error 139 with make.contigs

usegalaxy.org support
,
1

I am trying to follow the 16S Analysis Tutorial, which I have used successfully before, and I keep getting an error 139 when I try to run make.contigs on my data. Is there something wrong with my data? I tried with the tutorial data and it works fine with that.

Fatal error: Exit code 139 ()

Tool generated the following standard error:

        /corral4/main/jobs/062/207/62207533/tool_script.sh: line 23: 3775477 Done                    echo 'make.contigs( file=combo_fastq.dat, align=needleman, match=1, mismatch=-1, gapopen=-2, gapextend=-1, rename=True, processors='${GALAXY_SLOTS:-8}' )'
 3775478                       | sed 's/ //g'
 3775479 Segmentation fault      (core dumped) | mothur
 3775480                       | tee mothur.out.log
2

Hi @jkagle

The tool seems to be running out of resources when attempting to assemble your custom data into contigs.

That can be due to data quality issues, or some parameter issue, or a very large data volume. Start by making sure that you understand those very early steps in the protocol as described in the tutorial, then be sure to apply them to your own data. As a test, you could try sub-setting your own data to see if that works or not. It will be easier to test different data preparation steps and parameters with smaller data too. Then you can apply those methods to the whole set and proceed.

UseGalaxy.eu can probably process the largest amount of data with this tool. Just know: more processing resources will not compensate for problems in the data or parameters.

Please give that a try and let us know if we can help more. Thanks! :slight_smile:

Xref: related Q&A at mothur_make_contigs mothur