centrifuge-class died with signal 11 (SEGV) (core dumped)

[MRuinels]

Hi all,

I am quite new to command line programs and Linux but I am willing to run centrifuge on nanopore fastq data (bacteria metagenome). I have noticed that some previous issues were pointing to the same error (centrifuge-class died with signal 11 (SEGV) (core dumped)). I had a look on many of them but I could not find a solution for that problem and what is the reason of it. Is it due to the computing power or it's a problem in the data/command line?

Thanks a lot in advance Ciao Michi

[mourisl]

Can you show me the command you use? And can you show me the output when running Centrifuge with --verbose option?

[MRuinels]

Hi!thanks a lot for your reply! you can find the command as well as the output in the attached .txt file. I saw that with the --verbose option the error is now (ERR): centrifuge-class exited with value 1. Thanks in advance for your support! Ciao M. centrifuge_output_verbose.txt

[mourisl]

You need to put a -U before your read file.

[MRuinels]

hi!thanks for your answer. I have tried many other command version but I always got errors. I also moved the fastq.gz file in the same folder and unzipped it to fastq but did not work as well.

centrifuge -x abv -U Cad_16_all_passed.fastq -S output --report-file report

centrifuge -q -x abv -U Cad_16_all_passed.fastq -S output --report-file report

centrifuge -q -mm -x abv -U Cad_16_all_passed.fastq -S output --report-file report

My error was always:

Error: Encountered internal Centrifuge exception (#1) Command: /usr/local/bin/centrifuge-class --wrapper basic-0 -q -mm -x abv -S output --report-file report -U /tmp/114389.unp (ERR): centrifuge-class exited with value 1

I am just wondering if it's a problem of my PC. :( Thanks in advance

[mourisl]

Can you show me what the verbose says after adding the -U?

[MRuinels]

Hi! please find attached the output. The error is the same as before apparently. centrifuge_output_verbose_2.txt

[mourisl]

It seems you gave the wrong options "-s classification /mnt/hgfs/SHARED_LINUX/Centrifuge/abv" which I read from the txt file. However they were not in the commands you gave last week.

[mourisl]

Oh, and for verbose, you need to use --verbose, instead of -verbose.

[MRuinels]

Hi!sorry, yes I tried so many commands that I got confused in the end but yes, any command I was giving always gave the same error --> centrifuge-class died with signal 11 (SEGV) (core dumped)

Now I downloaded the index for the nt database instead of doing it myself and I transferred data to a server to free some space on my laptop and I get now a new error: (ERR): centrifuge-class died with signal 9 (KILL). I tried with -p 32 and -p 12 (despite my laptop only has 2 cores...I saw here that somebody had the same issue (https://github.com/infphilo/centrifuge/issues/82) but I still get this error.

I have to say that I am working on a laptop that is not that powerful and I fear that it might be related to that ...but already knowing that will save me some time and will oblige my boss to buy a workstation :)

Please find attached the real --verbose of this command.

Thanks a lot!M

verbose_centrifuge_output_nt.txt

[mourisl]

nt database requires more than 100GB memory now. I don't think your laptop can allocate this much memory and thus throws the signal 9 error.