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marbl / parsnp

Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
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-x option issue #108

Closed pasdidee closed 8 months ago

pasdidee commented 2 years ago

Could you tell me if the -x option to filter recombinaison is still working?

I have tried it and I receive this error message:

11:13:24 - [1;37mINFO [0m - <> 11:13:24 - [1;37mINFO [0m - No genbank file provided for reference annotations, skipping.. 11:13:25 - [1;37mINFO [0m - Running Parsnp multi-MUM search and libMUSCLE aligner... 11:16:28 - [1;37mINFO [0m - Running PhiPack on LCBs to detect recombination... Traceback (most recent call last): File "/opt/gensoft/exe/parsnp/1.5.4/bin/parsnp", line 1322, in if block_spos < chr_spos: TypeError: '<' not supported between instances of 'int' and 'list' slurmstepd: error: STEP 66553408.0 CANCELLED srun: Job step aborted: Waiting up to 32 seconds for job step to finish.

It seems to have an error in the original script. Is-it the case?

Thank you for your answer,

A bioinformatic noob user ;-)

bkille commented 2 years ago

Hi @pasdidee, thanks for using parsnp! That issue has been mentioned before in #87 and has since been fixed. If you update your parsnp version, you should no longer experience that failure.

-Bryce

pasdidee commented 2 years ago

Hi @bkille, thank for your answer. I have checked the version of parsnp used and it was Parsnp 1.5.4. I will retry my analysis with the 1.5.6 version (or the most recent one).

Thank you very much !

bkille commented 2 years ago

@pasdidee has the update resolved the issue?

pasdidee commented 2 years ago

Hi Bryce,

The issue seems to be resolved. ParSNP run well and complete the task without error. Unfortunately, I observe no difference between the tree and ggr file obtained with or without the -x option. Maybe I forget something else…

Thanks to ask news,

Pasdidee

Le 2 mars 2022 à 21:37, Bryce Kille @.**@.>> a écrit :

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bkille commented 8 months ago

Hi @pasdidee,

When running with -x, you should see a message

INFO: Running PhiPack on LCBs to detect recombination...

Running with -x will not change your output files, but it will provide an additional BED file parsnp.rec which contains the desired recombination information.