Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/60446498b55aa6efc029283a184293/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/b5375f6458a9bd31034f4aae58fe8f/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/4a4bf2afe7de789ec1bf0906becb61/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/60446498b55aa6efc029283a184293/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/b5375f6458a9bd31034f4aae58fe8f/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/60446498b55aa6efc029283a184293/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.Chimeric.out.junction
==> STAGING COMPLETE (7 inputs)
09:07:33 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[13660000], rate=12418181.82/min 09:08:49 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns.prelim
Use of uninitialized value $ctat_genome_lib in concatenation (.) or string at /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl line 18.
-1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.introns: identified 3557 cancer introns
09:08:50 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns.prelim
09:08:50 : INFO : Running: touch /tmp/nxf.8CucsSjEGe/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/prelim_introns.ok
09:08:50 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns.prelim --min_total_reads 5 > 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns
09:08:51 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns.prelim --min_total_reads 5 > 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns
09:08:51 : INFO : Running: touch /tmp/nxf.8CucsSjEGe/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/introns_filtered.ok
09:08:51 : INFO : -found 1622 cancer introns
09:08:51 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.introns --cancer_introns 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed
09:08:51 : INFO : Creating the BED File.
09:08:57 : INFO : Saving Bed File as 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed
09:08:58 : INFO : Execution Time = 0.11 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.introns --cancer_introns 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed
09:08:58 : INFO : Running: touch /tmp/nxf.8CucsSjEGe/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/intron_igv_bed.ok
09:08:58 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed --bam 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam --output_prefix 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2
[W::hts_idx_load3] The index file is older than the data file: 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
09:25:43 : INFO : Execution Time = 16.76 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed --bam 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam --output_prefix 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2
09:25:43 : INFO : Running: touch /tmp/nxf.8CucsSjEGe/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/reads_alignments_extracted.ok
09:25:43 : INFO : Running: samtools sort -o 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.bam
09:25:43 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.bam
09:25:43 : INFO : Running: touch /tmp/nxf.8CucsSjEGe/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/sort_cancer_intron_reads.ok
09:25:43 : INFO : Running: samtools sort -o 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.bam 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.bam
[bam_sort_core] merging from 68 files and 1 in-memory blocks...
09:42:06 : INFO : Execution Time = 16.38 minutes. CMD: samtools sort -o 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.bam 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.bam
09:42:06 : INFO : Running: touch /tmp/nxf.8CucsSjEGe/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/sort_gene_reads.ok
09:42:06 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.bam
Done with chr chr1.
Done with chr chr2.
Done with chr chr3.
Done with chr chr4.
Done with chr chr5.
Done with chr chr6.
Done with chr chr7.
Done with chr chr8.
Done with chr chr9.
Done with chr chr10.
Done with chr chr11.
Done with chr chr12.
Done with chr chr13.
Done with chr chr14.
Done with chr chr15.
Done with chr chr16.
Done with chr chr17.
Done with chr chr18.
Done with chr chr19.
Done with chr chr20.
Done with chr chr21.
Done with chr chr22.
09:48:13 : INFO : Execution Time = 6.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.bam
09:48:13 : INFO : Running: touch /tmp/nxf.8CucsSjEGe/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp.ok
09:48:13 : INFO : Running: samtools sort -o 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 2 files and 1 in-memory blocks...
09:48:49 : INFO : Execution Time = 0.61 minutes. CMD: samtools sort -o 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp
09:48:49 : INFO : Running: touch /tmp/nxf.8CucsSjEGe/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmpsorted.ok
09:48:49 : INFO : Running: samtools index 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam
09:48:53 : INFO : Execution Time = 0.07 minutes. CMD: samtools index 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam
09:48:53 : INFO : Running: touch /tmp/nxf.8CucsSjEGe/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.indexed.ok
09:48:53 : INFO : Running: samtools index 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam
09:48:53 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam
09:48:53 : INFO : Running: touch /tmp/nxf.8CucsSjEGe/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam.indexed.ok
09:48:53 : INFO : Running: create_report 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.ctat-splicing.igv.html --track-config 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2'
[W::hts_idx_load3] The index file is older than the data file: ctat_genome_lib_build_dir/refGene.sort.bed.gz.tbi
09:54:02 : INFO : Execution Time = 5.15 minutes. CMD: create_report 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.ctat-splicing.igv.html --track-config 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2'
09:54:02 : INFO : Running: touch /tmp/nxf.8CucsSjEGe/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/igv_create_html.ok
09:54:02 : INFO : done.