Bactopia-Sapelo2 - Revision history

Chelsea: /* Running Program */

2026-05-12T13:23:49Z

Running Program

← Older revision		Revision as of 09:23, 12 May 2026
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	[02:10:40] ERROR Writing to /tmp/bcftools.gTh9nG utils.py:550"		[02:10:40] ERROR Writing to /tmp/bcftools.gTh9nG utils.py:550"


			'''For errors such as "ModuleNotFoundError: No module named 'pkg_resources' "'''

			Ensure that the version of setuptools in your tbprofiler environment is less than or equal to 80.x. You check this by starting an interactive session, loading Bactopia, then activating your tbprofiler environment with "source activate ~/.bactopia/conda/bioconda--tb-profiler-6.6.3" and then "conda list". Then scroll to view the version of setuptools and change it if needed with "conda install setuptools=80.* "

	== Documentation ==		== Documentation ==

Chelsea: /* Running Program */

2026-04-29T19:05:34Z

Running Program

← Older revision		Revision as of 15:05, 29 April 2026
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	This module can be loaded directly: module load Bactopia/3.2.0-conda		This module can be loaded directly: module load Bactopia/3.2.0-conda
	== Running Program ==		== Running Program ==

			To load Bactopia, use <syntaxhighlight lang="bash">
			ml Bactopia/3.2.0-conda
			</syntaxhighlight>Please ensure you do not have any base conda environments active when running this program.


	'''For errors such as "FileNotFoundError: [Errno 2] No such file or directory: '/home/MyID/.bactopia/conda/bioconda--tb-profiler-6.6.3/share/snpeff-5.2-1/snpEff.config'"'''		'''For errors such as "FileNotFoundError: [Errno 2] No such file or directory: '/home/MyID/.bactopia/conda/bioconda--tb-profiler-6.6.3/share/snpeff-5.2-1/snpEff.config'"'''

Chelsea: /* Running Program */

2026-04-29T19:03:44Z

Running Program

← Older revision		Revision as of 15:03, 29 April 2026
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	== Running Program ==		== Running Program ==

			'''For errors such as "FileNotFoundError: [Errno 2] No such file or directory: '/home/MyID/.bactopia/conda/bioconda--tb-profiler-6.6.3/share/snpeff-5.2-1/snpEff.config'"'''

			Bactopia expects a snpEff.config file in /home/MyID/.bactopia/conda/bioconda--tb-profiler-6.6.3/share/snpeff-5.2-1/. If Bactopia installed a different version of snpeff (i.e. not 5.2-1), then you can create a symbolic link to your actual config file. First, check to see what version of snpeff you have installed with "ls /home/MyID/.bactopia/conda/bioconda--tb-profiler-6.6.3/share/" and look for a directory named snpeff-<version>. There should be one with the version as 5.2-1 and another with a different version. Your snpEff.config file should exist inside the directory that is not version 5.2-1 (there should not be a snpEff.config file in the 5.2-1 directory, but we will fix that). You will create a symbolic link in the snpeff-5.2-1directory to the actual snpEff.config file in the other snpeff-<version> directory using this command (change MyID to your own MyID and <version> to the other snpeff version that is not 5.2-1): ln -s /home/MyID/.bactopia/conda/bioconda--tb-profiler-6.6.3/share/snpeff-<version>/snpEff.config /home/MyID/.bactopia/conda/bioconda--tb-profiler-6.6.3/share/snpeff-5.2-1/snpEff.config


			'''For errors such as "ERROR Delly failed, skipping INFO Running snpEff ERROR Writing to /tmp/bcftools.gTh9nG "'''

			Edit your snpEff.config file so that the 'data.dir' path points to your actual database directory that contains Mycobacterium_tuberculosis_h37rv (which may be something like /home/MyID/.bactopia/conda/bioconda--tb-profiler-6.6.3/share/snpeff-5.2-1/data/).

			[02:10:40] ERROR Writing to /tmp/bcftools.gTh9nG utils.py:550"

	== Documentation ==		== Documentation ==

Chelsea: /* Documentation */

2026-04-21T14:36:47Z

Documentation

@@ Line 24: / Line 24: @@
 == Documentation ==
-<pre  class="gcommand">
+<pre class="gcommand">
-tbd
+[cft07037@b1-24 ~]$ ml Bactopia/3.2.0-conda
 </pre>

Chelsea: /* Running Program */

2026-04-21T14:36:02Z

Running Program

← Older revision		Revision as of 10:36, 21 April 2026
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	== Running Program ==		== Running Program ==

	~~tbd~~

Chelsea: /* Description */

2026-04-21T14:35:50Z

Description

← Older revision		Revision as of 10:35, 21 April 2026
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	== Description ==		== Description ==
			Bactopia is a flexible pipeline for complete analysis of bacterial genomes.
	~~tbd~~		This module can be loaded directly: module load Bactopia/3.2.0-conda

	== Running Program ==		== Running Program ==

Chelsea: Created page with "Category:Sapelo2Category:SoftwareCategory:Bioinformatics == Category == Bioinformatics == Program On == Sapelo2 == Version == 3.2.0 == Author / Distributor == Please see https://bactopia.github.io/v3.1.0/ == Description == tbd == Running Program == tbd == Documentation ==

tbd

2026-04-21T14:34:52Z

Created page with "Category:Sapelo2 Category:Software Category:Bioinformatics == Category == Bioinformatics == Program On == Sapelo2 == Version == 3.2.0 == Author / Distributor == Please see https://bactopia.github.io/v3.1.0/ == Description == tbd == Running Program == tbd == Documentation == <pre class="gcommand"> tbd </pre> Back to Top == System == 64-bit Linux"

New page

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
== Category ==

Bioinformatics

== Program On ==

Sapelo2

== Version ==
3.2.0

== Author / Distributor ==

Please see https://bactopia.github.io/v3.1.0/

== Description ==

tbd

== Running Program ==

tbd

== Documentation ==

<pre class="gcommand">
tbd
</pre>

[[#top|Back to Top]]

== System ==
64-bit Linux