Is it stuck when there is really low CPU usage?
Opened this issue · 3 comments
We just run twopaco
for thousands of bacterial genomes and now it's at:
Round 0, 0:4398046511104
Pass Filling Filtering
However, when we look at top
we see that while its loaded in memory there is only 0.3% cpu usage:
514.3g 512.2g 4368 D 0.3 33.9 209:34.18 twopaco
Is this normal or does this mean something is going wrong?
Hey @rickbeeloo , did it finish? Do you have enough free space on the disk?
@iminkin not yet, but I think that makes sense with thousands of genomes, however, an odd thing is that we have the:
/path/to/file/1.fna
/path/to/file/2.fna
/path/to/file/3.fna
/path/to/file/4.fna
...
--------------------------------------------------------------------------------
but sometimes there is the following below it:
Round 0, 0:4398046511104
Pass Filling Filtering
however, when I check later again this disappears and I see only the paths again. Nevertheless, now we see something happening:
512.0g 211.2g 4324 R 99.7 14.0 13:27.84 twopaco
It's hard to see how far it is and if it's not repeating
How much memory does your machine have and what was the command line you used to run twopaco? I would suggest using the largest filter size possible given your machine's RAM (see documentation here: https://github.com/medvedevgroup/TwoPaCo#twopaco-usage).