search

uni-halle / gerbil

A fast and memory-efficient k-mer counter with GPU-support
MIT License
34 stars 14 forks source link

Support of .fastq.gz failing? #22

Open svenrahmann opened 2 years ago

svenrahmann commented 2 years ago

I have a collection of 12 fairly large .fastq.gz files listed in 12 lines of a text file (absolut paths, all like /scratch/.../something.fastq.gz). I am calling gerbil -k 27 -e 50GB -l 3 -x h -i MYTEXTFILE.txt tmp gerbil-27

tmp exists as a subdirectory where I am calling.

I get ERROR: unexpected end of stream (thread[0])! Archive corrupt?! Sometimes I get this with several threads.

I get the same error if instead of the text file that lists my files, I directly put in one of the .fastq.gz files. I do not seem to be able to get gerbil to run on .fastq.gz With other tools, e.g. kmc3, I get the kmer counts just fine.

gerbil does run on a fasta.gz file that I have (but only after renaming .fna.gz to .fasta.gz).

Any ideas?

Paul-bunel commented 1 year ago

I have the exact same situation. I know I am late, but did you find any solution ?