Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/2397b408a8213734a173d8a752ccf8/tih_rna_sample_00097_23H5VFLT4_s12.Aligned.sortedByCoord.out.bam.bai
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/89/bbcba6ab78416d7efb405afcd63927/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/d08e67d90729dde14e85deda2ab47c/tih_rna_sample_00097_23H5VFLT4_s12.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/d08e67d90729dde14e85deda2ab47c/tih_rna_sample_00097_23H5VFLT4_s12.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/d08e67d90729dde14e85deda2ab47c/tih_rna_sample_00097_23H5VFLT4_s12.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/bbcba6ab78416d7efb405afcd63927/.command.run
==> STAGING COMPLETE (7 inputs)
09:04:34 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[9590000], rate=14385000.00/min 09:05:23 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00097_23H5VFLT4_s12.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00097_23H5VFLT4_s12.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.
-tih_rna_sample_00097_23H5VFLT4_s12.introns: identified 7425 cancer introns
09:05:24 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00097_23H5VFLT4_s12.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00097_23H5VFLT4_s12.cancer.introns.prelim
09:05:24 : INFO : Running: touch /tmp/nxf.sMZuVqw8hq/tih_rna_sample_00097_23H5VFLT4_s12.chckpts/prelim_introns.ok
09:05:24 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00097_23H5VFLT4_s12.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00097_23H5VFLT4_s12.cancer.introns
09:05:25 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00097_23H5VFLT4_s12.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00097_23H5VFLT4_s12.cancer.introns
09:05:25 : INFO : Running: touch /tmp/nxf.sMZuVqw8hq/tih_rna_sample_00097_23H5VFLT4_s12.chckpts/introns_filtered.ok
09:05:25 : INFO : -found 2991 cancer introns
09:05:25 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00097_23H5VFLT4_s12.introns --cancer_introns tih_rna_sample_00097_23H5VFLT4_s12.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00097_23H5VFLT4_s12.introns.for_IGV.bed
09:05:25 : INFO : Creating the BED File.
09:05:32 : INFO : Saving Bed File as tih_rna_sample_00097_23H5VFLT4_s12.introns.for_IGV.bed
09:05:32 : INFO : Execution Time = 0.12 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00097_23H5VFLT4_s12.introns --cancer_introns tih_rna_sample_00097_23H5VFLT4_s12.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00097_23H5VFLT4_s12.introns.for_IGV.bed
09:05:32 : INFO : Running: touch /tmp/nxf.sMZuVqw8hq/tih_rna_sample_00097_23H5VFLT4_s12.chckpts/intron_igv_bed.ok
09:05:32 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00097_23H5VFLT4_s12.introns.for_IGV.bed --bam tih_rna_sample_00097_23H5VFLT4_s12.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00097_23H5VFLT4_s12
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00097_23H5VFLT4_s12.Aligned.sortedByCoord.out.bam.bai
09:32:00 : INFO : Execution Time = 26.47 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00097_23H5VFLT4_s12.introns.for_IGV.bed --bam tih_rna_sample_00097_23H5VFLT4_s12.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00097_23H5VFLT4_s12
09:32:00 : INFO : Running: touch /tmp/nxf.sMZuVqw8hq/tih_rna_sample_00097_23H5VFLT4_s12.chckpts/reads_alignments_extracted.ok
09:32:00 : INFO : Running: samtools sort -o tih_rna_sample_00097_23H5VFLT4_s12.cancer_intron_reads.sorted.bam tih_rna_sample_00097_23H5VFLT4_s12.cancer_intron_reads.bam
09:32:01 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00097_23H5VFLT4_s12.cancer_intron_reads.sorted.bam tih_rna_sample_00097_23H5VFLT4_s12.cancer_intron_reads.bam
09:32:01 : INFO : Running: touch /tmp/nxf.sMZuVqw8hq/tih_rna_sample_00097_23H5VFLT4_s12.chckpts/sort_cancer_intron_reads.ok
09:32:01 : INFO : Running: samtools sort -o tih_rna_sample_00097_23H5VFLT4_s12.gene_reads.sorted.bam tih_rna_sample_00097_23H5VFLT4_s12.gene_reads.bam
[bam_sort_core] merging from 121 files and 1 in-memory blocks...
10:00:44 : INFO : Execution Time = 28.72 minutes. CMD: samtools sort -o tih_rna_sample_00097_23H5VFLT4_s12.gene_reads.sorted.bam tih_rna_sample_00097_23H5VFLT4_s12.gene_reads.bam
10:00:44 : INFO : Running: touch /tmp/nxf.sMZuVqw8hq/tih_rna_sample_00097_23H5VFLT4_s12.chckpts/sort_gene_reads.ok
10:00:44 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00097_23H5VFLT4_s12.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00097_23H5VFLT4_s12.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.
10:11:57 : INFO : Execution Time = 11.22 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00097_23H5VFLT4_s12.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00097_23H5VFLT4_s12.gene_reads.sorted.bam
10:11:57 : INFO : Running: touch /tmp/nxf.sMZuVqw8hq/tih_rna_sample_00097_23H5VFLT4_s12.chckpts/tih_rna_sample_00097_23H5VFLT4_s12.gene_reads.sorted.sifted.bam.tmp.ok
10:11:57 : INFO : Running: samtools sort -o tih_rna_sample_00097_23H5VFLT4_s12.gene_reads.sorted.sifted.bam tih_rna_sample_00097_23H5VFLT4_s12.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 9 files and 1 in-memory blocks...
10:14:30 : INFO : Execution Time = 2.54 minutes. CMD: samtools sort -o tih_rna_sample_00097_23H5VFLT4_s12.gene_reads.sorted.sifted.bam tih_rna_sample_00097_23H5VFLT4_s12.gene_reads.sorted.sifted.bam.tmp
10:14:30 : INFO : Running: touch /tmp/nxf.sMZuVqw8hq/tih_rna_sample_00097_23H5VFLT4_s12.chckpts/tih_rna_sample_00097_23H5VFLT4_s12.gene_reads.sorted.sifted.bam.tmpsorted.ok
10:14:30 : INFO : Running: samtools index tih_rna_sample_00097_23H5VFLT4_s12.gene_reads.sorted.sifted.bam
10:14:46 : INFO : Execution Time = 0.27 minutes. CMD: samtools index tih_rna_sample_00097_23H5VFLT4_s12.gene_reads.sorted.sifted.bam
10:14:46 : INFO : Running: touch /tmp/nxf.sMZuVqw8hq/tih_rna_sample_00097_23H5VFLT4_s12.chckpts/tih_rna_sample_00097_23H5VFLT4_s12.gene_reads.sorted.sifted.bam.indexed.ok
10:14:46 : INFO : Running: samtools index tih_rna_sample_00097_23H5VFLT4_s12.cancer_intron_reads.sorted.bam
10:14:46 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00097_23H5VFLT4_s12.cancer_intron_reads.sorted.bam
10:14:46 : INFO : Running: touch /tmp/nxf.sMZuVqw8hq/tih_rna_sample_00097_23H5VFLT4_s12.chckpts/tih_rna_sample_00097_23H5VFLT4_s12.cancer_intron_reads.sorted.bam.indexed.ok
10:14:46 : INFO : Running: create_report tih_rna_sample_00097_23H5VFLT4_s12.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00097_23H5VFLT4_s12.ctat-splicing.igv.html --track-config tih_rna_sample_00097_23H5VFLT4_s12.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00097_23H5VFLT4_s12'
[W::hts_idx_load3] The index file is older than the data file: ctat_genome_lib_build_dir/refGene.sort.bed.gz.tbi
10:23:30 : INFO : Execution Time = 8.74 minutes. CMD: create_report tih_rna_sample_00097_23H5VFLT4_s12.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00097_23H5VFLT4_s12.ctat-splicing.igv.html --track-config tih_rna_sample_00097_23H5VFLT4_s12.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00097_23H5VFLT4_s12'
10:23:30 : INFO : Running: touch /tmp/nxf.sMZuVqw8hq/tih_rna_sample_00097_23H5VFLT4_s12.chckpts/igv_create_html.ok
10:23:30 : INFO : done.