search

voutcn / megahit

Ultra-fast and memory-efficient (meta-)genome assembler
http://www.ncbi.nlm.nih.gov/pubmed/25609793
GNU General Public License v3.0
588 stars 134 forks source link

Convert reads to binary library step #297

Open RitaBogorad opened 3 years ago

RitaBogorad commented 3 years ago

Hello,

I am running the assembly of 19 pre-filtered with thimmomatic metatranscriptome sediment samples. However, the process seems to be stuck at the "Convert reads to binary library" step. From the other issues posted here, I saw that this step usually takes ~5 minutes, for me, it is been stuck already for 3 hours. Is this normal? Can you please recommend me how to fix this issue?

The log file: 2021-02-04 14:04:46 - MEGAHIT v1.2.9 2021-02-04 14:04:46 - Using megahit_core with POPCNT and BMI2 support 2021-02-04 14:04:46 - Convert reads to binary library 2021-02-04 14:04:46 - command /home/bioadmin/Downloads/MEGAHIT-1.2.9-Linux-x86_64-static/bin/megahit_core buildlib /home/mbogorad/2018/metatrans/2018/data/raw_fastq/megahit_out/tmp/reads.lib /home/mbogorad/2018/metatrans/2018/data/raw_fastq/megahit_out/tmp/reads.lib

The command I have used (on merged samples) megahit -1 par1.fastq.gz -2 par2.fastq.gz -o megahit_out --presets meta-large

Also, the megahit process is absent from the list of processes in htop....

Thank you in advance!

Rita

adamkova commented 3 years ago

Hi Rita,

I had the same issue, almost the same time. Was stuck for 1 day and I left it working, thinking that eventually the script will continue. I even used the --verbose option, thinking that I am missing some logs.

Turned out I probably didn't have enough space for the temporary files, and the output folder was not in a drive big enough for the task.

Changed the output folder destination to a drive with 2 TB, now it is buzzing at full capacity. Try it at least, might be the solution.

BR,

Adam

RitaBogorad commented 3 years ago

Hi, Adam, I managed to make this work by unzipping my files manually.. I saw in the other issues here that using your samples as .gz can cause problems and I figured out one of my files was giving a "unexpected end of file" error when gzip command was called. Try checking that as well maybe will help!