Proovread terminated with error
I run proovread with following command
perl proove/proovread/bin/proovread -l Lang_flnc.fasta.CDHIT.fasta -s normalized.fastq -o re
After running for 5 days, it terminated with the following error.
Reading normalized.fastq
Killed
[E::sam_parse1] incomplete aux field
[W::sam_read1] parse error at line 185663450
[main_samview] truncated file.
#------------------------------------------------------------------------------#
Exited at 'main'
'proove/proovread/bin/proovread', line 1320
Last call 'main::run_bwa'
'proove/proovread/bin/proovread', line 853
Any help will be appreciated. Thanks.
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Please read the README on post types. This is a
Questiontype post, not aForumtype post.This looks like a out-of-memory error. How much memory is available, what is the organism and how many threads have been used?
Thanks for the comment. My command looks like this
I have enough memory too.
You did not answer any of it. This error always occurred to me when I was out-of-memory, that is why I am asking. BWA can be pretty RAM-hungry at times. With 16-32 threads at times 60GB was not enough.
Sorry. I used 17 million reads from a non-model plant. I have 70 GB with 8 threads.