Segmentation fault (core dumped)

lmrodriguezr / nonpareil

Estimate metagenomic coverage and sequence diversity

http://enve-omics.ce.gatech.edu/nonpareil/

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Segmentation fault (core dumped) #30

Closed Freemacl closed 6 years ago

Freemacl commented 6 years ago

Hello,

I saw there were a couple of closed issues reporting something similar, but it seems like they were all corrected by updating. I am using Nonpareil v3.2, just installed today via conda.

I executed this command: nonpareil -s ~/pathto/seqs.fastq -T kmer -f fastq -t 2

Which produced this output: Nonpareil v3.2 [ 0.0] reading /home/imss/Vault/Community/NunavutWWTPMetagen/Reads/18SEPin4_R1.fastq [ 0.0] Picking 10000 random sequences [ 0.0] Started counting Segmentation fault (core dumped)

gunturus commented 6 years ago

can you output the first 10 lines of the fastq file. You are missing -b option on your command. -b refers to the prefix of the output files

Freemacl commented 6 years ago

Wow easy fix... Thank you for the quick response!

gunturus commented 6 years ago

I will make -b a requirement and give a proper message.

thank you for noticing the problem.