Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/e9fc6820dbb4f90a8f82151763124e/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/0a/ec6e1dffa9cc228870fc61fc169fc7/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/c5936724debd1d1973be64e82a53c1/rna_s1221_S42.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/c5936724debd1d1973be64e82a53c1/rna_s1221_S42.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/c5936724debd1d1973be64e82a53c1/rna_s1221_S42.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/ec6e1dffa9cc228870fc61fc169fc7/.command.run
==> STAGING COMPLETE (7 inputs)
20:37:32 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
[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 20:37:37 : 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
20:37:37 : 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
20:37:37 : INFO : Running: touch /tmp/nxf.fGxJvrcDUR/rna_s1221_S42.chckpts/prelim_introns.ok
20:37:37 : 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
20:37:37 : 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
20:37:37 : INFO : Running: touch /tmp/nxf.fGxJvrcDUR/rna_s1221_S42.chckpts/introns_filtered.ok
20:37:37 : INFO : -found 28 cancer introns
20:37:37 : 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
20:37:37 : INFO : Creating the BED File.
20:37:38 : INFO : Saving Bed File as rna_s1221_S42.introns.for_IGV.bed
20:37:38 : 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
20:37:38 : INFO : Running: touch /tmp/nxf.fGxJvrcDUR/rna_s1221_S42.chckpts/intron_igv_bed.ok
20:37:38 : 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
20:37:38 : 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
20:37:38 : INFO : Running: touch /tmp/nxf.fGxJvrcDUR/rna_s1221_S42.chckpts/reads_alignments_extracted.ok
20:37:39 : INFO : Running: samtools sort -o rna_s1221_S42.cancer_intron_reads.sorted.bam rna_s1221_S42.cancer_intron_reads.bam
20:37:39 : 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
20:37:39 : INFO : Running: touch /tmp/nxf.fGxJvrcDUR/rna_s1221_S42.chckpts/sort_cancer_intron_reads.ok
20:37:39 : INFO : Running: samtools sort -o rna_s1221_S42.gene_reads.sorted.bam rna_s1221_S42.gene_reads.bam
20:37:39 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o rna_s1221_S42.gene_reads.sorted.bam rna_s1221_S42.gene_reads.bam
20:37:39 : INFO : Running: touch /tmp/nxf.fGxJvrcDUR/rna_s1221_S42.chckpts/sort_gene_reads.ok
20:37:39 : 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.
20:37:40 : 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
20:37:40 : INFO : Running: touch /tmp/nxf.fGxJvrcDUR/rna_s1221_S42.chckpts/rna_s1221_S42.gene_reads.sorted.sifted.bam.tmp.ok
20:37:40 : INFO : Running: samtools sort -o rna_s1221_S42.gene_reads.sorted.sifted.bam rna_s1221_S42.gene_reads.sorted.sifted.bam.tmp
20:37:40 : 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
20:37:40 : INFO : Running: touch /tmp/nxf.fGxJvrcDUR/rna_s1221_S42.chckpts/rna_s1221_S42.gene_reads.sorted.sifted.bam.tmpsorted.ok
20:37:40 : INFO : Running: samtools index rna_s1221_S42.gene_reads.sorted.sifted.bam
20:37:40 : INFO : Execution Time = 0.00 minutes. CMD: samtools index rna_s1221_S42.gene_reads.sorted.sifted.bam
20:37:40 : INFO : Running: touch /tmp/nxf.fGxJvrcDUR/rna_s1221_S42.chckpts/rna_s1221_S42.gene_reads.sorted.sifted.bam.indexed.ok
20:37:40 : INFO : Running: samtools index rna_s1221_S42.cancer_intron_reads.sorted.bam
20:37:40 : INFO : Execution Time = 0.00 minutes. CMD: samtools index rna_s1221_S42.cancer_intron_reads.sorted.bam
20:37:40 : INFO : Running: touch /tmp/nxf.fGxJvrcDUR/rna_s1221_S42.chckpts/rna_s1221_S42.cancer_intron_reads.sorted.bam.indexed.ok
20:37:40 : 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'
20:37:43 : 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'
20:37:43 : INFO : Running: touch /tmp/nxf.fGxJvrcDUR/rna_s1221_S42.chckpts/igv_create_html.ok
20:37:43 : INFO : done.