ustacks - bad interpreter - galaxy-dev

7 Jul 2017

Good afternoon,

I will do my best!

Best Regards,
David

*From: *Yvan Le Bras <yvan.le-bras@mnhn.fr
<mailto:yvan.le-bras@mnhn.fr>>
*Date: *Friday, July 7, 2017 at 1:06 PM

*To: *David Meltzer <David.Meltzer@glasgow.ac.uk
<mailto:David.Meltzer@glasgow.ac.uk>>,
"galaxy-dev@lists.galaxyproject.org
<mailto:galaxy-dev@lists.galaxyproject.org>"
<galaxy-dev@lists.galaxyproject.org
<mailto:galaxy-dev@lists.galaxyproject.org>>
*Subject: *RE : [galaxy-dev] ustacks - bad interpreter

No problem, I was not writing my question clearly...

I suspect a pb with the stacks_summary related script... Can you
investigate it, I unfortunately can't work on it for now. .. Maybe
""just"" a missing python interpreter invocation somewhere. .. when
executing stacks_summary. ...

-------- Message d'origine --------
De : David Meltzer <David.Meltzer@glasgow.ac.uk
<mailto:David.Meltzer@glasgow.ac.uk>>
Date : 07/07/2017 13:47 (GMT+01:00)
À : Yvan Le Bras <yvan.le-bras@mnhn.fr
<mailto:yvan.le-bras@mnhn.fr>>, galaxy-dev@lists.galaxyproject.org
<mailto:galaxy-dev@lists.galaxyproject.org>
Objet : Re: [galaxy-dev] ustacks - bad interpreter

Good afternoon,

I apologize. I misunderstood the question. Yes, stacks_summary has
been installed correctly as have stacks and velvet.

Additionally, the tool is outputting three items into the history -

Summary from Stacks – red (error)

Ustacks.log – red (error)

Stacks from Data – green (successful)

Best Regards,

David Jacob Meltzer

*From: *galaxy-dev <galaxy-dev-bounces@lists.galaxyproject.org
<mailto:galaxy-dev-bounces@lists.galaxyproject.org>> on behalf of
David Meltzer <David.Meltzer@glasgow.ac.uk
<mailto:David.Meltzer@glasgow.ac.uk>>
*Date: *Friday, July 7, 2017 at 12:31 PM
*To: *Yvan Le Bras <yvan.le-bras@mnhn.fr
<mailto:yvan.le-bras@mnhn.fr>>, "galaxy-dev@lists.galaxyproject.org
<mailto:galaxy-dev@lists.galaxyproject.org>"
<galaxy-dev@lists.galaxyproject.org
<mailto:galaxy-dev@lists.galaxyproject.org>>
*Subject: *Re: [galaxy-dev] ustacks - bad interpreter

Good afternoon,

I am sorry. I don’t see a tool called stacks_summary installed on my
system or available on the toolshed.

Best Regards,

David

*From: *Yvan Le Bras <yvan.le-bras@mnhn.fr
<mailto:yvan.le-bras@mnhn.fr>>
*Date: *Friday, July 7, 2017 at 12:08 PM
*To: *David Meltzer <David.Meltzer@glasgow.ac.uk
<mailto:David.Meltzer@glasgow.ac.uk>>,
"galaxy-dev@lists.galaxyproject.org
<mailto:galaxy-dev@lists.galaxyproject.org>"
<galaxy-dev@lists.galaxyproject.org
<mailto:galaxy-dev@lists.galaxyproject.org>>
*Subject: *RE : [galaxy-dev] ustacks - bad interpreter

Hi David,

A pb with stacks_summary apparently... and ustacks is working well
apparently... Can you check you have stacks_summary well installed ?
I think it is but there is a pb using it...

Cheers,

Yvan 

Envoyé depuis mon appareil Samsung

-------- Message d'origine --------
De : David Meltzer <David.Meltzer@glasgow.ac.uk
<mailto:David.Meltzer@glasgow.ac.uk>>
Date : 07/07/2017 12:38 (GMT+01:00)
À : galaxy-dev@lists.galaxyproject.org
<mailto:galaxy-dev@lists.galaxyproject.org>
Objet : [galaxy-dev] ustacks - bad interpreter

Good morning,

I have a user attempting to run ustacks. They are receiving the
following error

Fatal error: Exit code 126 (Error in Stacks execution)

/home/big_galaxy/galaxy/database/jobs_directory/079/79363/tool_script.sh:
/home/big_galaxy/galaxy/tool_dependencies/_conda/envs/mulled-v1-8e6d35eac718a13db6458b9361ca87c93be9feed656f9938ebcc435642f3a0a3/bin/stacks_summary.py:
/home/big_galaxy/galaxy/tool_dependencies/_conda/envs/mulled-v1-8e6d35eac718a1:
bad interpreter: No such file or directory

The tool produces an additional output on the bug report –

ustacks parameters selected:

  Sample ID: 1

  Min depth of coverage to create a stack: 3

  Max distance allowed between stacks: 2

  Max distance allowed to align secondary reads: 4

  Max number of stacks allowed per de novo locus: 3

  Deleveraging algorithm: disabled

  Removal algorithm: enabled

  Model type: SNP

  Alpha significance level for model: 0.05

  Gapped alignments: disabled

Parsing stacks_inputs/ZU-6.fq

Loading RAD-Tags...done

Loaded 933120 RAD-Tags.

  Inserted 256463 elements into the RAD-Tags hash map.

  0 reads contained uncalled nucleotides that were modified.

65509 initial stacks were populated; 190954 stacks were set aside as
secondary reads.

Initial coverage mean: 10.9276; Std Dev: 25.3864; Max: 4650

Deleveraging trigger: 36; Removal trigger: 62

Calculating distance for removing repetitive stacks.

  Distance allowed between stacks: 1; searching with a k-mer length
of 35 (36 k-mers per read); 1 k-mer hits required.

Removing repetitive stacks.

  Removed 993 stacks.

  64677 stacks remain for merging.

Post-Repeat Removal, coverage depth Mean: 10.2655; Std Dev: 9.03472;
Max: 62

Calculating distance between stacks...

  Distance allowed between stacks: 2; searching with a k-mer length
of 23 (48 k-mers per read); 2 k-mer hits required.

Merging stacks, maximum allowed distance: 2 nucleotide(s)

  64677 stacks merged into 57327 loci; deleveraged 0 loci;
blacklisted 189 loci.

After merging, coverage depth Mean: 11.0747; Std Dev: 9.82823; Max: 91

Merging remainder radtags

  217265 remainder sequences left to merge.

  Distance allowed between stacks: 4; searching with a k-mer length
of 13 (58 k-mers per read); 6 k-mer hits required.

  Matched 26211 remainder reads; unable to match 191054 remainder reads.

After remainders merged, coverage depth Mean: 11.5347; Std Dev:
9.95581; Max: 93

Calling final consensus sequences, invoking SNP-calling model...

Number of utilized reads: 742066

Writing loci, SNPs, and alleles to 'stacks_outputs/'...

  Refetching sequencing IDs from stacks_inputs/ZU-6.fq... read
933120 sequence IDs.

done.

ustacks is done.

I am not sure what is causing the bad interpreter: No such file or
directory. The tools are correctly installed along with its
requisite conda packages.

Any help would be greatly appreciated.

Best Regards,

David

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