I try to run parsnp (downloaded binay) on my Manjaro (a flavour of Archlinux) laptop but the program fails with the following error:
$ parsnp -r ./0.0_ref/Scedosporium_apiospermum.ScApio1_0.31.dna.toplevel.fna -p 6 -c -d ./0.2_data 2>&1 | tee test_harvest1_Sapio.log
Warning: Cannot determine OS, defaulting to linux
|--Parsnp v1.2--|
For detailed documentation please see --> http://harvest.readthedocs.org/en/latest
sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook
sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook
sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook
sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook
sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook
sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook
-->Reading Genome (asm, fasta) files from ./0.2_data..
|->[OK]
-->Reading Genbank file(s) for reference (.gbk) ..
|->[WARNING]: no genbank file provided for reference annotations, skipping..
**ERROR**
The following command failed:
>>/tmp/_MEIkmsiuD/parsnp /home/ludo/Documents/01_professional/06_Projects_experiments/2016-2017_Angers/2016-2017_Scedosporium/01_Pipeline_CompGeno/05_Harvest/02_Ssapio_only/P_2016_10_25_175622540458/parsnpAligner.ini
Please veryify input data and restart Parsnp. If the problem persists please contact the Parsnp development team.
**ERROR**
**********************************************************************************************************************************************************************************************
SETTINGS:
|-refgenome: ./0.0_ref/Scedosporium_apiospermum.ScApio1_0.31.dna.toplevel.fna
|-aligner: libMUSCLE
|-seqdir: ./0.2_data
|-outdir: /home/ludo/Documents/01_professional/06_Projects_experiments/2016-2017_Angers/2016-2017_Scedosporium/01_Pipeline_CompGeno/05_Harvest/02_Ssapio_only/P_2016_10_25_175622540458
|-OS: linux
|-threads: 6
**********************************************************************************************************************************************************************************************
<<Parsnp started>>
-->Running Parsnp multi-MUM search and libMUSCLE aligner..
It's important to note here that the very same design works on the ubuntu laptop of a colleague (same folders, files, commands).
I thought first it was due to the small size of the /tmp folder (only 8GB) but when I changed it by setting 'TMPDIR="/home/ludo/tmp"', I got the very same error:
$ parsnp -r ./0.0_ref/Scedosporium_apiospermum.ScApio1_0.31.dna.toplevel.fna -p 6 -c -d ./0.2_data 2>&1 | tee test_harvest1_Sapio.log
Warning: Cannot determine OS, defaulting to linux
|--Parsnp v1.2--|
For detailed documentation please see --> http://harvest.readthedocs.org/en/latest
sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook
sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook
sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook
sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook
sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook
sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook
-->Reading Genome (asm, fasta) files from ./0.2_data..
|->[OK]
-->Reading Genbank file(s) for reference (.gbk) ..
|->[WARNING]: no genbank file provided for reference annotations, skipping..
**ERROR**
The following command failed:
>>/home/ludo/tmp/_MEI8uE6ZN/parsnp /home/ludo/Documents/01_professional/06_Projects_experiments/2016-2017_Angers/2016-2017_Scedosporium/01_Pipeline_CompGeno/05_Harvest/02_Ssapio_only/P_2016_10_25_175011659051/parsnpAligner.ini
Please veryify input data and restart Parsnp. If the problem persists please contact the Parsnp development team.
**ERROR**
**********************************************************************************************************************************************************************************************
SETTINGS:
|-refgenome: ./0.0_ref/Scedosporium_apiospermum.ScApio1_0.31.dna.toplevel.fna
|-aligner: libMUSCLE
|-seqdir: ./0.2_data
|-outdir: /home/ludo/Documents/01_professional/06_Projects_experiments/2016-2017_Angers/2016-2017_Scedosporium/01_Pipeline_CompGeno/05_Harvest/02_Ssapio_only/P_2016_10_25_175011659051
|-OS: linux
|-threads: 6
**********************************************************************************************************************************************************************************************
<<Parsnp started>>
-->Running Parsnp multi-MUM search and libMUSCLE aligner..
Important note: default python on Archlinux is python3, may that be a problem?
Thank you for any help!
Ludovic
PPS: so far trying to compile from the git source is not an option either as libMuscle fails to compile due to CXXFLAGS=’-fopenmp’.
I try to run parsnp (downloaded binay) on my Manjaro (a flavour of Archlinux) laptop but the program fails with the following error:
It's important to note here that the very same design works on the ubuntu laptop of a colleague (same folders, files, commands). I thought first it was due to the small size of the /tmp folder (only 8GB) but when I changed it by setting 'TMPDIR="/home/ludo/tmp"', I got the very same error:
Important note: default python on Archlinux is python3, may that be a problem?
Thank you for any help! Ludovic
PPS: so far trying to compile from the git source is not an option either as libMuscle fails to compile due to CXXFLAGS=’-fopenmp’.