search

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.
Other
126 stars 25 forks source link

parsnp run error due to readlinelib #61

Open alexadn opened 5 years ago

alexadn commented 5 years ago

I installed parsnp 1) via conda as part of a pipeline I want to use which brings its own envs. After recieving the error below: 2) via conda (bioconda) in an own dedicated parsnp env, and 3) from source as descibed on the redthedocs page. Im am working on Linux SUSE/SLES12. In all approaches I get the following error as soon as I start pasnp wih a test data set (parsnp -c -f GCF000008985.fasta -d assemby-folder/ -o outdir -p 8 -v) and even only with option -h:

Warning: Cannot determine OS, defaulting to linux |--Parsnp v1.2--| For detailed documentation please see --> http://harvest.readthedocs.org/en/latest sh: /tmp/_MEIgucblW/libreadline.so.6: no version information available (required by sh) sh: relocation error: sh: symbol rl_filename_stat_hook, version READLINE_6.3 not defined in file libreadline.so.6 with link time reference sh: /tmp/_MEIgucblW/libreadline.so.6: no version information available (required by sh) sh: relocation error: sh: symbol rl_filename_stat_hook, version READLINE_6.3 not defined in file libreadline.so.6 with link time reference sh: /tmp/_MEIgucblW/libreadline.so.6: no version information available (required by sh) sh: relocation error: sh: symbol rl_filename_stat_hook, version READLINE_6.3 not defined in file libreadline.so.6 with link time reference sh: /tmp/_MEIgucblW/libreadline.so.6: no version information available (required by sh) sh: relocation error: sh: symbol rl_filename_stat_hook, version READLINE_6.3 not defined in file libreadline.so.6 with link time reference sh: /tmp/_MEIgucblW/libreadline.so.6: no version information available (required by sh) sh: relocation error: sh: symbol rl_filename_stat_hook, version READLINE_6.3 not defined in file libreadline.so.6 with link time reference sh: /tmp/_MEIgucblW/libreadline.so.6: no version information available (required by sh) sh: relocation error: sh: symbol rl_filename_stat_hook, version READLINE_6.3 not defined in file libreadline.so.6 with link time reference option -f not recognized

below that error the usage manual is shown:

parsnp [options] [-g|-r|-q](see below) -d -p ...

Any help woul be appraciated. Thank you so much!

bkille commented 4 years ago

I installed parsnp 1) via conda as part of a pipeline I want to use which brings its own envs. After recieving the error below: 2) via conda (bioconda) in an own dedicated parsnp env, and 3) from source as descibed on the redthedocs page. Im am working on Linux SUSE/SLES12. In all approaches I get the following error as soon as I start pasnp wih a test data set (parsnp -c -f GCF000008985.fasta -d assemby-folder/ -o outdir -p 8 -v) and even only with option -h:

Warning: Cannot determine OS, defaulting to linux
|--Parsnp v1.2--|
For detailed documentation please see --> http://harvest.readthedocs.org/en/latest
sh: /tmp/_MEIgucblW/libreadline.so.6: no version information available (required by sh)
sh: relocation error: sh: symbol rl_filename_stat_hook, version READLINE_6.3 not defined in file libreadline.so.6 with link time reference
sh: /tmp/_MEIgucblW/libreadline.so.6: no version information available (required by sh)
sh: relocation error: sh: symbol rl_filename_stat_hook, version READLINE_6.3 not defined in file libreadline.so.6 with link time reference
sh: /tmp/_MEIgucblW/libreadline.so.6: no version information available (required by sh)
sh: relocation error: sh: symbol rl_filename_stat_hook, version READLINE_6.3 not defined in file libreadline.so.6 with link time reference
sh: /tmp/_MEIgucblW/libreadline.so.6: no version information available (required by sh)
sh: relocation error: sh: symbol rl_filename_stat_hook, version READLINE_6.3 not defined in file libreadline.so.6 with link time reference
sh: /tmp/_MEIgucblW/libreadline.so.6: no version information available (required by sh)
sh: relocation error: sh: symbol rl_filename_stat_hook, version READLINE_6.3 not defined in file libreadline.so.6 with link time reference
sh: /tmp/_MEIgucblW/libreadline.so.6: no version information available (required by sh)
sh: relocation error: sh: symbol rl_filename_stat_hook, version READLINE_6.3 not defined in file libreadline.so.6 with link time reference
option -f not recognized

#below that error the usage manual is shown:
parsnp [options] [-g|-r|-q](see below) -d <genome_dir> -p
...

Any help woul be appraciated. Thank you so much!

@alexadn Sorry for the late reply. These errors suggest that one of the binaries does not support your distribution of Linux. I'll look into seeing if we can get SUSE recognized/supported.

bkille commented 4 years ago

Can you try the 1.5 release? We've changed the binary to be more compatible w/ other OSs