Open drelo opened 2 years ago
Dear users, sorry to bother you again... I created a new environment, I installed metaplatanus
using the conda recipe and replaced the executables metaplatanus
(and all those included in sub_bin ) in the bin folder in the conda environment. I got the same error as described above. How can I properly install this?
Thanks for your help!
Andres
Sorry for the very late response.
I guess the error was caused by the absence of /usr/bin/time
command. I have removed this command in the main script (metaplatnuas in this repo).
Could you please try the following procedures?
chmod u+x metaplatanus
).mv metaplatanus /your-conda-env/bin/
).I'm sorry to bother you.
Dear Kajitani, Thanks for your help. I followed the instructions above... reinstalled metaplatanus in a new environment, downloaded the file, added permissions and moved the file to the bin folder, but the problem persist. How can I help to diagnose this better? Thanks in advance
metaplatanus version v1.3.0
Error: contig_assembly error!
Inappropriate ioctl for device
Thank you for trying and reporting the new script. I have been thinking about the cause.
Could you please show me the log file: out_intermediate/1_contig_asm/out.assembleLog
?
Thanks for your help, I checked that log and noticed I had one filename name wrong.
I still have to make the tgsgapcloser
work with it but I left the example data running for now.
Sorry to reopen this discussion. But I got the same ioctl error but in them iterative assembly step.
Do you have any idea how to fix this?
Ok I saw that does not support .gz for long reads so I now used the unzipped version of my long reads but the errors is still there
This is the output .gapLog
Dear Kajitani,
After reading the paper and the great performance of this software I am trying to use MetaPlatanus for an hybrid assembly of human gut metagenomes. I installed the conda version in a newly created environment following the instructions in a CentOS machine. Then I tried a run with the sample data...
metaplatanus -IP1 ./UPLOAD/PE_1.fq ./UPLOAD/PE_2.fq -ont ./UPLOAD/ONT.fq --o out > log 2>&1
The
out.assembleLog
says something like no folder here in Spanish due to my installation.cmd.bash: línea 10: /usr/bin/time: No existe el fichero o el directorio
Is there a way to fix this? Any help would be appreciated.Thanks for your help
Andrés