Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/88fd948cf6c83d1864c43a742149c2/659_ciJ-T1-TRNA-1_A23MVY2LT4_1.SJ.out.tab
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/a3/ea3b376c477ad2b120e54fe58c232d/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/88fd948cf6c83d1864c43a742149c2/659_ciJ-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/88fd948cf6c83d1864c43a742149c2/659_ciJ-T1-TRNA-1_A23MVY2LT4_1.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/ea3b376c477ad2b120e54fe58c232d/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/f269dfa04f260b7f33e0776e4a171c/659_ciJ-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (7 inputs)
09:26:08 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[10470000], rate=12317647.06/min
[10480000], rate=12329411.76/min
[10490000], rate=12341176.47/min
[10500000], rate=12352941.18/min
[10510000], rate=12364705.88/min
[10520000], rate=12376470.59/min
[10530000], rate=12388235.29/min
[10540000], rate=12400000.00/min
[10550000], rate=12411764.71/min
[10560000], rate=12423529.41/min
[10570000], rate=12435294.12/min
[10580000], rate=12207692.31/min
[10590000], rate=12219230.77/min
[10600000], rate=12230769.23/min
[10610000], rate=12242307.69/min
[10620000], rate=12253846.15/min
[10630000], rate=12265384.62/min
[10640000], rate=12276923.08/min
[10650000], rate=12288461.54/min
[10660000], rate=12300000.00/min
[10670000], rate=12311538.46/min
[10680000], rate=12323076.92/min
[10690000], rate=12334615.38/min
[10700000], rate=12346153.85/min
[10710000], rate=12357692.31/min
[10720000], rate=12369230.77/min 09:27:11 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_ciJ-T1-TRNA-1_A23MVY2LT4_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.
-659_ciJ-T1-TRNA-1_A23MVY2LT4_1.introns: identified 7611 cancer introns
09:27:12 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.cancer.introns.prelim
09:27:12 : INFO : Running: touch /tmp/nxf.CQsnGJwfWj/659_ciJ-T1-TRNA-1_A23MVY2LT4_1.chckpts/prelim_introns.ok
09:27:12 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.cancer.introns
09:27:13 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.cancer.introns
09:27:13 : INFO : Running: touch /tmp/nxf.CQsnGJwfWj/659_ciJ-T1-TRNA-1_A23MVY2LT4_1.chckpts/introns_filtered.ok
09:27:13 : INFO : -found 3020 cancer introns
09:27:13 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.introns --cancer_introns 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.introns.for_IGV.bed
09:27:13 : INFO : Creating the BED File.
09:27:20 : INFO : Saving Bed File as 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.introns.for_IGV.bed
09:27:20 : INFO : Execution Time = 0.12 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.introns --cancer_introns 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.introns.for_IGV.bed
09:27:20 : INFO : Running: touch /tmp/nxf.CQsnGJwfWj/659_ciJ-T1-TRNA-1_A23MVY2LT4_1.chckpts/intron_igv_bed.ok
09:27:20 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.introns.for_IGV.bed --bam 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_ciJ-T1-TRNA-1_A23MVY2LT4_1
[W::hts_idx_load3] The index file is older than the data file: 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
09:50:32 : INFO : Execution Time = 23.21 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.introns.for_IGV.bed --bam 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_ciJ-T1-TRNA-1_A23MVY2LT4_1
09:50:32 : INFO : Running: touch /tmp/nxf.CQsnGJwfWj/659_ciJ-T1-TRNA-1_A23MVY2LT4_1.chckpts/reads_alignments_extracted.ok
09:50:32 : INFO : Running: samtools sort -o 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.cancer_intron_reads.sorted.bam 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.cancer_intron_reads.bam
09:50:33 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.cancer_intron_reads.sorted.bam 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.cancer_intron_reads.bam
09:50:33 : INFO : Running: touch /tmp/nxf.CQsnGJwfWj/659_ciJ-T1-TRNA-1_A23MVY2LT4_1.chckpts/sort_cancer_intron_reads.ok
09:50:33 : INFO : Running: samtools sort -o 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.bam 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.bam
[bam_sort_core] merging from 108 files and 1 in-memory blocks...
10:15:36 : INFO : Execution Time = 25.06 minutes. CMD: samtools sort -o 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.bam 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.bam
10:15:36 : INFO : Running: touch /tmp/nxf.CQsnGJwfWj/659_ciJ-T1-TRNA-1_A23MVY2LT4_1.chckpts/sort_gene_reads.ok
10:15:36 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.bam
Done with chr chr1.
Done with chr chr2.
Done with chr chr3.
Done with chr chr4.
Done with chr chr5.
Done with chr chr6.
Done with chr chr7.
Done with chr chr8.
Done with chr chr9.
Done with chr chr10.
Done with chr chr11.
Done with chr chr12.
Done with chr chr13.
Done with chr chr14.
Done with chr chr15.
Done with chr chr16.
Done with chr chr17.
Done with chr chr18.
Done with chr chr19.
Done with chr chr20.
Done with chr chr21.
Done with chr chr22.
10:23:18 : INFO : Execution Time = 7.69 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.bam
10:23:18 : INFO : Running: touch /tmp/nxf.CQsnGJwfWj/659_ciJ-T1-TRNA-1_A23MVY2LT4_1.chckpts/659_ciJ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.sifted.bam.tmp.ok
10:23:18 : INFO : Running: samtools sort -o 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.sifted.bam 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 3 files and 1 in-memory blocks...
10:24:14 : INFO : Execution Time = 0.94 minutes. CMD: samtools sort -o 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.sifted.bam 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.sifted.bam.tmp
10:24:14 : INFO : Running: touch /tmp/nxf.CQsnGJwfWj/659_ciJ-T1-TRNA-1_A23MVY2LT4_1.chckpts/659_ciJ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
10:24:14 : INFO : Running: samtools index 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.sifted.bam
10:24:21 : INFO : Execution Time = 0.11 minutes. CMD: samtools index 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.sifted.bam
10:24:21 : INFO : Running: touch /tmp/nxf.CQsnGJwfWj/659_ciJ-T1-TRNA-1_A23MVY2LT4_1.chckpts/659_ciJ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.sifted.bam.indexed.ok
10:24:21 : INFO : Running: samtools index 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.cancer_intron_reads.sorted.bam
10:24:21 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.cancer_intron_reads.sorted.bam
10:24:21 : INFO : Running: touch /tmp/nxf.CQsnGJwfWj/659_ciJ-T1-TRNA-1_A23MVY2LT4_1.chckpts/659_ciJ-T1-TRNA-1_A23MVY2LT4_1.cancer_intron_reads.sorted.bam.indexed.ok
10:24:21 : INFO : Running: create_report 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.ctat-splicing.igv.html --track-config 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_ciJ-T1-TRNA-1_A23MVY2LT4_1'
10:30:55 : INFO : Execution Time = 6.57 minutes. CMD: create_report 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.ctat-splicing.igv.html --track-config 659_ciJ-T1-TRNA-1_A23MVY2LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_ciJ-T1-TRNA-1_A23MVY2LT4_1'
10:30:55 : INFO : Running: touch /tmp/nxf.CQsnGJwfWj/659_ciJ-T1-TRNA-1_A23MVY2LT4_1.chckpts/igv_create_html.ok
10:30:55 : INFO : done.