mothur

Segfault with screen.seqs

Hi, I am using latest version of mothur (1.44.3) in Ubuntu 18. I have followed MiSeq SOP guide and everything went fine until the step of re-screening for making sure that all sequences overlap the same regions:

Captura de pantalla 2021-01-31 a las 12.39.30

screen.seqs(fasta=example.trim.contigs.good.unique.align, 
count=example.trim.contigs.good.count_table, 
summary=example.trim.contigs.good.unique.summary, start=1, end=18928)

The process seems to run properly but at the last step I always get a segfault when remove.seqs is triggered to update the count table giving the following error:

/******************************************/
Running command: 
remove.seqs(accnos=example.trim.contigs.good.unique.bad.accnos.temp, 
count=example.trim.contigs.good.count_table)
[ERROR]: example.trim.contigs.good.unique.bad.accnos.temp is blank, aborting.
[ERROR]: You have no valid accnos file and accnos is required.
/******************************************/
Segmentation fault

Any idea about what could be going on?

Thank you.

Update: I have tried the same but forcing to execute in a single CPU (processors=1) and still getting the same error but no segfault was triggered (altough example.trim.contigs.good.good.count_table is a blank file).

/******************************************/
Running command: 
remove.seqs(accnos=example.trim.contigs.good.unique.bad.accnos.temp, 
count=example.trim.contigs.good.count_table)
[ERROR]: example.trim.contigs.good.unique.bad.accnos.temp is blank, aborting.
Using example.trim.contigs.good.unique.flip.accnos as input file for the accnos 
parameter.
Removed 6362 sequences from your count file.
Output File Names:
example.trim.contigs.good.pick.count_table
/******************************************/
Output File Names:
example.trim.contigs.good.unique.good.summary
example.trim.contigs.good.unique.good.align
example.trim.contigs.good.unique.bad.accnos
example.trim.contigs.good.good.count_table

Could you send your input files and log file to mothur.bugs@gmail.com?

Hi. The error was produced by lack of disk space as the files generated during the process were really huge. Thank you for your answer.

1 Like

This topic was automatically closed 10 days after the last reply. New replies are no longer allowed.