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DiltheyLab / MetaMaps

Long-read metagenomic analysis
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Script filterLowIdentityEntities.pl dies prematurely #72

Open mhajimorad opened 1 year ago

mhajimorad commented 1 year ago

Hello,

Thank you so much for the MetaMaps tool!

I believe I have been able to successfully perform a MetaMaps run, and the expected output files are produced.

I am interested in using the "filterLowIdentityEntities.pl" script to filter out low identity results. Upon running the script, it runs for a bit of time and produces a partial "-filtered.WIMP" file. I say it is partial because I receive the following message

Died at /util/../perlLib/taxTree.pm line 587

And while there are "definedGenomes" entries in the "-filtered.WIMP" file, there are no "family", "genus", "species", etc. lines in the "-filtered.WIMP" file (unlike the original WIMP file).

Is there a bug with the "filterLowIdentityEntities.pl" file?

Thank you!

AlexanderDilthey commented 1 year ago

Hey @mhajimorad,

Not sure what is going on here, but I have just pushed a code change that will output a more informative error message - could you pull, try again, and post the message here?

Best wishes

Alex

mhajimorad commented 1 year ago

Hi @AlexanderDilthey ,

Thank you for your message.

I pulled and ran the script again. In case it is useful, here is the instruction entered at the command line: perl ./util/filterLowIdentityEntities.pl --DB testbacteria --mappings ./mmresults_bac_retry2/bac_retry2_classification_results --identityThreshold 0.85

Please find below all the content that is printed to the terminal:

Median identity 83.083 - full distribution printed to ./mmresults_bac_retry2/bac_retry2_classification_results.extractedIdentities

With --identityThreshold 85 -- 35855 of 48913 *individual* best mappings are below that threshold.
Hit database genomes:
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Out of 2904, now remove 2641 because their median identity is below 85

Produced filtered file ./mmresults_bac_retry2/bac_retry2_classification_results.EM-filtered (41191 of 7722 alignments were filtered out).
$VAR1 = 'taxTree::get_ancestors_by_rank(..): Rank \'clade\' for node is already defined';
$VAR2 = '2615203';
$VAR3 = {
          'family' => '1853232',
          'phylum' => '976',
          'genus' => '89966',
          'class' => '768503',
          'order' => '768507',
          'clade' => '68336'
        };

And I have attached the "-filtered.WIMP" file. Note that it only contains "definedGenomes" entries, and no "family", "genus", "species", etc. lines.

bac_retry2_classification_results.EM-filtered.WIMP.txt

Thank you for all of your help!

AlexanderDilthey commented 1 year ago

Hi @mhajimorad,

Thank you for posting the error message!

It is still not clear to me what is going on here, but the error message certainly helps - it seems that that node 2615203 has multiple ancestors at the clade level.

Are you using the standard NCBI taxonomy?

I have pushed another change to the code that should make the error-throwing function a bit more robust - it will now not complain if the taxon IDs of ancestor nodes agree, in case there are multiple ancestors at a level. Could you give it another try?