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/1c/db61c47132439c13247ce527607ecc/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/4de7802266e95e36763fef62c5e2d8/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/11af243ec7377c7db6655d898327a0/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/db61c47132439c13247ce527607ecc/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/4de7802266e95e36763fef62c5e2d8/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/4de7802266e95e36763fef62c5e2d8/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam ==> STAGING COMPLETE (7 inputs) 07:27:03 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [110000], rate=6600000.00/min [120000], rate=7200000.00/min [130000], rate=7800000.00/min [140000], rate=8400000.00/min [150000], rate=9000000.00/min [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 [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=14100000.00/min [480000], rate=14400000.00/min [490000], rate=14700000.00/min [500000], rate=15000000.00/min [510000], rate=15300000.00/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 [990000], rate=19800000.00/min [1000000], rate=20000000.00/min [1010000], rate=20200000.00/min [1020000], rate=20400000.00/min [1030000], rate=20600000.00/min [1040000], rate=20800000.00/min [1050000], rate=21000000.00/min [1060000], rate=21200000.00/min [1070000], rate=21400000.00/min [1080000], rate=21600000.00/min [1090000], rate=21800000.00/min [1100000], rate=22000000.00/min [1110000], rate=22200000.00/min [1120000], rate=22400000.00/min [1130000], rate=22600000.00/min [1140000], rate=22800000.00/min [1150000], rate=23000000.00/min [1160000], rate=23200000.00/min [1170000], rate=17550000.00/min [1180000], rate=17700000.00/min [1190000], rate=17850000.00/min [1200000], rate=18000000.00/min [1210000], rate=18150000.00/min [1220000], rate=18300000.00/min [1230000], rate=18450000.00/min [1240000], rate=18600000.00/min [1250000], rate=18750000.00/min [1260000], rate=18900000.00/min [1270000], rate=19050000.00/min [1280000], rate=19200000.00/min [1290000], rate=19350000.00/min [1300000], rate=19500000.00/min [1310000], rate=19650000.00/min [1320000], rate=19800000.00/min [1330000], rate=19950000.00/min [1340000], rate=20100000.00/min [1350000], rate=20250000.00/min 07:27:11 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > ColoN_FFPE_L03_RNA_01_B23LG7FLT4_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. -ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.introns: identified 24 cancer introns 07:27:11 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer.introns.prelim 07:27:11 : INFO : Running: touch /tmp/nxf.z0ugrxM1og/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/prelim_introns.ok 07:27:11 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer.introns 07:27:12 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer.introns 07:27:12 : INFO : Running: touch /tmp/nxf.z0ugrxM1og/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/introns_filtered.ok 07:27:12 : INFO : -found 15 cancer introns 07:27:12 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.introns --cancer_introns ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed 07:27:12 : INFO : Creating the BED File. 07:27:13 : INFO : Saving Bed File as ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed 07:27:13 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.introns --cancer_introns ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed 07:27:13 : INFO : Running: touch /tmp/nxf.z0ugrxM1og/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/intron_igv_bed.ok 07:27:13 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed --bam ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1 [W::hts_idx_load3] The index file is older than the data file: ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai 07:27:13 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed --bam ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1 07:27:13 : INFO : Running: touch /tmp/nxf.z0ugrxM1og/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/reads_alignments_extracted.ok 07:27:13 : INFO : Running: samtools sort -o ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer_intron_reads.bam 07:27:13 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer_intron_reads.bam 07:27:13 : INFO : Running: touch /tmp/nxf.z0ugrxM1og/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/sort_cancer_intron_reads.ok 07:27:13 : INFO : Running: samtools sort -o ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.bam 07:27:13 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.bam 07:27:13 : INFO : Running: touch /tmp/nxf.z0ugrxM1og/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/sort_gene_reads.ok 07:27:13 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam Done with chr chr1. Done with chr chr3. Done with chr chr6. Done with chr chr7. Done with chr chr9. Done with chr chr11. Done with chr chr14. Done with chr chr16. Done with chr chr17. 07:27:14 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam 07:27:14 : INFO : Running: touch /tmp/nxf.z0ugrxM1og/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp.ok 07:27:14 : INFO : Running: samtools sort -o ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp 07:27:14 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp 07:27:14 : INFO : Running: touch /tmp/nxf.z0ugrxM1og/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 07:27:14 : INFO : Running: samtools index ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam 07:27:14 : INFO : Execution Time = 0.00 minutes. CMD: samtools index ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam 07:27:14 : INFO : Running: touch /tmp/nxf.z0ugrxM1og/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.indexed.ok 07:27:14 : INFO : Running: samtools index ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam 07:27:14 : INFO : Execution Time = 0.00 minutes. CMD: samtools index ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam 07:27:14 : INFO : Running: touch /tmp/nxf.z0ugrxM1og/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam.indexed.ok 07:27:14 : INFO : Running: create_report ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.ctat-splicing.igv.html --track-config ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1' 07:27:15 : INFO : Execution Time = 0.03 minutes. CMD: create_report ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.ctat-splicing.igv.html --track-config ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1' 07:27:15 : INFO : Running: touch /tmp/nxf.z0ugrxM1og/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/igv_create_html.ok 07:27:15 : INFO : done.