Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/2ed545fff25c6e0105af5ccec7b6eb/tih_rna_sample_00762_B23MVV7LT4_1.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/15/2ac6d5e7d4842a259dbf8d1b929742/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/eb4819a62a9d8788e02d0396cad486/tih_rna_sample_00762_B23MVV7LT4_1.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/2ac6d5e7d4842a259dbf8d1b929742/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/eb4819a62a9d8788e02d0396cad486/tih_rna_sample_00762_B23MVV7LT4_1.SJ.out.tab
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/eb4819a62a9d8788e02d0396cad486/tih_rna_sample_00762_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (7 inputs)

09:11:32 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes

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[9640000], rate=21422222.22/min 09:12:06 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00762_B23MVV7LT4_1.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > tih_rna_sample_00762_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_00762_B23MVV7LT4_1.introns: identified 8530 cancer introns
09:12:06 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00762_B23MVV7LT4_1.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > tih_rna_sample_00762_B23MVV7LT4_1.cancer.introns.prelim 
09:12:06 : INFO : Running: touch /tmp/nxf.hEzDi4jALq/tih_rna_sample_00762_B23MVV7LT4_1.chckpts/prelim_introns.ok
09:12:06 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00762_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5  > tih_rna_sample_00762_B23MVV7LT4_1.cancer.introns 
09:12:07 : 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_00762_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5  > tih_rna_sample_00762_B23MVV7LT4_1.cancer.introns 
09:12:07 : INFO : Running: touch /tmp/nxf.hEzDi4jALq/tih_rna_sample_00762_B23MVV7LT4_1.chckpts/introns_filtered.ok
09:12:07 : INFO : -found 3965 cancer introns
09:12:07 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00762_B23MVV7LT4_1.introns  --cancer_introns tih_rna_sample_00762_B23MVV7LT4_1.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed tih_rna_sample_00762_B23MVV7LT4_1.introns.for_IGV.bed 
09:12:07 : INFO :  Creating the BED File.
09:12:14 : INFO : Saving Bed File as tih_rna_sample_00762_B23MVV7LT4_1.introns.for_IGV.bed
09:12:14 : INFO : Execution Time = 0.12 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00762_B23MVV7LT4_1.introns  --cancer_introns tih_rna_sample_00762_B23MVV7LT4_1.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed tih_rna_sample_00762_B23MVV7LT4_1.introns.for_IGV.bed 
09:12:14 : INFO : Running: touch /tmp/nxf.hEzDi4jALq/tih_rna_sample_00762_B23MVV7LT4_1.chckpts/intron_igv_bed.ok
09:12:14 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00762_B23MVV7LT4_1.introns.for_IGV.bed  --bam tih_rna_sample_00762_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam  --output_prefix tih_rna_sample_00762_B23MVV7LT4_1 
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00762_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai
09:31:54 : INFO : Execution Time = 19.67 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00762_B23MVV7LT4_1.introns.for_IGV.bed  --bam tih_rna_sample_00762_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam  --output_prefix tih_rna_sample_00762_B23MVV7LT4_1 
09:31:54 : INFO : Running: touch /tmp/nxf.hEzDi4jALq/tih_rna_sample_00762_B23MVV7LT4_1.chckpts/reads_alignments_extracted.ok
09:31:54 : INFO : Running: samtools sort -o tih_rna_sample_00762_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00762_B23MVV7LT4_1.cancer_intron_reads.bam
09:31:54 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00762_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00762_B23MVV7LT4_1.cancer_intron_reads.bam
09:31:54 : INFO : Running: touch /tmp/nxf.hEzDi4jALq/tih_rna_sample_00762_B23MVV7LT4_1.chckpts/sort_cancer_intron_reads.ok
09:31:55 : INFO : Running: samtools sort -o tih_rna_sample_00762_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00762_B23MVV7LT4_1.gene_reads.bam
[bam_sort_core] merging from 125 files and 1 in-memory blocks...
09:54:18 : INFO : Execution Time = 22.40 minutes. CMD: samtools sort -o tih_rna_sample_00762_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00762_B23MVV7LT4_1.gene_reads.bam
09:54:18 : INFO : Running: touch /tmp/nxf.hEzDi4jALq/tih_rna_sample_00762_B23MVV7LT4_1.chckpts/sort_gene_reads.ok
09:54:18 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o tih_rna_sample_00762_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  tih_rna_sample_00762_B23MVV7LT4_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.
10:01:15 : INFO : Execution Time = 6.94 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o tih_rna_sample_00762_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  tih_rna_sample_00762_B23MVV7LT4_1.gene_reads.sorted.bam 
10:01:15 : INFO : Running: touch /tmp/nxf.hEzDi4jALq/tih_rna_sample_00762_B23MVV7LT4_1.chckpts/tih_rna_sample_00762_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp.ok
10:01:15 : INFO : Running: samtools sort -o tih_rna_sample_00762_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00762_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 4 files and 1 in-memory blocks...
10:02:04 : INFO : Execution Time = 0.81 minutes. CMD: samtools sort -o tih_rna_sample_00762_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00762_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp
10:02:04 : INFO : Running: touch /tmp/nxf.hEzDi4jALq/tih_rna_sample_00762_B23MVV7LT4_1.chckpts/tih_rna_sample_00762_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
10:02:04 : INFO : Running: samtools index tih_rna_sample_00762_B23MVV7LT4_1.gene_reads.sorted.sifted.bam 
10:02:10 : INFO : Execution Time = 0.10 minutes. CMD: samtools index tih_rna_sample_00762_B23MVV7LT4_1.gene_reads.sorted.sifted.bam 
10:02:10 : INFO : Running: touch /tmp/nxf.hEzDi4jALq/tih_rna_sample_00762_B23MVV7LT4_1.chckpts/tih_rna_sample_00762_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.indexed.ok
10:02:10 : INFO : Running: samtools index tih_rna_sample_00762_B23MVV7LT4_1.cancer_intron_reads.sorted.bam 
10:02:10 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00762_B23MVV7LT4_1.cancer_intron_reads.sorted.bam 
10:02:10 : INFO : Running: touch /tmp/nxf.hEzDi4jALq/tih_rna_sample_00762_B23MVV7LT4_1.chckpts/tih_rna_sample_00762_B23MVV7LT4_1.cancer_intron_reads.sorted.bam.indexed.ok
10:02:10 : INFO : Running: create_report tih_rna_sample_00762_B23MVV7LT4_1.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output tih_rna_sample_00762_B23MVV7LT4_1.ctat-splicing.igv.html  --track-config tih_rna_sample_00762_B23MVV7LT4_1.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: tih_rna_sample_00762_B23MVV7LT4_1' 
[W::hts_idx_load3] The index file is older than the data file: ctat_genome_lib_build_dir/refGene.sort.bed.gz.tbi
10:08:29 : INFO : Execution Time = 6.32 minutes. CMD: create_report tih_rna_sample_00762_B23MVV7LT4_1.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output tih_rna_sample_00762_B23MVV7LT4_1.ctat-splicing.igv.html  --track-config tih_rna_sample_00762_B23MVV7LT4_1.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: tih_rna_sample_00762_B23MVV7LT4_1' 
10:08:29 : INFO : Running: touch /tmp/nxf.hEzDi4jALq/tih_rna_sample_00762_B23MVV7LT4_1.chckpts/igv_create_html.ok
10:08:29 : INFO : done.