Segmentation fault on paired end reads for classify_metagenome.sh

[Syed Murtuza Baker]

Hello,
I am trying to use classify_metagenome.sh on a custom database in paired end mode. But it is always giving me error. The command I am using is

classify_metagenome.sh -P samples.R.txt samples.L.txt -R results.txt -n 8 -m 0

Where samples.R.txt holds
./Trimmo_out/NG-10502_A_tenuis_DNA_lib157247_5036_7_1_trimmed (please note I have to put the file name without the fastq extension, otherwise it complains)
 and samples.L.txt holds
./Trimmo_out/NG-10502_A_tenuis_DNA_lib157247_5036_7_2_trimmed

The error it is giving is

CLARK version 1.2.3 (UCR CS&E. Copyright 2013-2016 Rachid Ounit, roun...@cs.ucr.edu)
Loading database [$users/CLARK_DB/custom_1/db_central_k31_t3_s1610612741_m0.tsk.*] ...
Loading done (database size: 5523 MB read, with sampling factor 1)
Mode: Full using 8 CPU.
classify_metagenome.sh: line 172: 36169 Segmentation fault      (core dumped) $CLARKDIR/exe/CLARK $PARAMS

Could you please help to fix it.

Thank you.

Best Regards,
Syed

[Rachid]

Thank you for reporting this issue!

Could you please follow the directions for reporting any error/bug as indicated in the CLARK website or, rather, in this blog post (see below) ?

https://groups.google.com/d/msg/clarkusers/3m657VajTtg/LuewyqEuAQAJ

It's important to gather as much as information as possible, typically, is this reported error/bug is specific to your data? If so, could you please send it to us so we can reproduce it? What is your system configurations? ... etc. Please read all the instructions and let us know what is the outcome.

Best,

Rachid