mini_test

[Adam Blanchard]

Hi all,

I've installed anvio using pip on ubuntu 14.04. Everything seemed to go OK until I run the mini test. Firstly it doesn't find a version number, even though the version file shows 1.2.2.

Then it fails with:

Traceback (most recent call last):

  File "/usr/local/bin/anvi-init-bam", line 77, in <module>

    already_sorted = args.sorted))

  File "/usr/local/bin/anvi-init-bam", line 44, in init_bam_file

    pysam.sort(input_file_path, output_file_path)

  File "/usr/local/lib/python2.7/dist-packages/pysam/utils.py", line 65, in __call__

    "\n".join(stderr)))

pysam.utils.SamtoolsError: 'samtools returned with error 1: stdout=, stderr=[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files\n\nUsage: samtools sort [options...] [in.bam]\n\nOptions:\n\n  -l INT     Set compression level, from 0 (uncompressed) to 9 (best)\n\n  -m INT     Set maximum memory per thread; suffix K/M/G recognized [768M]\n\n  -n         Sort by read name\n\n  -o FILE    Write final output to FILE rather than standard output\n\n  -T PREFIX  Write temporary files to PREFIX.nnnn.bam\n\n  -@, --threads INT\n\n             Set number of sorting and compression threads [1]\n\n      --input-fmt-option OPT[=VAL]\n\n               Specify a single input file format option in the form\n\n               of OPTION or OPTION=VALUE\n\n  -O, --output-fmt FORMAT[,OPT[=VAL]]...\n\n               Specify output format (SAM, BAM, CRAM)\n\n      --output-fmt-option OPT[=VAL]\n\n               Specify a single output file format option in the form\n\n               of OPTION or OPTION=VALUE\n\n      --reference FILE\n\n               Reference sequence FASTA FILE [null]\n'

Any ideas

Thanks in advance

Adam

[Özcan Esen]

Hi Adam,

How did you get the mini_test? If you cloned or downloaded master branch, it is not compatible with 1.2.2,

you should get the mini test using 

git clone -b v1.2.2 --depth=1 https://github.com/meren/anvio.git

cd anvio/tests

./run_mini_test.sh

Excuse me if you already using the compatible mini_test.

Best Regards
Òzcan Esen

--
Anvi'o Paper: https://peerj.com/articles/1319/
Project Page: http://merenlab.org/projects/anvio/
Code Repository: https://github.com/meren/anvio
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[Adam Blanchard]

Hi Òzcan

Thanks for your prompt reply

I had cloned following the directions on http://merenlab.org/2015/05/01/installation/#running-the-mini-test which are the same as you have suggested.

i'm not quite sure why it isn't showing a version number either. The installation went smoothly after ironing out a few issues with hcluster hanging on install.

[Özcan Esen]

Hi Adam,

Sorry for the delay, I have tested it with clean Ubuntu. It seems it fails because pysam released new version which is not backwards compatible,

You can fix your installation with:
sudo pip install pysam==0.8.3

Best,
Özcan

--
Anvi'o Paper: https://peerj.com/articles/1319/
Project Page: http://merenlab.org/projects/anvio/
Code Repository: https://github.com/meren/anvio
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[Adam Blanchard]

Hi Òzcan

That did indeed fix things! Thank you very much, really excited about using Anvi'o!

Adam

[jne...@gmail.com]

Hi Ozcan,

Thanks a lot for answering this, I was banging my head not understanding what was wrong with my anvio install that was previously working like a charm.

For the sake of completion, I'm mostly posting to point that when:

sudo pip install anvio --upgrade

It'll upgrade pysam to 0.9.0. and the error is back.

[A. Murat Eren]

It is all my fault :/ I should have mentioned version numbers explicitly in the setup.py...

It is now fixed in the repository for v2, but stable releases from the v1 branch will continue to suffer.

To view this discussion on the web visit https://groups.google.com/d/msgid/anvio/f3f5a76c-9b72-4fef-a17f-e18528d2d775%40googlegroups.com.