search

hall-lab / speedseq

A flexible framework for rapid genome analysis and interpretation
MIT License
311 stars 116 forks source link

Speedseq Sv on exome data #109

Closed silenus092 closed 7 years ago

silenus092 commented 7 years ago

Hi I run SV by using the following command

speedseq sv -t 8 -o /mnt/speedSeq_data/SR03/SR03 -x /opt/speedseq/annotations/ceph18.b37.lumpy.exclude.2014-01-15.bed -g -d -B /mnt/speedSeq_data/SR03/SR03.bam -D /mnt/speedSeq_data/SR03/SR03.discordants.bam -S /mnt/speedSeq_data/SR03/SR03.splitters.bam -R /mnt/speedSeq_data/RefGRch37/human_g1k_v37.fasta -K /opt/speedseq/bin/speedseq.config -T /mnt/speedSeq_data/tmp/

And then speedseq generated error log as below;

Can't open file '/mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root'. Error in : file /mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root does not exist Can't open file '/mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root'. Error in : file /mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root does not exist Can't open file '/mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root'. Error in : file /mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root does not exist Can't open file '/mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root'. Error in : file /mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root does not exist Can't open file '/mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root'. Can't find all necessary histograms for chromosome '22' in file /mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root. Error in : file /mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root does not exist Can't open file '/mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root'. Error in : file /mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root does not exist Can't open file '/mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root'. Error in : file /mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root does not exist Can't open file '/mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root'. Error in : file /mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root does not exist Can't open file '/mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root'. Error in : file /mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root does not exist Can't open file '/mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root'. Can't find all necessary histograms for chromosome '22' in file /mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root. Error in : file /mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root does not exist Can't open file '/mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root'. Error in : file /mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root does not exist Can't open file '/mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root'. Error in : file /mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root does not exist Can't open file '/mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root'. Error in : file /mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root does not exist Can't open file '/mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root'. Error in : file /mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root does not exist Can't open file '/mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root'. Can't find all necessary histograms for chromosome '22' in file /mnt/speedSeq_data/tmp//cnvnator-temp/SR03.bam.hist.root. Traceback (most recent call last): File "/opt/speedseq//bin/annotate_rd.py", line 350, in sys.exit(main()) File "/opt/speedseq//bin/annotate_rd.py", line 342, in main sv_readdepth(args.input_vcf, args.sample, args.root, args.window, args.output_vcf, args.debug, args.cnvnator) File "/opt/speedseq//bin/annotate_rd.py", line 321, in sv_readdepth var.genotype(sample).set_format('CN', cn_list[i]) IndexError: list index out of range

Thanks, Note

cc2qe commented 7 years ago

SpeedSeq is intended for WGS data, not exome data. While some of the modules are adaptable to exome sequence, the SV modules will not work.

silenus092 commented 7 years ago

Thank you very much

again , I used WGS data instead , and called SV same command above.The speedseq generated error log as below;

Error in : file /mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root does not exist Can't open file '/mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root'. Error in : file /mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root does not exist Can't open file '/mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root'. Error in : file /mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root does not exist Can't open file '/mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root'. Error in : file /mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root does not exist Can't open file '/mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root'. Error in : file /mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root does not exist Can't open file '/mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root'. Can't find all necessary histograms for chromosome 'GL000219.1' in file /mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root. Error in : file /mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root does not exist Can't open file '/mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root'. Error in : file /mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root does not exist Can't open file '/mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root'. Error in : file /mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root does not exist Can't open file '/mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root'. Error in : file /mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root does not exist Can't open file '/mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root'. Error in : file /mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root does not exist Can't open file '/mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root'. Can't find all necessary histograms for chromosome 'GL000224.1' in file /mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root. Error in : file /mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root does not exist Can't open file '/mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root'. Error in : file /mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root does not exist Can't open file '/mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root'. Error in : file /mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root does not exist Can't open file '/mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root'. Error in : file /mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root does not exist Can't open file '/mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root'. Error in : file /mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root does not exist Can't open file '/mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root'. Can't find all necessary histograms for chromosome 'GL000224.1' in file /mnt/speedSeq_data/tmp/cnvnator-temp/C747.bam.hist.root. Traceback (most recent call last): File "/opt/speedseq//bin/annotate_rd.py", line 350, in sys.exit(main()) File "/opt/speedseq//bin/annotate_rd.py", line 342, in main sv_readdepth(args.input_vcf, args.sample, args.root, args.window, args.output_vcf, args.debug, args.cnvnator) File "/opt/speedseq//bin/annotate_rd.py", line 321, in sv_readdepth var.genotype(sample).set_format('CN', cn_list[i]) IndexError: list index out of range

Moreover , any recommend for SV annotation ?

Many thanks, Note