Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/43d0eeeb57f6e794c1328833b6aa50/aih-tih-sc-331e97-R1_A23WJ53LT4_1.Chimeric.out.junction
  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/2a/ba1fadc8532b14facf3f4a43966849/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/44d478988b781361bbb43743242093/aih-tih-sc-331e97-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/ba1fadc8532b14facf3f4a43966849/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/43d0eeeb57f6e794c1328833b6aa50/aih-tih-sc-331e97-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/43d0eeeb57f6e794c1328833b6aa50/aih-tih-sc-331e97-R1_A23WJ53LT4_1.SJ.out.tab
==> STAGING COMPLETE (7 inputs)

07:45:36 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes

[10000], rate=600000.00/min 
[20000], rate=1200000.00/min 
[30000], rate=1800000.00/min 
[40000], rate=2400000.00/min 
[50000], rate=3000000.00/min 
[60000], rate=3600000.00/min 07:45:42 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-331e97-R1_A23WJ53LT4_1.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > aih-tih-sc-331e97-R1_A23WJ53LT4_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.
-aih-tih-sc-331e97-R1_A23WJ53LT4_1.introns: identified 10 cancer introns
07:45:42 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-331e97-R1_A23WJ53LT4_1.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > aih-tih-sc-331e97-R1_A23WJ53LT4_1.cancer.introns.prelim 
07:45:42 : INFO : Running: touch /tmp/nxf.Fh7fzcTlM2/aih-tih-sc-331e97-R1_A23WJ53LT4_1.chckpts/prelim_introns.ok
07:45:42 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-331e97-R1_A23WJ53LT4_1.cancer.introns.prelim --min_total_reads 5  > aih-tih-sc-331e97-R1_A23WJ53LT4_1.cancer.introns 
07:45:42 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-331e97-R1_A23WJ53LT4_1.cancer.introns.prelim --min_total_reads 5  > aih-tih-sc-331e97-R1_A23WJ53LT4_1.cancer.introns 
07:45:42 : INFO : Running: touch /tmp/nxf.Fh7fzcTlM2/aih-tih-sc-331e97-R1_A23WJ53LT4_1.chckpts/introns_filtered.ok
07:45:42 : INFO : -found 1 cancer introns
07:45:42 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-331e97-R1_A23WJ53LT4_1.introns  --cancer_introns aih-tih-sc-331e97-R1_A23WJ53LT4_1.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed aih-tih-sc-331e97-R1_A23WJ53LT4_1.introns.for_IGV.bed 
07:45:43 : INFO :  Creating the BED File.
07:45:43 : INFO : Saving Bed File as aih-tih-sc-331e97-R1_A23WJ53LT4_1.introns.for_IGV.bed
07:45:43 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-331e97-R1_A23WJ53LT4_1.introns  --cancer_introns aih-tih-sc-331e97-R1_A23WJ53LT4_1.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed aih-tih-sc-331e97-R1_A23WJ53LT4_1.introns.for_IGV.bed 
07:45:43 : INFO : Running: touch /tmp/nxf.Fh7fzcTlM2/aih-tih-sc-331e97-R1_A23WJ53LT4_1.chckpts/intron_igv_bed.ok
07:45:43 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-331e97-R1_A23WJ53LT4_1.introns.for_IGV.bed  --bam aih-tih-sc-331e97-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam  --output_prefix aih-tih-sc-331e97-R1_A23WJ53LT4_1 
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-331e97-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
07:45:43 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-331e97-R1_A23WJ53LT4_1.introns.for_IGV.bed  --bam aih-tih-sc-331e97-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam  --output_prefix aih-tih-sc-331e97-R1_A23WJ53LT4_1 
07:45:43 : INFO : Running: touch /tmp/nxf.Fh7fzcTlM2/aih-tih-sc-331e97-R1_A23WJ53LT4_1.chckpts/reads_alignments_extracted.ok
07:45:43 : INFO : Running: samtools sort -o aih-tih-sc-331e97-R1_A23WJ53LT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-331e97-R1_A23WJ53LT4_1.cancer_intron_reads.bam
07:45:43 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o aih-tih-sc-331e97-R1_A23WJ53LT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-331e97-R1_A23WJ53LT4_1.cancer_intron_reads.bam
07:45:43 : INFO : Running: touch /tmp/nxf.Fh7fzcTlM2/aih-tih-sc-331e97-R1_A23WJ53LT4_1.chckpts/sort_cancer_intron_reads.ok
07:45:43 : INFO : Running: samtools sort -o aih-tih-sc-331e97-R1_A23WJ53LT4_1.gene_reads.sorted.bam aih-tih-sc-331e97-R1_A23WJ53LT4_1.gene_reads.bam
07:45:44 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o aih-tih-sc-331e97-R1_A23WJ53LT4_1.gene_reads.sorted.bam aih-tih-sc-331e97-R1_A23WJ53LT4_1.gene_reads.bam
07:45:44 : INFO : Running: touch /tmp/nxf.Fh7fzcTlM2/aih-tih-sc-331e97-R1_A23WJ53LT4_1.chckpts/sort_gene_reads.ok
07:45:44 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o aih-tih-sc-331e97-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  aih-tih-sc-331e97-R1_A23WJ53LT4_1.gene_reads.sorted.bam 
Done with chr chr1.
07:45:44 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o aih-tih-sc-331e97-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  aih-tih-sc-331e97-R1_A23WJ53LT4_1.gene_reads.sorted.bam 
07:45:44 : INFO : Running: touch /tmp/nxf.Fh7fzcTlM2/aih-tih-sc-331e97-R1_A23WJ53LT4_1.chckpts/aih-tih-sc-331e97-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam.tmp.ok
07:45:44 : INFO : Running: samtools sort -o aih-tih-sc-331e97-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-331e97-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam.tmp
07:45:44 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o aih-tih-sc-331e97-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-331e97-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam.tmp
07:45:44 : INFO : Running: touch /tmp/nxf.Fh7fzcTlM2/aih-tih-sc-331e97-R1_A23WJ53LT4_1.chckpts/aih-tih-sc-331e97-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
07:45:44 : INFO : Running: samtools index aih-tih-sc-331e97-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam 
07:45:44 : INFO : Execution Time = 0.00 minutes. CMD: samtools index aih-tih-sc-331e97-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam 
07:45:44 : INFO : Running: touch /tmp/nxf.Fh7fzcTlM2/aih-tih-sc-331e97-R1_A23WJ53LT4_1.chckpts/aih-tih-sc-331e97-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam.indexed.ok
07:45:44 : INFO : Running: samtools index aih-tih-sc-331e97-R1_A23WJ53LT4_1.cancer_intron_reads.sorted.bam 
07:45:44 : INFO : Execution Time = 0.00 minutes. CMD: samtools index aih-tih-sc-331e97-R1_A23WJ53LT4_1.cancer_intron_reads.sorted.bam 
07:45:44 : INFO : Running: touch /tmp/nxf.Fh7fzcTlM2/aih-tih-sc-331e97-R1_A23WJ53LT4_1.chckpts/aih-tih-sc-331e97-R1_A23WJ53LT4_1.cancer_intron_reads.sorted.bam.indexed.ok
07:45:44 : INFO : Running: create_report aih-tih-sc-331e97-R1_A23WJ53LT4_1.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output aih-tih-sc-331e97-R1_A23WJ53LT4_1.ctat-splicing.igv.html  --track-config aih-tih-sc-331e97-R1_A23WJ53LT4_1.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: aih-tih-sc-331e97-R1_A23WJ53LT4_1' 
07:45:44 : INFO : Execution Time = 0.00 minutes. CMD: create_report aih-tih-sc-331e97-R1_A23WJ53LT4_1.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output aih-tih-sc-331e97-R1_A23WJ53LT4_1.ctat-splicing.igv.html  --track-config aih-tih-sc-331e97-R1_A23WJ53LT4_1.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: aih-tih-sc-331e97-R1_A23WJ53LT4_1' 
07:45:44 : INFO : Running: touch /tmp/nxf.Fh7fzcTlM2/aih-tih-sc-331e97-R1_A23WJ53LT4_1.chckpts/igv_create_html.ok
07:45:44 : INFO : done.