Hello there,
I am calling variants on 800 exome samples using Haplotypercaller for some reasons the caller stopped the analysis on certain location on chromosome 5 (after 5 weeks and i have 10 weeks to go). The error is below (one of the samples was malformed)
_INFO 02:04:51,540 ProgressMeter - chr5:180670788 1.05846818873E11 4.5 w 25.0 s 31.7% 14.1 w 9.6 w
INFO 02:06:01,736 ProgressMeter - chr5:180687847 1.05853600709E11 4.5 w 25.0 s 31.7% 14.1 w 9.6 w
INFO 02:07:01,737 ProgressMeter - chr5:180687847 1.05853600709E11 4.5 w 25.0 s 31.7% 14.1 w 9.6 w
INFO 02:08:11,738 ProgressMeter - chr5:180687847 1.05853600709E11 4.5 w 25.0 s 31.7% 14.1 w 9.6 w
INFO 02:09:11,739 ProgressMeter - chr5:180687847 1.05853600709E11 4.5 w 25.0 s 31.7% 14.1 w 9.6 w
INFO 02:10:11,740 ProgressMeter - chr5:180687847 1.05853600709E11 4.5 w 25.0 s 31.7% 14.1 w 9.6 w
INFO 02:11:11,741 ProgressMeter - chr5:180687847 1.05853600709E11 4.5 w 25.0 s 31.7% 14.1 w 9.6 w
ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.8-1-0-gf15c1c3ef):
ERROR
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions https://software.broadinstitute.org/gatk
ERROR
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR
ERROR MESSAGE: File /media/daruma/sea/sample483.fastq.gz.mdup.realigned.fixed.recal.bai is malformed: Premature end-of-file while reading BAM index file sample483.fastq.gz.mdup.realigned.fixed.recal.bai. It's likely that this file is truncated or corrupt -- Please try re-indexing the corresponding BAM file.
_
I will re analysis the sample and want to resume the analysis to speed up the process i was wondering if Haplotypecaller has resume function. If it doesnt what is the best way to work around the issue?
- shall i modify the exome target file ? if yes, shall i start from the begining of chroomsome 5 or find the closer position to where the analysis stopped ?
- why not including resume feature by feeding the analysis VCF file where it was stopped?
would like to hear other suggestions that was not mentioned
Thanks in advance 