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dnanexus-archive / parliament2

Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
Apache License 2.0
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Problem with a 7Mb targeted capture panel Illumina sequencing. "No such file or directory" error, cannot generate results. #61

Closed nelsonchanhk closed 5 years ago

nelsonchanhk commented 5 years ago

Hello, it's my first time to use parliament2. I tried the docker version but apparently, the above error appears for every chromosome region and I cannot generate results. My script and error are as follows. Thank you!

sudo docker run -v /home/nelson/OPERATION/RedCellNGS/old_no_indelrealignment/Processed_bam_vcf_1/raw:/home/dnanexus/in -v /home/nelson/OPERATION/RedCellNGS/temp_parliament:/home/dnanexus/out -v /home/nelson/OPERATION/RedCellNGS/ref:/home/dnanexus/ref dnanexus/parliament2:v0.1.9-13-g37d63065 --bam /home/dnanexus/in/HBD1/HBD1.bam -r /home/dnanexus/ref/Homo_sapiens_assembly38.fasta WARNING: Did not detect any SV modules requested by the user through command-line flags. Running with default SV modules: Breakdancer, Breakseq, Manta, CNVnator, Lumpy, and Delly Deletion Set up and index BAM/CRAM BAM file and index both exist in the mounted volume; continuing Generate contigs Launching jobs that cannot be parallelized by contig BreakSeq Manta parliament2.sh: line 167: /home/dnanexus/out/log_files/manta_logs//home/dnanexus/in/HBD1/HBD1.manta.stdout.log: No such file or directory parliament2.sh: line 154: /home/dnanexus/out/log_files/breakseq_logs//home/dnanexus/in/HBD1/HBD1.breakseq.stdout.log: No such file or directory Processing bam input.bam Read group NB501576: ignoring insert sizes above 1205 First read: 0 16211 Launching jobs parallelized by contig samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr1 Running Breakdancer for contig chr1 parliament2.sh: line 208: /home/dnanexus/out/log_files/breakdancer_logs//home/dnanexus/in/HBD1/HBD1.breakdancer.chr1.stderr.log: No such file or directory Running CNVnator for contig chr1 parliament2.sh: line 216: /home/dnanexus/out/log_files/cnvnator_logs//home/dnanexus/in/HBD1/HBD1.cnvnator.chr1.stdout.log: No such file or directory Running sambamba view parliament2.sh: line 224: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr1.stderr.log: No such file or directory Running sambamba index parliament2.sh: line 226: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr1.stdout.log: No such file or directory Running Delly (deletions) for contig chr1 parliament2.sh: line 232: /home/dnanexus/out/log_files/delly_deletion_logs//home/dnanexus/in/HBD1/HBD1.delly_deletion.chr1.stdout.log: No such file or directory Running Lumpy for contig chr1 parliament2.sh: line 264: /home/dnanexus/out/log_files/lumpy_logs//home/dnanexus/in/HBD1/HBD1.lumpy.1.stdout.log: No such file or directory samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr2 Running Breakdancer for contig chr2 parliament2.sh: line 208: /home/dnanexus/out/log_files/breakdancer_logs//home/dnanexus/in/HBD1/HBD1.breakdancer.chr2.stderr.log: No such file or directory Running CNVnator for contig chr2 parliament2.sh: line 216: /home/dnanexus/out/log_files/cnvnator_logs//home/dnanexus/in/HBD1/HBD1.cnvnator.chr2.stdout.log: No such file or directory Running sambamba view parliament2.sh: line 224: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr2.stderr.log: No such file or directory Running sambamba index parliament2.sh: line 226: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr2.stdout.log: No such file or directory Running Delly (deletions) for contig chr2 parliament2.sh: line 232: /home/dnanexus/out/log_files/delly_deletion_logs//home/dnanexus/in/HBD1/HBD1.delly_deletion.chr2.stdout.log: No such file or directory Running Lumpy for contig chr2 parliament2.sh: line 264: /home/dnanexus/out/log_files/lumpy_logs//home/dnanexus/in/HBD1/HBD1.lumpy.2.stdout.log: No such file or directory samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr3 Running Breakdancer for contig chr3 parliament2.sh: line 208: /home/dnanexus/out/log_files/breakdancer_logs//home/dnanexus/in/HBD1/HBD1.breakdancer.chr3.stderr.log: No such file or directory Running CNVnator for contig chr3 parliament2.sh: line 216: /home/dnanexus/out/log_files/cnvnator_logs//home/dnanexus/in/HBD1/HBD1.cnvnator.chr3.stdout.log: No such file or directory Running sambamba view parliament2.sh: line 224: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr3.stderr.log: No such file or directory Running sambamba index parliament2.sh: line 226: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr3.stdout.log: No such file or directory Running Delly (deletions) for contig chr3 parliament2.sh: line 232: /home/dnanexus/out/log_files/delly_deletion_logs//home/dnanexus/in/HBD1/HBD1.delly_deletion.chr3.stdout.log: No such file or directory Running Lumpy for contig chr3 parliament2.sh: line 264: /home/dnanexus/out/log_files/lumpy_logs//home/dnanexus/in/HBD1/HBD1.lumpy.3.stdout.log: No such file or directory samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr4 Running Breakdancer for contig chr4 parliament2.sh: line 208: /home/dnanexus/out/log_files/breakdancer_logs//home/dnanexus/in/HBD1/HBD1.breakdancer.chr4.stderr.log: No such file or directory Running CNVnator for contig chr4 parliament2.sh: line 216: /home/dnanexus/out/log_files/cnvnator_logs//home/dnanexus/in/HBD1/HBD1.cnvnator.chr4.stdout.log: No such file or directory Running sambamba view parliament2.sh: line 224: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr4.stderr.log: No such file or directory Running sambamba index parliament2.sh: line 226: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr4.stdout.log: No such file or directory Running Delly (deletions) for contig chr4 parliament2.sh: line 232: /home/dnanexus/out/log_files/delly_deletion_logs//home/dnanexus/in/HBD1/HBD1.delly_deletion.chr4.stdout.log: No such file or directory Running Lumpy for contig chr4 parliament2.sh: line 264: /home/dnanexus/out/log_files/lumpy_logs//home/dnanexus/in/HBD1/HBD1.lumpy.4.stdout.log: No such file or directory samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr5 Running Breakdancer for contig chr5 parliament2.sh: line 208: /home/dnanexus/out/log_files/breakdancer_logs//home/dnanexus/in/HBD1/HBD1.breakdancer.chr5.stderr.log: No such file or directory Running CNVnator for contig chr5 parliament2.sh: line 216: /home/dnanexus/out/log_files/cnvnator_logs//home/dnanexus/in/HBD1/HBD1.cnvnator.chr5.stdout.log: No such file or directory Running sambamba view parliament2.sh: line 224: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr5.stderr.log: No such file or directory Running sambamba index parliament2.sh: line 226: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr5.stdout.log: No such file or directory Running Delly (deletions) for contig chr5 parliament2.sh: line 232: /home/dnanexus/out/log_files/delly_deletion_logs//home/dnanexus/in/HBD1/HBD1.delly_deletion.chr5.stdout.log: No such file or directory Running Lumpy for contig chr5 parliament2.sh: line 264: /home/dnanexus/out/log_files/lumpy_logs//home/dnanexus/in/HBD1/HBD1.lumpy.5.stdout.log: No such file or directory samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr6 Running Breakdancer for contig chr6 parliament2.sh: line 208: /home/dnanexus/out/log_files/breakdancer_logs//home/dnanexus/in/HBD1/HBD1.breakdancer.chr6.stderr.log: No such file or directory Running CNVnator for contig chr6 parliament2.sh: line 216: /home/dnanexus/out/log_files/cnvnator_logs//home/dnanexus/in/HBD1/HBD1.cnvnator.chr6.stdout.log: No such file or directory Running sambamba view parliament2.sh: line 224: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr6.stderr.log: No such file or directory Running sambamba index parliament2.sh: line 226: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr6.stdout.log: No such file or directory Running Delly (deletions) for contig chr6 parliament2.sh: line 232: /home/dnanexus/out/log_files/delly_deletion_logs//home/dnanexus/in/HBD1/HBD1.delly_deletion.chr6.stdout.log: No such file or directory Running Lumpy for contig chr6 parliament2.sh: line 264: /home/dnanexus/out/log_files/lumpy_logs//home/dnanexus/in/HBD1/HBD1.lumpy.6.stdout.log: No such file or directory samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr7 Running Breakdancer for contig chr7 parliament2.sh: line 208: /home/dnanexus/out/log_files/breakdancer_logs//home/dnanexus/in/HBD1/HBD1.breakdancer.chr7.stderr.log: No such file or directory Running CNVnator for contig chr7 parliament2.sh: line 216: /home/dnanexus/out/log_files/cnvnator_logs//home/dnanexus/in/HBD1/HBD1.cnvnator.chr7.stdout.log: No such file or directory Running sambamba view parliament2.sh: line 224: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr7.stderr.log: No such file or directory Running sambamba index parliament2.sh: line 226: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr7.stdout.log: No such file or directory Running Delly (deletions) for contig chr7 parliament2.sh: line 232: /home/dnanexus/out/log_files/delly_deletion_logs//home/dnanexus/in/HBD1/HBD1.delly_deletion.chr7.stdout.log: No such file or directory Running Lumpy for contig chr7 parliament2.sh: line 264: /home/dnanexus/out/log_files/lumpy_logs//home/dnanexus/in/HBD1/HBD1.lumpy.7.stdout.log: No such file or directory samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr8 Running Breakdancer for contig chr8 parliament2.sh: line 208: /home/dnanexus/out/log_files/breakdancer_logs//home/dnanexus/in/HBD1/HBD1.breakdancer.chr8.stderr.log: No such file or directory Running CNVnator for contig chr8 parliament2.sh: line 216: /home/dnanexus/out/log_files/cnvnator_logs//home/dnanexus/in/HBD1/HBD1.cnvnator.chr8.stdout.log: No such file or directory Running sambamba view parliament2.sh: line 224: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr8.stderr.log: No such file or directory Running sambamba index parliament2.sh: line 226: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr8.stdout.log: No such file or directory Running Delly (deletions) for contig chr8 parliament2.sh: line 232: /home/dnanexus/out/log_files/delly_deletion_logs//home/dnanexus/in/HBD1/HBD1.delly_deletion.chr8.stdout.log: No such file or directory Running Lumpy for contig chr8 parliament2.sh: line 264: /home/dnanexus/out/log_files/lumpy_logs//home/dnanexus/in/HBD1/HBD1.lumpy.8.stdout.log: No such file or directory samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr9 Running Breakdancer for contig chr9 parliament2.sh: line 208: /home/dnanexus/out/log_files/breakdancer_logs//home/dnanexus/in/HBD1/HBD1.breakdancer.chr9.stderr.log: No such file or directory Running CNVnator for contig chr9 parliament2.sh: line 216: /home/dnanexus/out/log_files/cnvnator_logs//home/dnanexus/in/HBD1/HBD1.cnvnator.chr9.stdout.log: No such file or directory Running sambamba view parliament2.sh: line 224: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr9.stderr.log: No such file or directory Running sambamba index parliament2.sh: line 226: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr9.stdout.log: No such file or directory Running Delly (deletions) for contig chr9 parliament2.sh: line 232: /home/dnanexus/out/log_files/delly_deletion_logs//home/dnanexus/in/HBD1/HBD1.delly_deletion.chr9.stdout.log: No such file or directory Running Lumpy for contig chr9 parliament2.sh: line 264: /home/dnanexus/out/log_files/lumpy_logs//home/dnanexus/in/HBD1/HBD1.lumpy.9.stdout.log: No such file or directory samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr10 Running Breakdancer for contig chr10 parliament2.sh: line 208: /home/dnanexus/out/log_files/breakdancer_logs//home/dnanexus/in/HBD1/HBD1.breakdancer.chr10.stderr.log: No such file or directory Running CNVnator for contig chr10 parliament2.sh: line 216: /home/dnanexus/out/log_files/cnvnator_logs//home/dnanexus/in/HBD1/HBD1.cnvnator.chr10.stdout.log: No such file or directory Running sambamba view parliament2.sh: line 224: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr10.stderr.log: No such file or directory Running sambamba index parliament2.sh: line 226: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr10.stdout.log: No such file or directory Running Delly (deletions) for contig chr10 parliament2.sh: line 232: /home/dnanexus/out/log_files/delly_deletion_logs//home/dnanexus/in/HBD1/HBD1.delly_deletion.chr10.stdout.log: No such file or directory Running Lumpy for contig chr10 parliament2.sh: line 264: /home/dnanexus/out/log_files/lumpy_logs//home/dnanexus/in/HBD1/HBD1.lumpy.10.stdout.log: No such file or directory samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr11 Running Breakdancer for contig chr11 parliament2.sh: line 208: /home/dnanexus/out/log_files/breakdancer_logs//home/dnanexus/in/HBD1/HBD1.breakdancer.chr11.stderr.log: No such file or directory Running CNVnator for contig chr11 parliament2.sh: line 216: /home/dnanexus/out/log_files/cnvnator_logs//home/dnanexus/in/HBD1/HBD1.cnvnator.chr11.stdout.log: No such file or directory Running sambamba view parliament2.sh: line 224: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr11.stderr.log: No such file or directory Running sambamba index parliament2.sh: line 226: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr11.stdout.log: No such file or directory Running Delly (deletions) for contig chr11 parliament2.sh: line 232: /home/dnanexus/out/log_files/delly_deletion_logs//home/dnanexus/in/HBD1/HBD1.delly_deletion.chr11.stdout.log: No such file or directory Running Lumpy for contig chr11 parliament2.sh: line 264: /home/dnanexus/out/log_files/lumpy_logs//home/dnanexus/in/HBD1/HBD1.lumpy.11.stdout.log: No such file or directory samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr12 Running Breakdancer for contig chr12 parliament2.sh: line 208: /home/dnanexus/out/log_files/breakdancer_logs//home/dnanexus/in/HBD1/HBD1.breakdancer.chr12.stderr.log: No such file or directory Running CNVnator for contig chr12 parliament2.sh: line 216: /home/dnanexus/out/log_files/cnvnator_logs//home/dnanexus/in/HBD1/HBD1.cnvnator.chr12.stdout.log: No such file or directory Running sambamba view parliament2.sh: line 224: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr12.stderr.log: No such file or directory Running sambamba index parliament2.sh: line 226: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr12.stdout.log: No such file or directory Running Delly (deletions) for contig chr12 parliament2.sh: line 232: /home/dnanexus/out/log_files/delly_deletion_logs//home/dnanexus/in/HBD1/HBD1.delly_deletion.chr12.stdout.log: No such file or directory Running Lumpy for contig chr12 parliament2.sh: line 264: /home/dnanexus/out/log_files/lumpy_logs//home/dnanexus/in/HBD1/HBD1.lumpy.12.stdout.log: No such file or directory samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr13 Running Breakdancer for contig chr13 parliament2.sh: line 208: /home/dnanexus/out/log_files/breakdancer_logs//home/dnanexus/in/HBD1/HBD1.breakdancer.chr13.stderr.log: No such file or directory Running CNVnator for contig chr13 parliament2.sh: line 216: /home/dnanexus/out/log_files/cnvnator_logs//home/dnanexus/in/HBD1/HBD1.cnvnator.chr13.stdout.log: No such file or directory Running sambamba view parliament2.sh: line 224: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr13.stderr.log: No such file or directory Running sambamba index parliament2.sh: line 226: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr13.stdout.log: No such file or directory Running Delly (deletions) for contig chr13 parliament2.sh: line 232: /home/dnanexus/out/log_files/delly_deletion_logs//home/dnanexus/in/HBD1/HBD1.delly_deletion.chr13.stdout.log: No such file or directory Running Lumpy for contig chr13 parliament2.sh: line 264: /home/dnanexus/out/log_files/lumpy_logs//home/dnanexus/in/HBD1/HBD1.lumpy.13.stdout.log: No such file or directory samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr14 Running Breakdancer for contig chr14 parliament2.sh: line 208: /home/dnanexus/out/log_files/breakdancer_logs//home/dnanexus/in/HBD1/HBD1.breakdancer.chr14.stderr.log: No such file or directory Running CNVnator for contig chr14 parliament2.sh: line 216: /home/dnanexus/out/log_files/cnvnator_logs//home/dnanexus/in/HBD1/HBD1.cnvnator.chr14.stdout.log: No such file or directory Running sambamba view parliament2.sh: line 224: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr14.stderr.log: No such file or directory Running sambamba index parliament2.sh: line 226: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr14.stdout.log: No such file or directory Running Delly (deletions) for contig chr14 parliament2.sh: line 232: /home/dnanexus/out/log_files/delly_deletion_logs//home/dnanexus/in/HBD1/HBD1.delly_deletion.chr14.stdout.log: No such file or directory Running Lumpy for contig chr14 parliament2.sh: line 264: /home/dnanexus/out/log_files/lumpy_logs//home/dnanexus/in/HBD1/HBD1.lumpy.14.stdout.log: No such file or directory samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr15 Running Breakdancer for contig chr15 parliament2.sh: line 208: /home/dnanexus/out/log_files/breakdancer_logs//home/dnanexus/in/HBD1/HBD1.breakdancer.chr15.stderr.log: No such file or directory Running CNVnator for contig chr15 parliament2.sh: line 216: /home/dnanexus/out/log_files/cnvnator_logs//home/dnanexus/in/HBD1/HBD1.cnvnator.chr15.stdout.log: No such file or directory Running sambamba view parliament2.sh: line 224: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr15.stderr.log: No such file or directory Running sambamba index parliament2.sh: line 226: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr15.stdout.log: No such file or directory Running Delly (deletions) for contig chr15 parliament2.sh: line 232: /home/dnanexus/out/log_files/delly_deletion_logs//home/dnanexus/in/HBD1/HBD1.delly_deletion.chr15.stdout.log: No such file or directory Running Lumpy for contig chr15 parliament2.sh: line 264: /home/dnanexus/out/log_files/lumpy_logs//home/dnanexus/in/HBD1/HBD1.lumpy.15.stdout.log: No such file or directory samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr16 Running Breakdancer for contig chr16 parliament2.sh: line 208: /home/dnanexus/out/log_files/breakdancer_logs//home/dnanexus/in/HBD1/HBD1.breakdancer.chr16.stderr.log: No such file or directory Running CNVnator for contig chr16 parliament2.sh: line 216: /home/dnanexus/out/log_files/cnvnator_logs//home/dnanexus/in/HBD1/HBD1.cnvnator.chr16.stdout.log: No such file or directory Running sambamba view parliament2.sh: line 224: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr16.stderr.log: No such file or directory Running sambamba index parliament2.sh: line 226: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr16.stdout.log: No such file or directory Running Delly (deletions) for contig chr16 parliament2.sh: line 232: /home/dnanexus/out/log_files/delly_deletion_logs//home/dnanexus/in/HBD1/HBD1.delly_deletion.chr16.stdout.log: No such file or directory Running Lumpy for contig chr16 parliament2.sh: line 264: /home/dnanexus/out/log_files/lumpy_logs//home/dnanexus/in/HBD1/HBD1.lumpy.16.stdout.log: No such file or directory samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr17 Running Breakdancer for contig chr17 parliament2.sh: line 208: /home/dnanexus/out/log_files/breakdancer_logs//home/dnanexus/in/HBD1/HBD1.breakdancer.chr17.stderr.log: No such file or directory Running CNVnator for contig chr17 parliament2.sh: line 216: /home/dnanexus/out/log_files/cnvnator_logs//home/dnanexus/in/HBD1/HBD1.cnvnator.chr17.stdout.log: No such file or directory Running sambamba view parliament2.sh: line 224: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr17.stderr.log: No such file or directory Running sambamba index parliament2.sh: line 226: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr17.stdout.log: No such file or directory Running Delly (deletions) for contig chr17 parliament2.sh: line 232: /home/dnanexus/out/log_files/delly_deletion_logs//home/dnanexus/in/HBD1/HBD1.delly_deletion.chr17.stdout.log: No such file or directory Running Lumpy for contig chr17 parliament2.sh: line 264: /home/dnanexus/out/log_files/lumpy_logs//home/dnanexus/in/HBD1/HBD1.lumpy.17.stdout.log: No such file or directory samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr18 Running Breakdancer for contig chr18 parliament2.sh: line 208: /home/dnanexus/out/log_files/breakdancer_logs//home/dnanexus/in/HBD1/HBD1.breakdancer.chr18.stderr.log: No such file or directory Running CNVnator for contig chr18 parliament2.sh: line 216: /home/dnanexus/out/log_files/cnvnator_logs//home/dnanexus/in/HBD1/HBD1.cnvnator.chr18.stdout.log: No such file or directory Running sambamba view parliament2.sh: line 224: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr18.stderr.log: No such file or directory Running sambamba index parliament2.sh: line 226: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr18.stdout.log: No such file or directory Running Delly (deletions) for contig chr18 parliament2.sh: line 232: /home/dnanexus/out/log_files/delly_deletion_logs//home/dnanexus/in/HBD1/HBD1.delly_deletion.chr18.stdout.log: No such file or directory Running Lumpy for contig chr18 parliament2.sh: line 264: /home/dnanexus/out/log_files/lumpy_logs//home/dnanexus/in/HBD1/HBD1.lumpy.18.stdout.log: No such file or directory samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr19 Running Breakdancer for contig chr19 parliament2.sh: line 208: /home/dnanexus/out/log_files/breakdancer_logs//home/dnanexus/in/HBD1/HBD1.breakdancer.chr19.stderr.log: No such file or directory Running CNVnator for contig chr19 parliament2.sh: line 216: /home/dnanexus/out/log_files/cnvnator_logs//home/dnanexus/in/HBD1/HBD1.cnvnator.chr19.stdout.log: No such file or directory Running sambamba view parliament2.sh: line 224: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr19.stderr.log: No such file or directory Running sambamba index parliament2.sh: line 226: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr19.stdout.log: No such file or directory Running Delly (deletions) for contig chr19 parliament2.sh: line 232: /home/dnanexus/out/log_files/delly_deletion_logs//home/dnanexus/in/HBD1/HBD1.delly_deletion.chr19.stdout.log: No such file or directory Running Lumpy for contig chr19 parliament2.sh: line 264: /home/dnanexus/out/log_files/lumpy_logs//home/dnanexus/in/HBD1/HBD1.lumpy.19.stdout.log: No such file or directory samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr20 Running Breakdancer for contig chr20 parliament2.sh: line 208: /home/dnanexus/out/log_files/breakdancer_logs//home/dnanexus/in/HBD1/HBD1.breakdancer.chr20.stderr.log: No such file or directory Running CNVnator for contig chr20 parliament2.sh: line 216: /home/dnanexus/out/log_files/cnvnator_logs//home/dnanexus/in/HBD1/HBD1.cnvnator.chr20.stdout.log: No such file or directory Running sambamba view parliament2.sh: line 224: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr20.stderr.log: No such file or directory Running sambamba index parliament2.sh: line 226: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr20.stdout.log: No such file or directory Running Delly (deletions) for contig chr20 parliament2.sh: line 232: /home/dnanexus/out/log_files/delly_deletion_logs//home/dnanexus/in/HBD1/HBD1.delly_deletion.chr20.stdout.log: No such file or directory Running Lumpy for contig chr20 parliament2.sh: line 264: /home/dnanexus/out/log_files/lumpy_logs//home/dnanexus/in/HBD1/HBD1.lumpy.20.stdout.log: No such file or directory samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr21 Running Breakdancer for contig chr21 parliament2.sh: line 208: /home/dnanexus/out/log_files/breakdancer_logs//home/dnanexus/in/HBD1/HBD1.breakdancer.chr21.stderr.log: No such file or directory Running CNVnator for contig chr21 parliament2.sh: line 216: /home/dnanexus/out/log_files/cnvnator_logs//home/dnanexus/in/HBD1/HBD1.cnvnator.chr21.stdout.log: No such file or directory Running sambamba view parliament2.sh: line 224: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr21.stderr.log: No such file or directory Running sambamba index parliament2.sh: line 226: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr21.stdout.log: No such file or directory Running Delly (deletions) for contig chr21 parliament2.sh: line 232: /home/dnanexus/out/log_files/delly_deletion_logs//home/dnanexus/in/HBD1/HBD1.delly_deletion.chr21.stdout.log: No such file or directory Running Lumpy for contig chr21 parliament2.sh: line 264: /home/dnanexus/out/log_files/lumpy_logs//home/dnanexus/in/HBD1/HBD1.lumpy.21.stdout.log: No such file or directory samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chr22 Running Breakdancer for contig chr22 parliament2.sh: line 208: /home/dnanexus/out/log_files/breakdancer_logs//home/dnanexus/in/HBD1/HBD1.breakdancer.chr22.stderr.log: No such file or directory Running CNVnator for contig chr22 parliament2.sh: line 216: /home/dnanexus/out/log_files/cnvnator_logs//home/dnanexus/in/HBD1/HBD1.cnvnator.chr22.stdout.log: No such file or directory Running sambamba view parliament2.sh: line 224: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr22.stderr.log: No such file or directory Running sambamba index parliament2.sh: line 226: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chr22.stdout.log: No such file or directory Running Delly (deletions) for contig chr22 parliament2.sh: line 232: /home/dnanexus/out/log_files/delly_deletion_logs//home/dnanexus/in/HBD1/HBD1.delly_deletion.chr22.stdout.log: No such file or directory Running Lumpy for contig chr22 parliament2.sh: line 264: /home/dnanexus/out/log_files/lumpy_logs//home/dnanexus/in/HBD1/HBD1.lumpy.22.stdout.log: No such file or directory samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chrX Running Breakdancer for contig chrX parliament2.sh: line 208: /home/dnanexus/out/log_files/breakdancer_logs//home/dnanexus/in/HBD1/HBD1.breakdancer.chrX.stderr.log: No such file or directory Running CNVnator for contig chrX parliament2.sh: line 216: /home/dnanexus/out/log_files/cnvnator_logs//home/dnanexus/in/HBD1/HBD1.cnvnator.chrX.stdout.log: No such file or directory Running sambamba view parliament2.sh: line 224: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chrX.stderr.log: No such file or directory Running sambamba index parliament2.sh: line 226: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chrX.stdout.log: No such file or directory Running Delly (deletions) for contig chrX parliament2.sh: line 232: /home/dnanexus/out/log_files/delly_deletion_logs//home/dnanexus/in/HBD1/HBD1.delly_deletion.chrX.stdout.log: No such file or directory Running Lumpy for contig chrX parliament2.sh: line 264: /home/dnanexus/out/log_files/lumpy_logs//home/dnanexus/in/HBD1/HBD1.lumpy.23.stdout.log: No such file or directory samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Running on contig chrY Running Breakdancer for contig chrY parliament2.sh: line 208: /home/dnanexus/out/log_files/breakdancer_logs//home/dnanexus/in/HBD1/HBD1.breakdancer.chrY.stderr.log: No such file or directory Running CNVnator for contig chrY parliament2.sh: line 216: /home/dnanexus/out/log_files/cnvnator_logs//home/dnanexus/in/HBD1/HBD1.cnvnator.chrY.stdout.log: No such file or directory Running sambamba view parliament2.sh: line 224: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chrY.stderr.log: No such file or directory Running sambamba index parliament2.sh: line 226: /home/dnanexus/out/log_files/sambamba_logs//home/dnanexus/in/HBD1/HBD1.sambamba.chrY.stdout.log: No such file or directory Running Delly (deletions) for contig chrY parliament2.sh: line 232: /home/dnanexus/out/log_files/delly_deletion_logs//home/dnanexus/in/HBD1/HBD1.delly_deletion.chrY.stdout.log: No such file or directory Running Lumpy for contig chrY parliament2.sh: line 264: /home/dnanexus/out/log_files/lumpy_logs//home/dnanexus/in/HBD1/HBD1.lumpy.24.stdout.log: No such file or directory Converting results to VCF format Convert Lumpy results to VCF format Convert Manta results to VCF format No outputs of Manta found. Continuing. Convert Breakdancer results to VCF format Convert CNVnator results to VCF format Convert Breakseq results to VCF format No outputs of Breakseq found. Continuing. Convert Delly deletion results to VCF format cat: output.cnvnator_calls-1: No such file or directory cat: output.cnvnator_calls-2: No such file or directory cat: output.cnvnator_calls-3: No such file or directory cat: output.cnvnator_calls-4: No such file or directory cat: output.cnvnator_calls-5: No such file or directory cat: output.cnvnator_calls-6: No such file or directory cat: output.cnvnator_calls-7: No such file or directory cat: output.cnvnator_calls-8: No such file or directory cat: output.cnvnator_calls-9: No such file or directory cat: output.cnvnator_calls-10: No such file or directory cat: output.cnvnator_calls-11: No such file or directory cat: output.cnvnator_calls-12: No such file or directory cat: output.cnvnator_calls-13: No such file or directory cat: output.cnvnator_calls-14: No such file or directory cat: output.cnvnator_calls-15: No such file or directory cat: output.cnvnator_calls-16: No such file or directory cat: output.cnvnator_calls-17: No such file or directory cat: output.cnvnator_calls-18: No such file or directory cat: output.cnvnator_calls-19: No such file or directory cat: output.cnvnator_calls-20: No such file or directory cat: output.cnvnator_calls-21: No such file or directory cat: output.cnvnator_calls-22: No such file or directory cat: output.cnvnator_calls-23: No such file or directory cat: output.cnvnator_calls-24: No such file or directory ls: cannot access *.vcf: No such file or directory cp: cannot create regular file '/home/dnanexus/out/sv_caller_results//home/dnanexus/in/HBD1/HBD1.breakdancer.ctx': No such file or directory find: `breakseq2': No such file or directory No Breakseq log files found. cp: cannot create regular file '/home/dnanexus/out/sv_caller_results//home/dnanexus/in/HBD1/HBD1.breakdancer.vcf': No such file or directory cp: cannot create regular file '/home/dnanexus/out/sv_caller_results//home/dnanexus/in/HBD1/HBD1.delly.deletion.vcf': No such file or directory cp: cannot create regular file '/home/dnanexus/out/sv_caller_results//home/dnanexus/in/HBD1/HBD1.lumpy.vcf': No such file or directory Reading calls ... cp: cannot create regular file '/home/dnanexus/out/sv_caller_results//home/dnanexus/in/HBD1/HBD1.cnvnator.vcf': No such file or directory cp: cannot create regular file '/home/dnanexus/out/sv_caller_results//home/dnanexus/in/HBD1/HBD1.cnvnator.output': No such file or directory

AndrewCarroll commented 5 years ago

Hi Nelson,

I'm sorry, Parliament2 is designed to work for WGS samples. It isn't designed to call SVs in either exomes or target capture. If you would like to try generating output and use the fact that Parliament2 pre-installs the tools, you might like to try deselecting all but the individual methods and seeing which will produce output for target capture as structured here. CNVnator will certainly not work, but some of the others might.

Thanks, Andrew