Error on Speedseq SV

[silenus092]

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