ioctl error with conda version

[drelo]

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

etaplatanus version v1.3.0
Error: contig_assembly error!
Inappropriate ioctl for device

ls out_intermediate/1_contig_asm/
cmd.bash  cmd.stderr  cmd.stdout  out.assembleLog

The out.assembleLogsays 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

[drelo]

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

[rkajitani]

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?

1. Download the updated metaplatanus.
2. Add execution permission (chmod u+x metaplatanus).
3. Replace your metaplatanus with the new one (mv metaplatanus /your-conda-env/bin/).
4. Re-run metaplatanus.

I'm sorry to bother you.

[drelo]

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

[rkajitani]

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?

[drelo]

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.

[Unaimend]

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?

[Unaimend]

[Unaimend]

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