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petermr / tigr2ess

Materials for TIGR2ESS workshop in Delhi Feb 2019 - joint UK(Cambridge) - India project on Food Security.
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ami20190217_status_on_Linux #46

Closed vinitamehlawat closed 5 years ago

vinitamehlawat commented 5 years ago

Sir

Using getpapers i tried getpapers -q 'ocimum tenuiflorum' -o ocimumten_xml -x -k 100 and get result files in folder ocimumten_xml i run `ami-search-cooccur ocimumten_xml/ gene plantparts country species drugs I got stuck there by 2 points: It takes Much time more than 30 min and i quite this job in between I got many files as in previous one ami-jar But using new jar(20190217) i got one new file that is species.binomial.document.xml (same for gene ,plantparts,country) & Did not get cooccur folder in my ocimumten_xml folder.

1.This is command i use in this image and i forcefully quite this after 30 min.

ami_search_command

2.Here i am attaching image of error shown when i only use plantarts country and gene in ami-search-cooccur

ami_search_error

please correct me if i am doing something wrong with this new ami-jar commands or something else

petermr commented 5 years ago

Thank you, this is an excellent report. (It is better to include the actual output as text rather than a screenshot as I can cut and paste).

I think the problem is that some papers are very large and contain large numbers of species or genes. I will try to add a commandline switch that aborts papers which are too large. I will run the same job, and try to trap the problem.

It is not your fault - it's a bug.

Well done.