high memory usage for mecat2cns

[billzt]

The README noticed that the memory requirement of mecat2cns is about 1/4 of the total size of the reads. For example, if the reads are of total size 1GB, then mecat2cns will occupy about 250MB memory.

However, the size of my PacBio reads is 45GB. When I run the following steps, the memory usage has risen to ~1TB

mecat2pw -j 0 -d reads.fa -o reads.fa.can -w dir_pw -t 24 -n 50 -x 1
mecat2cns -i 0 -t 32 -x 1 reads.fa.can reads.fa reads.correct.fa

( I use NanoPore instead of PacBio mode to keep more corrected reads)

[xiaochuanle]

@billzt Please use -x 0 for the pacbio data set. You can make the -r and -a in mecat2cns smaller if you want to get more corrected reads.

[wingwingWY]

@xiaochuanle I met the same problem. I run mecat2cns on 2GB nanopore data, the memory has risen to ~1TB and killed .

[ZhuangYb]

Facing same problem here, with 60Gb, pacbio data, it only processed 1/30 of the whole data and the memory usage raised to 1TB and got killed. Is it supposed to be 15GB at most?

[xujiabao127]

I met the same problem, my data is 12G and the memory raised 2T ,so the task was been killed.

[xujiabao127]

For 12GB pacbio reads，I tried the -x 0 -r 0.4 -a 1000 for pacbio reads but the memory was still Large， 1T，can you solved the problem? @xiaochuanle