Work Directory

Attempt
1
S3 Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/99d04f466788e380ff145b548e516e

Files (108)

Name Size Modified
.command.begin 6 bytes May 27, 2026 8:37 AM
.command.err 5.1 KB May 27, 2026 8:47 AM
.command.log 35.5 KB May 27, 2026 8:47 AM
.command.out 29.6 KB May 27, 2026 8:47 AM
.command.run 14.2 KB May 27, 2026 8:36 AM
.command.sh 590 bytes May 27, 2026 8:36 AM
.command.trace 286 bytes May 27, 2026 8:47 AM
.command.yaml 3.9 KB May 27, 2026 8:36 AM
.exitcode 1 byte May 27, 2026 8:47 AM
FusionInspector.log 39.4 KB May 27, 2026 8:47 AM
chckpts_dir/EM_adj_counts.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/add_FFPM.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/add_splice_info.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/annot_filter.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/append_microH_info.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/blast_filter.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/coalesce_junc_n_span.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/cp_consol_bam.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/cp_contigs_file_workdir 0 bytes May 27, 2026 8:47 AM
chckpts_dir/cp_final.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/cp_gtf_file_workdir.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/create_fi_igvjs.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/cytoband.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/filter_by_frag_threshs.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/final.abridged.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/fusion_annotator.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/fusion_coding_region_effect.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/fusion_contigs.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/fusion_reports_html.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/index_consol_bam.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/init_EM_adj_counts.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/init_spanning_reads_bam.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/mark_dup_reads.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/mark_dups_reads.index.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/merged_contig_fai.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/merged_contig_gtf_to_bed.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/microH.dat.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/prep_igv_extract_junc_reads.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/prep_igv_junc_reads_bam.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/prep_igv_juncspan_fmt.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/prep_igv_pfam_bed.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/prep_igv_pfam_gff3.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/prep_igv_sam_frag_coordss.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/prep_igv_seqsim_bed.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/prep_igv_seqsim_gff3.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/prep_spanning_reads.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/rna_s1221_S42.bed.bedsort.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/rna_s1221_S42.bed.bgzip.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/rna_s1221_S42.bed.tabix.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/rna_s1221_S42.junction_reads.bam.bam_to_bed.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/rna_s1221_S42.junction_reads.bam.bedsort.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/rna_s1221_S42.junction_reads.bam.bgzip.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/rna_s1221_S42.junction_reads.bam.tabix.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/rna_s1221_S42.spanning_reads.bam.bam_to_bed.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/rna_s1221_S42.spanning_reads.bam.bedsort.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/rna_s1221_S42.spanning_reads.bam.bgzip.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/rna_s1221_S42.spanning_reads.bam.tabix.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/run_STAR.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/samtools_idx_junc_reads_bam.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/samtools_index_span_reads_bam.ok 0 bytes May 27, 2026 8:47 AM
chckpts_dir/span_reads_acc.ok 0 bytes May 27, 2026 8:47 AM
fi_workdir/Log.final.out 2.0 KB May 27, 2026 8:47 AM
fi_workdir/Log.out 20.6 KB May 27, 2026 8:47 AM
fi_workdir/Log.progress.out 364 bytes May 27, 2026 8:47 AM
fi_workdir/SJ.out.tab 6.2 MB May 27, 2026 8:47 AM
fi_workdir/_STARgenome/exonGeTrInfo.tab 64.6 KB May 27, 2026 8:47 AM
fi_workdir/_STARgenome/exonInfo.tab 31.1 KB May 27, 2026 8:47 AM
fi_workdir/_STARgenome/geneInfo.tab 1.1 KB May 27, 2026 8:47 AM
fi_workdir/_STARgenome/sjdbInfo.txt 10.8 MB May 27, 2026 8:47 AM
fi_workdir/_STARgenome/sjdbList.fromGTF.out.tab 14.4 KB May 27, 2026 8:47 AM
fi_workdir/_STARgenome/sjdbList.out.tab 9.5 MB May 27, 2026 8:47 AM
fi_workdir/_STARgenome/transcriptInfo.tab 16.7 KB May 27, 2026 8:47 AM
fi_workdir/microH.dat 84.6 KB May 27, 2026 8:47 AM
fi_workdir/pipeliner.1152.cmds 879 bytes May 27, 2026 8:47 AM
fi_workdir/rna_s1221_S42.fa 498.9 KB May 27, 2026 8:47 AM
fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary 131.1 KB May 27, 2026 8:47 AM
fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj 131.3 KB May 27, 2026 8:47 AM
fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh 131.3 KB May 27, 2026 8:47 AM
fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo 131.5 KB May 27, 2026 8:47 AM
fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter 131.5 KB May 27, 2026 8:47 AM
fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.info 131.5 KB May 27, 2026 8:47 AM
fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter 131.5 KB May 27, 2026 8:47 AM
fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter.info 131.5 KB May 27, 2026 8:47 AM
fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_junction_read_accs 18.3 KB May 27, 2026 8:47 AM
fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_spanning_read_accs 588 bytes May 27, 2026 8:47 AM
fi_workdir/rna_s1221_S42.gtf 2.1 MB May 27, 2026 8:47 AM
fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam 1.8 MB May 27, 2026 8:47 AM
fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.bai 2.9 KB May 27, 2026 8:47 AM
fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.failed_reads_during_span_analysis 171.9 KB May 27, 2026 8:47 AM
fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam 159.0 KB May 27, 2026 8:47 AM
fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junction_info 19.1 KB May 27, 2026 8:47 AM
fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_span_reads.sam 1.0 KB May 27, 2026 8:47 AM
fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_spanning_info 113.0 KB May 27, 2026 8:47 AM
fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.read_align_counts.idx 4.8 MB May 27, 2026 8:47 AM
fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.read_align_counts.idx.ok 0 bytes May 27, 2026 8:47 AM
fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.spanning_reads_want.idx 8.0 KB May 27, 2026 8:47 AM
fi_workdir/rna_s1221_S42.star.sortedByCoord.out.bam 2.8 MB May 27, 2026 8:47 AM
fi_workdir/rna_s1221_S42.star.sortedByCoord.out.bam.bai 3.0 KB May 27, 2026 8:47 AM
fi_workdir/rna_s1221_S42.star.sortedByCoord.out.bam.bai.ok 0 bytes May 27, 2026 8:47 AM
fi_workdir/rna_s1221_S42.star.sortedByCoord.out.bam.ok 0 bytes May 27, 2026 8:47 AM
fi_workdir/star_align.ok 0 bytes May 27, 2026 8:47 AM
rna_s1221_S42.FusionInspector.fusions.abridged.tsv 2.2 KB May 27, 2026 8:47 AM
rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 44.3 KB May 27, 2026 8:47 AM
rna_s1221_S42.FusionInspector.fusions.tsv 131.7 KB May 27, 2026 8:47 AM
rna_s1221_S42.fusion_inspector_web.html 268.4 KB May 27, 2026 8:47 AM
versions.yml 103 bytes May 27, 2026 8:47 AM