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DiltheyLab / MetaMaps

Long-read metagenomic analysis
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meta::getTaxonIDsFromMappingsFile(std::string): Assertion `mappingsStream.is_open()' failed #16

Closed sylvain-ri closed 4 years ago

sylvain-ri commented 5 years ago

Hello,

I ran metamaps mapDirectly, and get the output.x files. I am not sure what to expect from this first step, but the .output file (without .1 or .x) is sometimes missing, and this seems a first issue discussed here: https://github.com/DiltheyLab/MetaMaps/issues/7#issuecomment-440191480

In the second step, i am getting the following error. Commands:

conda activate metamap-0.1
metamaps classify --threads 12 --DB /path/to/miniSeq+H --mappings /path/to/file/nanopore_file.metamaps_standard_output

Error:

metamaps: src/meta/fEM.h:1362: std::set<std::basic_string<char> > meta::getTaxonIDsFromMappingsFile(std::string): Assertion `mappingsStream.is_open()' failed.
/.../source_activate.sh: line 36: 213339 Aborted                 (core dumped) "$@"

Could you help on this issue ? Thank you in advance, Sylvain

AlexanderDilthey commented 4 years ago

Hi @Earwelen, could you post the full command you use for the mapping step?

sylvain-ri commented 4 years ago

Hi @AlexanderDilthey , If I remember the issue was the memory usage. Using qsub on a server, i specified a memory requirement but the usage was much more than the target max memory (something like 52GB while targeting for 30GB) and it generated errors. Not sure why, but the memory consumption was close to the double of the specified amount. Thank you.

AlexanderDilthey commented 4 years ago

@Earwelen Thank you for getting back to us on this! Yes, this behavior is known and documented; but perhaps we have to increase the recommended factor between parameter value and available memory.