2026-06-08 12:55:42,478 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.D0FM3SWIx1/fi_workdir/microH.dat /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
2026-06-08 12:55:42,478 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/append_microH_info.ok
2026-06-08 12:55:42,479 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv
2026-06-08 12:55:42,482 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv
2026-06-08 12:55:42,482 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/cp_final.ok
2026-06-08 12:55:42,484 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv
2026-06-08 12:55:42,499 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv
2026-06-08 12:55:42,499 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/final.abridged.ok
2026-06-08 12:55:42,501 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.D0FM3SWIx1 --json_outfile /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1
2026-06-08 12:55:42,522 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.D0FM3SWIx1 --json_outfile /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1
2026-06-08 12:55:42,522 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/create_fi_igvjs.ok
2026-06-08 12:55:42,524 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.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html
2026-06-08 12:55:44,798 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.04 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.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html
2026-06-08 12:55:44,798 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/fusion_reports_html.ok
2026-06-08 12:55:44,800 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.D0FM3SWIx1/ctat_genome_lib_build_dir > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated
2026-06-08 12:55:44,830 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.D0FM3SWIx1/ctat_genome_lib_build_dir > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated
2026-06-08 12:55:44,830 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/fusion_annotator.ok
2026-06-08 12:55:44,832 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.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.D0FM3SWIx1/ctat_genome_lib_build_dir > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
2026-06-08 12:55:44,908 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.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.D0FM3SWIx1/ctat_genome_lib_build_dir > /tmp/nxf.D0FM3SWIx1/1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
2026-06-08 12:55:44,908 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.D0FM3SWIx1/chckpts_dir/fusion_coding_region_effect.ok