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DiltheyLab / MetaMaps

Long-read metagenomic analysis
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Error in classify step #7

Closed nllg closed 5 years ago

nllg commented 5 years ago

Hello, I am testing your tool and I get this error when I run: ./metamaps classify --mappings classification_results.1 --DB databases/miniSeq+H

The error is as follows: Min. reads for 'U' = 10000

metamaps: src/meta/fEM.h:350: std::map<std::__cxx11::basic_string, long unsigned int> meta::getMappingStats(std::__cxx11::string): Assertion `statsStream.is_open()' failed.

Thank you in advance!

Nathaly

AlexanderDilthey commented 5 years ago

Hi Nathaly,

You should probably use --mappings classification_results instead of --mappings classification_results.1, unless you explicitly specified -o classification_results.1 when mapping.

If the output file classification_results (i.e. without the .1) is not present, then something went wrong with the mapping step.

Best,

Alex

nllg commented 5 years ago

ok, then it might be that the mapping step didn't work out. I will run the mapping step again. Thank you very much! Cheers, Nathaly

nllg commented 5 years ago

Hi Alex,

I ran the mapping step again. I used the following command: metamaps mapDirectly --all -r /databases/miniSeq+H/DB.fa -q reads.fasta -o classification_results

The program ran for 8 days and once again, the output was classification_results.1 As expected, when I ran the classify step, I got the same error as before:

Min. reads for 'U' = 10000

metamaps: src/meta/fEM.h:350: std::map<std::__cxx11::basic_string, long unsigned int> meta::getMappingStats(std::__cxx11::string): Assertion `statsStream.is_open()' failed.

Do you have any suggestions?

Thank you very much,

Nathaly

AlexanderDilthey commented 5 years ago

Hi Nathaly, Can you post the classify command you used? Thanks, Alex

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From: nllg notifications@github.com Sent: Monday, November 19, 2018 10:45 To: DiltheyLab/MetaMaps Cc: Alexander Dilthey; Comment Subject: Re: [DiltheyLab/MetaMaps] Error in classify step (#7)

Hi Alex,

I ran the mapping step again. I used the following command: metamaps mapDirectly --all -r /databases/miniSeq+H/DB.fa -q reads.fasta -o classification_results

The program ran for 8 days and once again, the output was classification_results.1 As expected, when I ran the classify step, I got the same error as before:

Min. reads for 'U' = 10000

metamaps: src/meta/fEM.h:350: std::map<std::__cxx11::basic_string, long unsigned int> meta::getMappingStats(std::__cxx11::string): Assertion `statsStream.is_open()' failed.

Do you have any suggestions?

Thank you very much,

Nathaly

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nllg commented 5 years ago

I used: ./metamaps classify --mappings classification_results.1 --DB databases/miniSeq+H

because the output was still classification_results.1, even though I specified that the output should be named classification_results (without the .1)

AlexanderDilthey commented 5 years ago

Thank you! If the file without the .1 doesn’t exist, mapping has failed. Can you capture exit code and output with /usr/bin/time -v ... &> output.txt, where you substitute the ‚...‘ with your mapping command?

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From: nllg notifications@github.com Sent: Monday, November 19, 2018 11:24 To: DiltheyLab/MetaMaps Cc: Alexander Dilthey; Comment Subject: Re: [DiltheyLab/MetaMaps] Error in classify step (#7)

I used: ./metamaps classify --mappings classification_results.1 --DB databases/miniSeq+H

because the output was still classification_results.1, even though I specified that the output should be named classification_results (without the .1)

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/DiltheyLab/MetaMaps/issues/7#issuecomment-439843933, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AGFsacexAv5PZrJN6Mg6ipgtbt9TngVOks5uwob0gaJpZM4YSaBr.