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MBoemo / DNAscent

Software for detecting regions of BrdU and EdU incorporation in Oxford Nanopore reads.
https://www.boemogroup.org/
GNU General Public License v3.0
26 stars 13 forks source link

Fail to open pod5 files for indexing, version 4.0.3 #71

Closed musikutiv closed 1 month ago

musikutiv commented 1 month ago

I have problems getting DNAscent to run for detecting BrdU. same problem for different runs on FLO-MIN114

DNAscent index -f ${POD_PATH} Failed to query batch count: Invalid: null file passed to C API terminate called after throwing an instance of 'BadPod5Field' what(): pod5 field could not be opened.

pod5 recover ${POD_PATH} None of the 4 files given need recovery

anything I can do to solve the problem, do you have test pod5 files to test if there is a problem with my executable that I compiled from source?

MBoemo commented 1 month ago

Could be a problem with your compilation but my bet would be permissions and/or paths. POD5 files have been submitted here and are still being processed, but they should be publicly available in the coming days. https://www.ebi.ac.uk/ena/browser/view/PRJEB80561

musikutiv commented 1 month ago

thanks for the quick reply, that helped me to identify the problem: the pod5 directory contained hidden files .*.pod5 that caused the problem. after rm .* everything is fine.

MBoemo commented 1 month ago

Great! Give a shout if you run into any other problems.