Closed nllg closed 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
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
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
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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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)
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)
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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
Thank you in advance!
Nathaly