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Proovread terminated with error
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12 months ago
prp291 • 50
United States

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.

proovread bwa • 122 views
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Please read the README on post types. This is a Question type post, not a Forum type post.

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This looks like a out-of-memory error. How much memory is available, what is the organism and how many threads have been used?

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Thanks for the comment. My command looks like this

   perl proove/proovread/bin/proovread -l Lang_flnc.fasta.CDHIT.fasta -s normalized.fastq -o re

I have enough memory too.

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How much memory is available, what is the organism and how many threads have been used?

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.

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Sorry. I used 17 million reads from a non-model plant. I have 70 GB with 8 threads.

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