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/3e/2339f57fe6541d889d1002e247ae99/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/5d298b7528f78dc4019c240b840ae9/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/5d298b7528f78dc4019c240b840ae9/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/2339f57fe6541d889d1002e247ae99/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/78b9b7248ed477c45cdc4cbb1b53b1/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/5d298b7528f78dc4019c240b840ae9/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.SJ.out.tab
==> STAGING COMPLETE (7 inputs)
07:36:04 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[1470000], rate=22050000.00/min 07:36:13 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.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_CH0_T1_RNA_SLD_01_A23T55JLT4_1.introns: identified 1613 cancer introns
07:36:14 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim
07:36:14 : INFO : Running: touch /tmp/nxf.ejg3AsAkku/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/prelim_introns.ok
07:36:14 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim --min_total_reads 5 > 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns
07:36:14 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim --min_total_reads 5 > 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns
07:36:14 : INFO : Running: touch /tmp/nxf.ejg3AsAkku/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/introns_filtered.ok
07:36:14 : INFO : -found 164 cancer introns
07:36:14 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.introns --cancer_introns 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed
07:36:14 : INFO : Creating the BED File.
07:36:15 : INFO : Saving Bed File as 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed
07:36:15 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.introns --cancer_introns 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed
07:36:15 : INFO : Running: touch /tmp/nxf.ejg3AsAkku/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/intron_igv_bed.ok
07:36:15 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed --bam 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai
07:37:19 : INFO : Execution Time = 1.07 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed --bam 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1
07:37:19 : INFO : Running: touch /tmp/nxf.ejg3AsAkku/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/reads_alignments_extracted.ok
07:37:19 : INFO : Running: samtools sort -o 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.bam
07:37:19 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.bam
07:37:19 : INFO : Running: touch /tmp/nxf.ejg3AsAkku/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/sort_cancer_intron_reads.ok
07:37:20 : INFO : Running: samtools sort -o 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.bam
[bam_sort_core] merging from 4 files and 1 in-memory blocks...
07:38:45 : INFO : Execution Time = 1.42 minutes. CMD: samtools sort -o 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.bam
07:38:45 : INFO : Running: touch /tmp/nxf.ejg3AsAkku/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/sort_gene_reads.ok
07:38:45 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam
Done with chr chr1.
Done with chr chr2.
Done with chr chr3.
Done with chr chr4.
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Done with chr chr19.
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Done with chr chr22.
07:39:15 : INFO : Execution Time = 0.50 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam
07:39:15 : INFO : Running: touch /tmp/nxf.ejg3AsAkku/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
07:39:15 : INFO : Running: samtools sort -o 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp
07:39:27 : INFO : Execution Time = 0.20 minutes. CMD: samtools sort -o 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp
07:39:27 : INFO : Running: touch /tmp/nxf.ejg3AsAkku/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
07:39:27 : INFO : Running: samtools index 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam
07:39:28 : INFO : Execution Time = 0.03 minutes. CMD: samtools index 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam
07:39:28 : INFO : Running: touch /tmp/nxf.ejg3AsAkku/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
07:39:28 : INFO : Running: samtools index 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam
07:39:28 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam
07:39:28 : INFO : Running: touch /tmp/nxf.ejg3AsAkku/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
07:39:28 : INFO : Running: create_report 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.ctat-splicing.igv.html --track-config 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1'
07:42:45 : INFO : Execution Time = 3.28 minutes. CMD: create_report 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.ctat-splicing.igv.html --track-config 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1'
07:42:45 : INFO : Running: touch /tmp/nxf.ejg3AsAkku/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/igv_create_html.ok
07:42:45 : INFO : done.