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/51/cab0da90a81b3c6519d742ad89774f/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/4a9a668e5d29be97fb696b366879b5/tih_rna_sample_00740_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/fa03111fd317d3f4f6c8b0e948aec3/tih_rna_sample_00740_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/4a9a668e5d29be97fb696b366879b5/tih_rna_sample_00740_B23MVV7LT4_1.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/4a9a668e5d29be97fb696b366879b5/tih_rna_sample_00740_B23MVV7LT4_1.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/cab0da90a81b3c6519d742ad89774f/.command.run
==> STAGING COMPLETE (7 inputs)
08:42:51 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[10950000], rate=21900000.00/min
[10960000], rate=21920000.00/min
[10970000], rate=21940000.00/min
[10980000], rate=21960000.00/min
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[11010000], rate=22020000.00/min
[11020000], rate=22040000.00/min
[11030000], rate=22060000.00/min
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[11280000], rate=21832258.06/min
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[11420000], rate=22103225.81/min
[11430000], rate=22122580.65/min
[11440000], rate=22141935.48/min
[11450000], rate=22161290.32/min
[11460000], rate=22180645.16/min
[11470000], rate=22200000.00/min
[11480000], rate=22219354.84/min
[11490000], rate=21543750.00/min
[11500000], rate=21562500.00/min
[11510000], rate=21581250.00/min
[11520000], rate=21600000.00/min
[11530000], rate=21618750.00/min
[11540000], rate=21637500.00/min
[11550000], rate=21656250.00/min
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[11590000], rate=21731250.00/min
[11600000], rate=21750000.00/min 08:43:31 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00740_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00740_B23MVV7LT4_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.
-tih_rna_sample_00740_B23MVV7LT4_1.introns: identified 7956 cancer introns
08:43:31 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00740_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00740_B23MVV7LT4_1.cancer.introns.prelim
08:43:31 : INFO : Running: touch /tmp/nxf.hq53zUa3dp/tih_rna_sample_00740_B23MVV7LT4_1.chckpts/prelim_introns.ok
08:43:31 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00740_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00740_B23MVV7LT4_1.cancer.introns
08:43:32 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00740_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00740_B23MVV7LT4_1.cancer.introns
08:43:32 : INFO : Running: touch /tmp/nxf.hq53zUa3dp/tih_rna_sample_00740_B23MVV7LT4_1.chckpts/introns_filtered.ok
08:43:32 : INFO : -found 3732 cancer introns
08:43:32 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00740_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00740_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00740_B23MVV7LT4_1.introns.for_IGV.bed
08:43:32 : INFO : Creating the BED File.
08:43:38 : INFO : Saving Bed File as tih_rna_sample_00740_B23MVV7LT4_1.introns.for_IGV.bed
08:43:39 : INFO : Execution Time = 0.11 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00740_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00740_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00740_B23MVV7LT4_1.introns.for_IGV.bed
08:43:39 : INFO : Running: touch /tmp/nxf.hq53zUa3dp/tih_rna_sample_00740_B23MVV7LT4_1.chckpts/intron_igv_bed.ok
08:43:39 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00740_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00740_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00740_B23MVV7LT4_1
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00740_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai
09:03:35 : INFO : Execution Time = 19.93 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00740_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00740_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00740_B23MVV7LT4_1
09:03:35 : INFO : Running: touch /tmp/nxf.hq53zUa3dp/tih_rna_sample_00740_B23MVV7LT4_1.chckpts/reads_alignments_extracted.ok
09:03:35 : INFO : Running: samtools sort -o tih_rna_sample_00740_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00740_B23MVV7LT4_1.cancer_intron_reads.bam
09:03:35 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00740_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00740_B23MVV7LT4_1.cancer_intron_reads.bam
09:03:35 : INFO : Running: touch /tmp/nxf.hq53zUa3dp/tih_rna_sample_00740_B23MVV7LT4_1.chckpts/sort_cancer_intron_reads.ok
09:03:35 : INFO : Running: samtools sort -o tih_rna_sample_00740_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00740_B23MVV7LT4_1.gene_reads.bam