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License: Other
Genomic Origin Through Taxonomic CHAllenge (GOTTCHA) v2 BETA
License: Other
Hello,
I tested GOTTCHA2 on a set of nanopore reads I had. The reads were mapped to the signature database but the run failed with the following error:
Traceback (most recent call last):
File "/home/scott/GOTTCHA2/gottcha2.py", line 717, in
res_df = roll_up_taxonomy(res, db_stats, argvs.relAbu, argvs.dbLevel , argvs.minCov, argvs.minReads, argvs.minLen, argvs.maxZscore)
File "/home/scott/GOTTCHA2/gottcha2.py", line 449, in roll_up_taxonomy
str_df['LVL_NAME'] = str_df['TAXID'].apply(lambda x: gt.taxid2lineageDICT(x, True, True)[rank]['name'])
File "/home/scott/miniconda3/envs/SeqAnalysis/lib/python3.6/site-packages/pandas/core/series.py", line 3848, in apply
mapped = lib.map_infer(values, f, convert=convert_dtype)
File "pandas/_libs/lib.pyx", line 2329, in pandas._libs.lib.map_infer
File "/home/scott/GOTTCHA2/gottcha2.py", line 449, in
str_df['LVL_NAME'] = str_df['TAXID'].apply(lambda x: gt.taxid2lineageDICT(x, True, True)[rank]['name'])
TypeError: string indices must be integers
I have also attached the log file.
Any help would be appreciated.
Thanks,
Scott
Guppy_v3.gottcha_species.gottcha_species.log
Hi,
i tried to use GOTTCHA2 with SAM file and I obtained this message error:
[00:00:00] Starting GOTTCHA (v2.1.7)
[00:00:00] Arguments and dependencies checked:
Traceback (most recent call last):
File "./gottcha2.py", line 667, in
print_message( " Input reads : %s" % [x.name for x in argvs.input], argvs.silent, begin_t, logfile )
TypeError: 'NoneType' object is not iterable
Could you help me please
Alex
In order to create a bioconda recipe, gottcha2 needs to be uploaded into pypi.
The steps to take to complete this are:
[] Develop against the bioconda branch
[] Build gottcha2 dist and push to test-pypi
[] Test against test-pypi install
[] Once successful, push to master
[] From master, build dist and push to pypi
Hello,
I am trying to download the taxonomy dmp species signature index files (https://edge-lanl.gov/rest_of_path). I am redirected to https://lanal.gov/errors/system-notification.php with the following message displayed:
System Unavailable
We are currently performing system maintenance.
I have been receiving this message for about a month now. Is there another download location for these files? This also affects downloading databases/tools for the EDGE and PanGIA as they are in the same root path.
Thanks,
Scott
Hello,
It seems that GOTTCHA2 can use two reference databases for classification, namely, RefSeq BacteriaArchaeaViruses and RefSeq Fungal. But I cannot find the Refseq Fungal database at https://edge-dl.lanl.gov/GOTTCHA2/RefSeq-Release90/
Could you please help with this? Or let me know when the database is uploaded.
Many thanks for your help.
HY
I am following the installation protocol but have a problem with decompressing the RefSeq-r90.cg.BacteriaArchaeaViruses.species.fna.tar. I keep getting the following error:
tar: This does not look like a tar archive
tar: Skipping to next header
tar: Exiting with failure status due to previous errors.
I believe the problem is that the downloaded file is actually an HTML document and not .fna.
head RefSeq-r90.cg.BacteriaArchaeaViruses.species.fna.tar
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" class="ui-mobile" lang="en">
<head>
<title>
System Unavailable
</title>
<meta content="width=device-width, initial-scale=1, user-scalable=no" name="viewport"/>
<meta content="text/html;charset=utf-8" http-equiv="content-type"/>
<meta content="IE=edge" http-equiv="X-UA-Compatible"/>
<meta content="Los Alamos National Laboratory, Operated by Los Alamos National Security, LLC, for the U.S. Department of Energy" name="author"/>
Any idea what is wrong?
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