Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/a08acf255317d4582ce245333d6e77/rna_s1221_S42.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/e4/423965aff2a31b22a7fdd71052ea7f/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/4d40ad7538894f3daef343612a34d4/rna_s1221_S42.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/4d40ad7538894f3daef343612a34d4/rna_s1221_S42.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/4d40ad7538894f3daef343612a34d4/rna_s1221_S42.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/423965aff2a31b22a7fdd71052ea7f/.command.run ==> STAGING COMPLETE (7 inputs) 21:57:40 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [220000], rate=13200000.00/min [230000], rate=13800000.00/min [240000], rate=14400000.00/min [250000], rate=15000000.00/min [260000], rate=15600000.00/min [270000], rate=16200000.00/min [280000], rate=16800000.00/min [290000], rate=17400000.00/min [300000], rate=18000000.00/min [310000], rate=18600000.00/min [320000], rate=19200000.00/min [330000], rate=19800000.00/min [340000], rate=20400000.00/min [350000], rate=21000000.00/min [360000], rate=21600000.00/min [370000], rate=22200000.00/min [380000], rate=22800000.00/min [390000], rate=23400000.00/min [400000], rate=24000000.00/min [410000], rate=24600000.00/min [420000], rate=25200000.00/min [430000], rate=25800000.00/min [440000], rate=26400000.00/min [450000], rate=27000000.00/min [460000], rate=27600000.00/min [470000], rate=28200000.00/min [480000], rate=28800000.00/min [490000], rate=29400000.00/min [500000], rate=30000000.00/min [510000], rate=30600000.00/min [520000], rate=31200000.00/min [530000], rate=31800000.00/min [540000], rate=32400000.00/min [550000], rate=33000000.00/min 21:57:45 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file rna_s1221_S42.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > rna_s1221_S42.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_s1221_S42.introns: identified 1033 cancer introns 21:57:45 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file rna_s1221_S42.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > rna_s1221_S42.cancer.introns.prelim 21:57:45 : INFO : Running: touch /tmp/nxf.UW1TgExS9J/rna_s1221_S42.chckpts/prelim_introns.ok 21:57:45 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates rna_s1221_S42.cancer.introns.prelim --min_total_reads 5 > rna_s1221_S42.cancer.introns 21:57:45 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates rna_s1221_S42.cancer.introns.prelim --min_total_reads 5 > rna_s1221_S42.cancer.introns 21:57:45 : INFO : Running: touch /tmp/nxf.UW1TgExS9J/rna_s1221_S42.chckpts/introns_filtered.ok 21:57:45 : INFO : -found 28 cancer introns 21:57:45 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns rna_s1221_S42.introns --cancer_introns rna_s1221_S42.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed rna_s1221_S42.introns.for_IGV.bed 21:57:45 : INFO : Creating the BED File. 21:57:46 : INFO : Saving Bed File as rna_s1221_S42.introns.for_IGV.bed 21:57:46 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns rna_s1221_S42.introns --cancer_introns rna_s1221_S42.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed rna_s1221_S42.introns.for_IGV.bed 21:57:46 : INFO : Running: touch /tmp/nxf.UW1TgExS9J/rna_s1221_S42.chckpts/intron_igv_bed.ok 21:57:46 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed rna_s1221_S42.introns.for_IGV.bed --bam rna_s1221_S42.Aligned.sortedByCoord.out.bam --output_prefix rna_s1221_S42 [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai 21:57:46 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed rna_s1221_S42.introns.for_IGV.bed --bam rna_s1221_S42.Aligned.sortedByCoord.out.bam --output_prefix rna_s1221_S42 21:57:46 : INFO : Running: touch /tmp/nxf.UW1TgExS9J/rna_s1221_S42.chckpts/reads_alignments_extracted.ok 21:57:46 : INFO : Running: samtools sort -o rna_s1221_S42.cancer_intron_reads.sorted.bam rna_s1221_S42.cancer_intron_reads.bam 21:57:46 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o rna_s1221_S42.cancer_intron_reads.sorted.bam rna_s1221_S42.cancer_intron_reads.bam 21:57:46 : INFO : Running: touch /tmp/nxf.UW1TgExS9J/rna_s1221_S42.chckpts/sort_cancer_intron_reads.ok 21:57:46 : INFO : Running: samtools sort -o rna_s1221_S42.gene_reads.sorted.bam rna_s1221_S42.gene_reads.bam 21:57:47 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o rna_s1221_S42.gene_reads.sorted.bam rna_s1221_S42.gene_reads.bam 21:57:47 : INFO : Running: touch /tmp/nxf.UW1TgExS9J/rna_s1221_S42.chckpts/sort_gene_reads.ok 21:57:47 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o rna_s1221_S42.gene_reads.sorted.sifted.bam.tmp --keep_secondary rna_s1221_S42.gene_reads.sorted.bam Done with chr chr1. Done with chr chr2. Done with chr chr3. Done with chr chr4. Done with chr chr6. Done with chr chr7. Done with chr chr8. Done with chr chr9. Done with chr chr12. Done with chr chr15. Done with chr chr16. Done with chr chr17. 21:57:47 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o rna_s1221_S42.gene_reads.sorted.sifted.bam.tmp --keep_secondary rna_s1221_S42.gene_reads.sorted.bam 21:57:47 : INFO : Running: touch /tmp/nxf.UW1TgExS9J/rna_s1221_S42.chckpts/rna_s1221_S42.gene_reads.sorted.sifted.bam.tmp.ok 21:57:47 : INFO : Running: samtools sort -o rna_s1221_S42.gene_reads.sorted.sifted.bam rna_s1221_S42.gene_reads.sorted.sifted.bam.tmp 21:57:48 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o rna_s1221_S42.gene_reads.sorted.sifted.bam rna_s1221_S42.gene_reads.sorted.sifted.bam.tmp 21:57:48 : INFO : Running: touch /tmp/nxf.UW1TgExS9J/rna_s1221_S42.chckpts/rna_s1221_S42.gene_reads.sorted.sifted.bam.tmpsorted.ok 21:57:48 : INFO : Running: samtools index rna_s1221_S42.gene_reads.sorted.sifted.bam 21:57:48 : INFO : Execution Time = 0.00 minutes. CMD: samtools index rna_s1221_S42.gene_reads.sorted.sifted.bam 21:57:48 : INFO : Running: touch /tmp/nxf.UW1TgExS9J/rna_s1221_S42.chckpts/rna_s1221_S42.gene_reads.sorted.sifted.bam.indexed.ok 21:57:48 : INFO : Running: samtools index rna_s1221_S42.cancer_intron_reads.sorted.bam 21:57:48 : INFO : Execution Time = 0.00 minutes. CMD: samtools index rna_s1221_S42.cancer_intron_reads.sorted.bam 21:57:48 : INFO : Running: touch /tmp/nxf.UW1TgExS9J/rna_s1221_S42.chckpts/rna_s1221_S42.cancer_intron_reads.sorted.bam.indexed.ok 21:57:48 : INFO : Running: create_report rna_s1221_S42.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output rna_s1221_S42.ctat-splicing.igv.html --track-config rna_s1221_S42.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: rna_s1221_S42' 21:57:51 : INFO : Execution Time = 0.05 minutes. CMD: create_report rna_s1221_S42.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output rna_s1221_S42.ctat-splicing.igv.html --track-config rna_s1221_S42.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: rna_s1221_S42' 21:57:51 : INFO : Running: touch /tmp/nxf.UW1TgExS9J/rna_s1221_S42.chckpts/igv_create_html.ok 21:57:51 : INFO : done.