2026-06-08 11:35:46,040 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv --gtf /tmp/nxf.C1XRhGIdM9/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.C1XRhGIdM9/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2 --shrink_introns --max_intron_length 1000
2026-06-08 11:35:53,973 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_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv --gtf /tmp/nxf.C1XRhGIdM9/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.C1XRhGIdM9/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2 --shrink_introns --max_intron_length 1000
2026-06-08 11:35:53,973 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/fusion_contigs.ok
2026-06-08 11:35:53,975 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fa
2026-06-08 11:35:53,978 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fa
2026-06-08 11:35:53,978 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/cp_contigs_file_workdir
2026-06-08 11:35:53,980 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.gtf /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.gtf
2026-06-08 11:35:53,986 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.gtf /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.gtf
2026-06-08 11:35:53,986 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/cp_gtf_file_workdir.ok
2026-06-08 11:35:53,988 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.C1XRhGIdM9/cytoBand.txt
2026-06-08 11:35:54,149 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.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.C1XRhGIdM9/cytoBand.txt
2026-06-08 11:35:54,150 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/cytoband.ok
2026-06-08 11:35:54,151 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.bed
2026-06-08 11:35:54,669 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.bed
2026-06-08 11:35:54,669 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/merged_contig_gtf_to_bed.ok
2026-06-08 11:35:54,671 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.bed > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed
2026-06-08 11:35:54,673 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.bed > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed
2026-06-08 11:35:54,673 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.bed.bedsort.ok
2026-06-08 11:35:54,675 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed
2026-06-08 11:35:54,689 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed
2026-06-08 11:35:54,689 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.bed.bgzip.ok
2026-06-08 11:35:54,691 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed.gz
2026-06-08 11:35:54,698 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed.gz
2026-06-08 11:35:54,698 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.bed.tabix.ok
2026-06-08 11:35:54,699 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools faidx /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fa
2026-06-08 11:35:54,712 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fa
2026-06-08 11:35:54,712 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/merged_contig_fai.ok
2026-06-08 11:35:54,714 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.C1XRhGIdM9/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.gtf --CPU 8 --out_prefix 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star --out_dir /tmp/nxf.C1XRhGIdM9/fi_workdir --reads "/tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz"
2026-06-08 12:44:18,106 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 68.39 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.C1XRhGIdM9/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.gtf --CPU 8 --out_prefix 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star --out_dir /tmp/nxf.C1XRhGIdM9/fi_workdir --reads "/tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz"
2026-06-08 12:44:18,106 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/run_STAR.ok
2026-06-08 12:44:18,108 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --remove_dups
2026-06-08 12:45:14,202 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.93 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --remove_dups
2026-06-08 12:45:14,202 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/mark_dup_reads.ok
2026-06-08 12:45:14,204 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam
2026-06-08 12:45:21,300 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.12 minutes. CMD: samtools index /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam
2026-06-08 12:45:21,300 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/mark_dups_reads.index.ok
2026-06-08 12:45:21,302 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.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
2026-06-08 12:51:48,198 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 6.45 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
2026-06-08 12:51:48,198 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok
2026-06-08 12:51:48,201 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.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
2026-06-08 13:11:02,402 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 19.24 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
2026-06-08 13:11:02,402 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok
2026-06-08 13:11:02,405 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary
2026-06-08 13:11:02,584 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.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary
2026-06-08 13:11:02,584 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/coalesce_junc_n_span.ok
2026-06-08 13:11:02,586 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj
2026-06-08 13:11:02,645 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.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj
2026-06-08 13:11:02,645 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/init_EM_adj_counts.ok
2026-06-08 13:11:02,646 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.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
2026-06-08 13:11:02,675 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.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
2026-06-08 13:11:02,675 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/filter_by_frag_threshs.ok
2026-06-08 13:11:02,677 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs
2026-06-08 13:11:02,697 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs
2026-06-08 13:11:02,697 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/prep_igv_extract_junc_reads.ok
2026-06-08 13:11:02,699 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.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam"
2026-06-08 13:11:02,818 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.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam"
2026-06-08 13:11:02,818 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/prep_igv_junc_reads_bam.ok
2026-06-08 13:11:02,820 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam
2026-06-08 13:11:02,833 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam
2026-06-08 13:11:02,834 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/samtools_idx_junc_reads_bam.ok
2026-06-08 13:11:02,835 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed
2026-06-08 13:11:03,075 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.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed
2026-06-08 13:11:03,076 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bam_to_bed.ok
2026-06-08 13:11:03,077 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed
2026-06-08 13:11:03,084 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed
2026-06-08 13:11:03,084 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bedsort.ok
2026-06-08 13:11:03,086 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed
2026-06-08 13:11:03,106 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed
2026-06-08 13:11:03,107 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bgzip.ok
2026-06-08 13:11:03,108 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed.gz
2026-06-08 13:11:03,116 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed.gz
2026-06-08 13:11:03,116 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.tabix.ok
2026-06-08 13:11:03,118 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs
2026-06-08 13:11:03,138 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs
2026-06-08 13:11:03,138 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/span_reads_acc.ok
2026-06-08 13:11:03,140 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools view -H /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam
2026-06-08 13:11:03,145 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam
2026-06-08 13:11:03,146 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/init_spanning_reads_bam.ok
2026-06-08 13:11:03,147 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam || :
2026-06-08 13:11:03,184 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.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam || :
2026-06-08 13:11:03,184 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/prep_spanning_reads.ok
2026-06-08 13:11:03,186 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam
2026-06-08 13:11:03,190 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam
2026-06-08 13:11:03,191 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/samtools_index_span_reads_bam.ok
2026-06-08 13:11:03,192 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed
2026-06-08 13:11:03,208 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.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed
2026-06-08 13:11:03,208 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bam_to_bed.ok
2026-06-08 13:11:03,209 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed
2026-06-08 13:11:03,211 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed
2026-06-08 13:11:03,211 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bedsort.ok
2026-06-08 13:11:03,213 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed
2026-06-08 13:11:03,218 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed
2026-06-08 13:11:03,218 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bgzip.ok
2026-06-08 13:11:03,220 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed.gz
2026-06-08 13:11:03,224 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed.gz
2026-06-08 13:11:03,224 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.tabix.ok
2026-06-08 13:11:03,226 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam
2026-06-08 13:11:03,328 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam
2026-06-08 13:11:03,328 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/cp_consol_bam.ok
2026-06-08 13:11:03,330 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam
2026-06-08 13:11:10,394 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.12 minutes. CMD: samtools index /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam
2026-06-08 13:11:10,395 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/index_consol_bam.ok
2026-06-08 13:11:10,396 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam --max_insert_size 10000000
2026-06-08 13:14:09,156 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 2.98 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam --max_insert_size 10000000
2026-06-08 13:14:09,156 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/prep_igv_sam_frag_coordss.ok
2026-06-08 13:14:09,158 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.igv.FusionJuncSpan
2026-06-08 13:14:12,374 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.05 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.igv.FusionJuncSpan
2026-06-08 13:14:12,374 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/prep_igv_juncspan_fmt.ok
2026-06-08 13:14:12,376 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3
2026-06-08 13:14:12,697 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3
2026-06-08 13:14:12,697 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/prep_igv_pfam_gff3.ok
2026-06-08 13:14:12,699 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.bed
2026-06-08 13:14:12,815 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.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.bed
2026-06-08 13:14:12,815 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/prep_igv_pfam_bed.ok
2026-06-08 13:14:12,817 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.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3
2026-06-08 13:14:12,897 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.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3
2026-06-08 13:14:12,897 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/prep_igv_seqsim_gff3.ok
2026-06-08 13:14:12,899 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.bed
2026-06-08 13:14:12,921 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.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.bed
2026-06-08 13:14:12,921 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/prep_igv_seqsim_bed.ok
2026-06-08 13:14:12,923 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.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fa > /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
2026-06-08 13:14:13,046 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.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fa > /tmp/nxf.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
2026-06-08 13:14:13,046 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/add_splice_info.ok
2026-06-08 13:14:13,048 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.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
2026-06-08 13:14:13,227 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.C1XRhGIdM9/fi_workdir/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
2026-06-08 13:14:13,228 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/blast_filter.ok
2026-06-08 13:14:13,230 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.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.C1XRhGIdM9/ctat_genome_lib_build_dir
2026-06-08 13:14:13,256 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.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.C1XRhGIdM9/ctat_genome_lib_build_dir
2026-06-08 13:14:13,256 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/annot_filter.ok
2026-06-08 13:14:13,258 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
2026-06-08 13:14:13,304 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.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
2026-06-08 13:14:13,304 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/EM_adj_counts.ok
2026-06-08 13:14:13,306 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
2026-06-08 13:19:52,866 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 5.66 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
2026-06-08 13:19:52,866 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/add_FFPM.ok
2026-06-08 13:19:52,868 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.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fa --gtf /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.C1XRhGIdM9/fi_workdir/microH.dat
2026-06-08 13:19:53,436 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fa --gtf /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.C1XRhGIdM9/fi_workdir/microH.dat
2026-06-08 13:19:53,436 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/microH.dat.ok
2026-06-08 13:19:53,438 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.C1XRhGIdM9/fi_workdir/microH.dat /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
2026-06-08 13:19:53,566 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.C1XRhGIdM9/fi_workdir/microH.dat /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
2026-06-08 13:19:53,567 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/append_microH_info.ok
2026-06-08 13:19:53,569 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv
2026-06-08 13:19:53,572 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv
2026-06-08 13:19:53,572 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/cp_final.ok
2026-06-08 13:19:53,574 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv
2026-06-08 13:19:53,592 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv
2026-06-08 13:19:53,592 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/final.abridged.ok
2026-06-08 13:19:53,594 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.C1XRhGIdM9 --json_outfile /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --file_prefix 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2
2026-06-08 13:19:53,615 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.C1XRhGIdM9 --json_outfile /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --file_prefix 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2
2026-06-08 13:19:53,615 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/create_fi_igvjs.ok
2026-06-08 13:19:53,616 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.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --input_file_prefix 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2 --html_output /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.html
2026-06-08 13:19:55,683 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.03 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.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --input_file_prefix 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2 --html_output /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.html
2026-06-08 13:19:55,683 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/fusion_reports_html.ok
2026-06-08 13:19:55,684 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.C1XRhGIdM9/ctat_genome_lib_build_dir > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated
2026-06-08 13:19:55,728 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.C1XRhGIdM9/ctat_genome_lib_build_dir > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated
2026-06-08 13:19:55,728 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/fusion_annotator.ok
2026-06-08 13:19:55,729 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.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.C1XRhGIdM9/ctat_genome_lib_build_dir > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
2026-06-08 13:19:56,012 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.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.C1XRhGIdM9/ctat_genome_lib_build_dir > /tmp/nxf.C1XRhGIdM9/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
2026-06-08 13:19:56,012 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.C1XRhGIdM9/chckpts_dir/fusion_coding_region_effect.ok