opera error bwa mapping

[H1889]

Hi. When running an analysis with opera-ms an error is produced:

Error in during bwa mapping.

I hace checked /intermediate_files/polished_assembly/bwa.err, and this is shown:

[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files
Usage: samtools sort [options...] [in.bam]
Options:
-l INT Set compression level, from 0 (uncompressed) to 9 (best)
-m INT Set maximum memory per thread; suffix K/M/G recognized [768M]
-n Sort by read name
-t TAG Sort by value of TAG. Uses position as secondary index (or read name if -n is set)
-o FILE Write final output to FILE rather than standard output
-T PREFIX Write temporary files to PREFIX.nnnn.bam
--no-PG do not add a PG line
--input-fmt-option OPT[=VAL]
Specify a single input file format option in the form
of OPTION or OPTION=VALUE
-O, --output-fmt FORMAT[,OPT[=VAL]]...
Specify output format (SAM, BAM, CRAM)
--output-fmt-option OPT[=VAL]
Specify a single output file format option in the form
of OPTION or OPTION=VALUE
--reference FILE
Reference sequence FASTA FILE [null]
-@, --threads INT
Number of additional threads to use [0]
--verbosity INT
Set level of verbosity
[M::main_mem] read 1117024 sequences (320000554 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] skip orientation FR as there are not enough pairs
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1117024 reads in 5923.134 CPU sec, 494.192 real sec

And the /intermediate_files/polished_assembly/bwa.out is empty

thank you in advance

[jsgounot]

Hi,

very interesting, it looks like it's similar to issue #67. I still don't know what's happening here. I will come back to you as soon as I know more. Please keep me updated if you find something on your own.

Could you please indicate to me which perl you're using?

regards,
jsgounot

[H1889]

Thanks for the fast reponse, my machine is Ubuntu 20.04.3 LTS (GNU/Linux 4.15.0-147-generic x86_64

and perl -V:
Summary of my perl5 (revision 5 version 30 subversion 0) configuration:

Platform:
osname=linux
osvers=4.19.0
archname=x86_64-linux-gnu-thread-multi
uname='linux localhost 4.19.0 #1 smp debian 4.19.0 x86_64 gnulinux '

best

[emblab-westlake]

Hi,
Has this problem been solved? I look forward to your sharing your experience.
best wishes

[jsgounot]

Hi, I'm slowly working on a global rewritting of the software and I didn't precisely find the origin of this issue. It looks like this is related to BWA version, which might fail now with some specific reads formatting. A potential fix would be to use a new BWA version (or minimap2) and link it to OPERA-MS by modifying the bwa path in the OPERA-MS directory (with a softlink for example). Sorry to not be able to provide a better solution right now.

[cyhofe]

Hi everyone,
I encountered the same problem and wanted to know if there is a solution to this problem by now?

[jsgounot]

Hi @cyhofe, I never found why this issue happens on some computer but not on others. Could you please share the tail of your bwa file? Otherwise, you can also run the polishing step (bwa-mem + pilon) and the result should be the same.