PSMC Illegal division by zero

Question

[YocelynGG]

Dear all,

I'm using PSMC for many genomes, and only for two genomes, I received an error after performing the command psmc2history.pl

Error:
Illegal division by zero at /PATH/psmc_plot.pl line 119

I performed 100 PSMC bootstrap replicates and I concatenated these files to run the command: psmc2history.pl

I have seen the same error in other groups, but they have not figured out a solution.

I'm wondering if you could help me to fix and understand this error.

Thanks in advance,

Best,
Yocelyn

[thjnant]

Hi,

I am having the same error. I was wondering if you found a solution to this problem? Thank you, Homa

[wtchoga]

@ _r_am have you managed to get the solution? I am getting the same error.

[jcolella.jc]

Same issue. 2/40 genomes failed. Any progress on a solution?

[gubrins]

same error here, any solution?

Answer 1

[Darija]

Do your .psmc bootstraped files have the same size. I had the same issue and the problem was that my .psmc files had different sizes, after I re ran the bootstrap and got the same sizes everything was ok. Also, when concatenating, be careful to include the correct files.. that was also one of the errors I had.

[gubrins]

Can you update the code for performing bootstrap with PSMC? I'm having a problem in this line:

seq 100 | xargs -i echo psmc -N25 -t15 -r5 -b -p "4+25*2+4+6" \
    -o round-{}.psmc split.fa | sh

[YocelynGG]

Hi, I have used this code, and works perfectly

seq 100 | xargs -P 10 -Iz psmc -N25 -t15 -r5 -b -p "4+25*2+4+6" -o round-{z}.psmc split.psmcfa