Structural variations (SV calling using Parliament2)

Question

[Nitha]

Hi All,

I am using Parliament2 docker version (installed in centos 7) to identify the structural variants. Able to pull the Parliament 2 image successfully but while running the tool, the very first command itself not able to read input. As mentioned in Readme file, all the file required are kept in folder, but still it throws error

**Errors:**  
**--1st way (more than 1 sample used)**    
```[root@lab bam_files]# docker run -v /home/br/Parliament2/bam_files/:/home/dnanexus/in -v /home/cbr/Parliament2/bam_files/outputs/:/home/br/Parliament2/bam_files/out dnanexus/parliament2 --bam *.bam --bai *.bai -r /home/br/Parliament2/bam_files/ref-gen/GRCh38_full_analysis_set_plus_decoy_hla.fa --breakdancer --cnvnator --manta --genotype ``` 
usage: parliament2.py [-h] --bam BAM [--bai BAI] -r REF_GENOME [--fai FAI]  
                      [--prefix PREFIX] [--filter_short_contigs]  
                      [--breakdancer] [--breakseq] [--manta] [--cnvnator]  
                      [--lumpy] [--delly_deletion] [--delly_insertion]  
                      [--delly_inversion] [--delly_duplication] [--genotype]  
                      [--svviz] [--svviz_only_validated_candidates]  
**parliament2.py: error: unrecognized arguments:** sample1.bam sample2.bam sample3.bam sample4.bam sample5.bam sample1.bai sample2.bai sample3.bai sample4.bai sample5.bai  

**2nd way ( used only one samples, still it shows error)**  

```[root@lab bam_files]# docker run -v /home/br/Parliament2/bam_files/:/home/dnanexus/in -v /home/cbr/Parliament2/bam_files/outputs/:/home/cbr/Parliament2/bam_files/out dnanexus/parliament2 --bam sample1.bam --bai sample1.bai -r /home/br/Parliament2/bam_files/ref-gen/GRCh38_full_analysis_set_plus_decoy_hla.fa --breakdancer --cnvnator --manta --genotype```  
**ERROR: An invalid (nonexistent) input file has been specified.**  
Traceback (most recent call last):  
  File "/home/dnanexus/parliament2.py", line 80, in <module>  
    main()  
  File "/home/dnanexus/parliament2.py", line 76, in main  
    run_parliament(args.bam, args.bai, ref_genome_name, args.fai, prefix, args.filter_short_contigs, args.breakdancer, args.breakseq, args.manta, args.cnvnator, args.lumpy, args.delly_deletion, args.delly_insertion, args.delly_inversion, args.delly_duplication, args.genotype, args.svviz, args.svviz_only_validated_candidates, args.dnanexus)  
  File "/home/dnanexus/parliament2.py", line 49, in run_parliament  
    subprocess.check_call(['bash', 'parliament2.sh', bam, bai, ref_genome, fai, prefix, str(filter_short_contigs), str(breakdancer), str(breakseq), str(manta), str(cnvnator), str(lumpy), str(delly_deletion), str(delly_insertion), str(delly_inversion), str(delly_duplication), str(genotype), str(svviz), str(svviz_only_validated_candidates), str(dnanexus)])
  File "/miniconda/lib/python2.7/subprocess.py", line 190, in check_call  
    raise CalledProcessError(retcode, cmd)  
subprocess.CalledProcessError: Command '['bash', 'parliament2.sh', '/home/dnanexus/in/sample1.bam', '/home/dnanexus/in/sample1.bai', '/home/dnanexus/in//home/br/Parliament2/bam_files/ref-gen/GRCh38_full_analysis_set_plus_decoy_hla.fa', '/home/dnanexus/in/None', 'sample1', 'False', 'True', 'False', 'True', 'True', 'False', 'False', 'False', 'False', 'False', 'True', 'False', 'False', 'False']' returned non-zero exit status 1

Could any one help me, how to sort out this error?

Thanks in advance

[namaring12]

Hi ! Hope everything is going well with you.

I have tried to run Parliament2 to detect structural variants using one sample, and it seems like I got the same error message as you. Did you solve the problem? I don't know what am I doing wrong as I followed the command line as in the guidelines.

The following is the command line I used to call S.V:

docker run -v /storage/F2101/:/home/dnanexus/in -v /storage/PopGen/outputcnv/:/home/dnanexus/out dnanexus/parliament2:latest --bam NELBRAMLGA000000023.sorted.bam -r /storage/F2101/reference/ARS-UCD1.2_Btau5.0.1Y.fa --breakdancer --cnvnator --manta --lumpy --delly_deletion --delly_insertion --delly_inversion --delly_duplication --genotype --svviz --svviz_only_validated

I have around 150 samples to run, and I don't know certainly how to run them simultaneously (i.e. in a loop) in order to optimize my analysis. Did you find a way to do this?

[GenoMax]

/home/dnanexus is an example directory. Do you have a directory with that name? If not then you need to substitute that with your own directory.

You must mount two local volumes -- one that contains the inputs (.bam and .fa.gz) and one in which you wish to place the files generated by Parliament2.