search

DRL / blobtools

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
GNU General Public License v3.0
187 stars 44 forks source link

division by zero when creating #48

Closed ishengtsai closed 5 years ago

ishengtsai commented 7 years ago

Hi,

I was running blobtools but failed at first stage:

/home/ijt/bin/blobtools/blobtools create -i ref.fa -b 180bp-pe.sorted.bam -t assembly.vs.uniref90.dmnd -o first

and

Traceback (most recent call last): File "/home/ijt/bin/blobtools/bloblib/create.py", line 115, in <module> main() File "/home/ijt/bin/blobtools/bloblib/create.py", line 108, in main blobDb.parseCoverage(covLibObjs=cov_libs, no_base_cov=None, prefix=prefix) File "/home/ijt/bin/blobtools/bloblib/BtCore.py", line 355, in parseCoverage cov = base_cov / self.dict_of_blobs[name].agct_count ZeroDivisionError: division by zero

Any suggestions would be great!

DRL commented 7 years ago

Hi ishengtsai,

could it be that you have an empty sequence in your assembly file?

cheers,

dom

kaylahardwick commented 6 years ago

Hello,

I'm just wondering if this issue was ever resolved? I got the same error, and I don't have any empty sequences in my assembly file.

Thanks in advance for your help!

DRL commented 6 years ago

Hi kaylahardwick,

this happens when either the bam file is empty or you have empty sequences (composed of N's alone0 in your fasta.

if this persist please send me a dropbox link to your files and the command you ran, so I can reproduce the error.

cheers,

dom