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gottcha2's Issues

Problem at start with sam file

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

Add gottcha2 to pypi

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

Fungi database

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

System Unavailable

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

Run failed after processing SAM file

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

RefSeq-r90.cg.fna.tar issues

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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