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/c8/df1f42043faf347b6152170b79ce4b/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/825e6edc2b8d8b2b70055dde5a7a95/rna_s1200_S21.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/825e6edc2b8d8b2b70055dde5a7a95/rna_s1200_S21.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/825e6edc2b8d8b2b70055dde5a7a95/rna_s1200_S21.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/df1f42043faf347b6152170b79ce4b/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/f1149b8715780589b3b3ec8eaab375/rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (7 inputs)
04:04:47 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
[160000], rate=9600000.00/min
[170000], rate=10200000.00/min
[180000], rate=10800000.00/min
[190000], rate=11400000.00/min
[200000], rate=12000000.00/min
[210000], rate=12600000.00/min
[220000], rate=13200000.00/min
[230000], rate=13800000.00/min
[240000], rate=14400000.00/min 04:04:54 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file rna_s1200_S21.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > rna_s1200_S21.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.
-rna_s1200_S21.introns: identified 1141 cancer introns
04:04:55 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file rna_s1200_S21.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > rna_s1200_S21.cancer.introns.prelim
04:04:55 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/prelim_introns.ok
04:04:55 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates rna_s1200_S21.cancer.introns.prelim --min_total_reads 5 > rna_s1200_S21.cancer.introns
04:04:55 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates rna_s1200_S21.cancer.introns.prelim --min_total_reads 5 > rna_s1200_S21.cancer.introns
04:04:55 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/introns_filtered.ok
04:04:55 : INFO : -found 17 cancer introns
04:04:55 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns rna_s1200_S21.introns --cancer_introns rna_s1200_S21.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed rna_s1200_S21.introns.for_IGV.bed
04:04:56 : INFO : Creating the BED File.
04:04:56 : INFO : Saving Bed File as rna_s1200_S21.introns.for_IGV.bed
04:04:56 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns rna_s1200_S21.introns --cancer_introns rna_s1200_S21.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed rna_s1200_S21.introns.for_IGV.bed
04:04:56 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/intron_igv_bed.ok
04:04:56 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed rna_s1200_S21.introns.for_IGV.bed --bam rna_s1200_S21.Aligned.sortedByCoord.out.bam --output_prefix rna_s1200_S21
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
04:04:57 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed rna_s1200_S21.introns.for_IGV.bed --bam rna_s1200_S21.Aligned.sortedByCoord.out.bam --output_prefix rna_s1200_S21
04:04:57 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/reads_alignments_extracted.ok
04:04:57 : INFO : Running: samtools sort -o rna_s1200_S21.cancer_intron_reads.sorted.bam rna_s1200_S21.cancer_intron_reads.bam
04:04:57 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o rna_s1200_S21.cancer_intron_reads.sorted.bam rna_s1200_S21.cancer_intron_reads.bam
04:04:57 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/sort_cancer_intron_reads.ok
04:04:57 : INFO : Running: samtools sort -o rna_s1200_S21.gene_reads.sorted.bam rna_s1200_S21.gene_reads.bam
04:04:57 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o rna_s1200_S21.gene_reads.sorted.bam rna_s1200_S21.gene_reads.bam
04:04:57 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/sort_gene_reads.ok
04:04:58 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o rna_s1200_S21.gene_reads.sorted.sifted.bam.tmp --keep_secondary rna_s1200_S21.gene_reads.sorted.bam
Done with chr chr1.
Done with chr chr2.
Done with chr chr6.
Done with chr chr7.
Done with chr chr8.
Done with chr chr9.
Done with chr chr12.
Done with chr chr17.
Done with chr chr20.
04:04:58 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o rna_s1200_S21.gene_reads.sorted.sifted.bam.tmp --keep_secondary rna_s1200_S21.gene_reads.sorted.bam
04:04:58 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/rna_s1200_S21.gene_reads.sorted.sifted.bam.tmp.ok
04:04:58 : INFO : Running: samtools sort -o rna_s1200_S21.gene_reads.sorted.sifted.bam rna_s1200_S21.gene_reads.sorted.sifted.bam.tmp
04:04:58 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o rna_s1200_S21.gene_reads.sorted.sifted.bam rna_s1200_S21.gene_reads.sorted.sifted.bam.tmp
04:04:58 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/rna_s1200_S21.gene_reads.sorted.sifted.bam.tmpsorted.ok
04:04:58 : INFO : Running: samtools index rna_s1200_S21.gene_reads.sorted.sifted.bam
04:04:58 : INFO : Execution Time = 0.00 minutes. CMD: samtools index rna_s1200_S21.gene_reads.sorted.sifted.bam
04:04:58 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/rna_s1200_S21.gene_reads.sorted.sifted.bam.indexed.ok
04:04:58 : INFO : Running: samtools index rna_s1200_S21.cancer_intron_reads.sorted.bam
04:04:58 : INFO : Execution Time = 0.00 minutes. CMD: samtools index rna_s1200_S21.cancer_intron_reads.sorted.bam
04:04:58 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/rna_s1200_S21.cancer_intron_reads.sorted.bam.indexed.ok
04:04:58 : INFO : Running: create_report rna_s1200_S21.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output rna_s1200_S21.ctat-splicing.igv.html --track-config rna_s1200_S21.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: rna_s1200_S21'
[W::hts_idx_load3] The index file is older than the data file: ctat_genome_lib_build_dir/refGene.sort.bed.gz.tbi
04:05:01 : INFO : Execution Time = 0.04 minutes. CMD: create_report rna_s1200_S21.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output rna_s1200_S21.ctat-splicing.igv.html --track-config rna_s1200_S21.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: rna_s1200_S21'
04:05:01 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/igv_create_html.ok
04:05:01 : INFO : done.