Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/aec77973b89d81529313915b9c4e31/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.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/5d/c242f728c89feaaf2eb67364dae0cc/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/ec3a10410562e6c89a0256d8bfdf6b/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/ec3a10410562e6c89a0256d8bfdf6b/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/c242f728c89feaaf2eb67364dae0cc/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/ec3a10410562e6c89a0256d8bfdf6b/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Chimeric.out.junction ==> STAGING COMPLETE (7 inputs) 20:13:00 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [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=15600000.00/min [530000], rate=15900000.00/min [540000], rate=16200000.00/min [550000], rate=16500000.00/min [560000], rate=16800000.00/min [570000], rate=17100000.00/min [580000], rate=17400000.00/min [590000], rate=17700000.00/min [600000], rate=18000000.00/min [610000], rate=18300000.00/min [620000], rate=18600000.00/min [630000], rate=18900000.00/min [640000], rate=19200000.00/min [650000], rate=19500000.00/min [660000], rate=19800000.00/min [670000], rate=20100000.00/min [680000], rate=20400000.00/min [690000], rate=20700000.00/min [700000], rate=21000000.00/min [710000], rate=21300000.00/min [720000], rate=21600000.00/min [730000], rate=21900000.00/min [740000], rate=22200000.00/min [750000], rate=22500000.00/min [760000], rate=22800000.00/min [770000], rate=23100000.00/min [780000], rate=23400000.00/min [790000], rate=23700000.00/min [800000], rate=24000000.00/min [810000], rate=16200000.00/min [820000], rate=16400000.00/min [830000], rate=16600000.00/min [840000], rate=16800000.00/min [850000], rate=17000000.00/min [860000], rate=17200000.00/min [870000], rate=17400000.00/min [880000], rate=17600000.00/min [890000], rate=17800000.00/min [900000], rate=18000000.00/min [910000], rate=18200000.00/min [920000], rate=18400000.00/min [930000], rate=18600000.00/min [940000], rate=18800000.00/min [950000], rate=19000000.00/min [960000], rate=19200000.00/min [970000], rate=19400000.00/min [980000], rate=19600000.00/min 20:13:08 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_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. -BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns: identified 24 cancer introns 20:13:08 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer.introns.prelim 20:13:08 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/prelim_introns.ok 20:13:08 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer.introns.prelim --min_total_reads 5 > BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer.introns 20:13:09 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer.introns.prelim --min_total_reads 5 > BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer.introns 20:13:09 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/introns_filtered.ok 20:13:09 : INFO : -found 12 cancer introns 20:13:09 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns --cancer_introns BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed 20:13:09 : INFO : Creating the BED File. 20:13:10 : INFO : Saving Bed File as BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed 20:13:10 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns --cancer_introns BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed 20:13:10 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/intron_igv_bed.ok 20:13:10 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed --bam BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --output_prefix BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2 [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai 20:13:28 : INFO : Execution Time = 0.30 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed --bam BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --output_prefix BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2 20:13:28 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/reads_alignments_extracted.ok 20:13:28 : INFO : Running: samtools sort -o BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.sorted.bam BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.bam 20:13:28 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.sorted.bam BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.bam 20:13:28 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/sort_cancer_intron_reads.ok 20:13:28 : INFO : Running: samtools sort -o BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.bam BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.bam [bam_sort_core] merging from 1 files and 1 in-memory blocks... 20:13:50 : INFO : Execution Time = 0.36 minutes. CMD: samtools sort -o BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.bam BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.bam 20:13:50 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/sort_gene_reads.ok 20:13:50 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.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 chr12. Done with chr chr14. Done with chr chr15. 20:13:54 : INFO : Execution Time = 0.07 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.bam 20:13:54 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp.ok 20:13:54 : INFO : Running: samtools sort -o BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp 20:13:54 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp 20:13:54 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmpsorted.ok 20:13:54 : INFO : Running: samtools index BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam 20:13:54 : INFO : Execution Time = 0.00 minutes. CMD: samtools index BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam 20:13:54 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.indexed.ok 20:13:54 : INFO : Running: samtools index BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.sorted.bam 20:13:54 : INFO : Execution Time = 0.00 minutes. CMD: samtools index BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.sorted.bam 20:13:54 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.sorted.bam.indexed.ok 20:13:54 : INFO : Running: create_report BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.ctat-splicing.igv.html --track-config BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2' 20:13:56 : INFO : Execution Time = 0.03 minutes. CMD: create_report BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.ctat-splicing.igv.html --track-config BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2' 20:13:56 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/igv_create_html.ok 20:13:56 : INFO : done.