Unable to convert string="-nan": some files fail, some don't

[santinson]

Hello Gabriel,

I have been running schmutzi on 9 double-stranded libraries but it is failing in some of the files, I don't really know why. I am getting this error:

cannot open file1.deam.config at ~/bin/schmutzi.pl line 578.
cannot open file1.deam.config at ~/bin/schmutzi.pl line 578.
Libgab.cpp: destringify() Unable to convert string="-nan"

I am using bam files exclusively mapped to the mitochondria, and coverage is between 22x and 60x for the files that have failed, so I understand this should not be the issue. I have also run both mapDamage and Calico, but the files that are failing have more or less the same values as the those that have worked, and in any case they look like normal aDNA samples. Lastly, I ran a previous version of these files (before I merged two separate sequencing runs of the same samples), and it worked with all of them.

I would be very grateful if you could help me out, as I really don't know what to do.

Thank you!!

MapDamage:
File | 3pGtoA | 5pCtoT
File 1 | 0.16 | 0.18
File 3 | 0.22 | 0.23
Average | 0.21 | 0.22

Calico:
File | Cont | CI_low | CI_up
File 1 | 0.031 | 0.017 | 0.045
File 3 | 0.019 | 0.014 | 0.024
Average | 0.031 | 0.025 | 0.037

[grenaud]

Dear Santinson, sorry, did you manage to solve this problem? normally, NAN is due to lack of data.