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-boun...@lists.galaxyproject.org> on behalf of 
David Meltzer <david.melt...@glasgow.ac.uk>
Date: Friday, July 7, 2017 at 12:31 PM
To: Yvan Le Bras <yvan.le-b...@mnhn.fr>, "galaxy-dev@lists.galaxyproject.org" 
<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-b...@mnhn.fr>
Date: Friday, July 7, 2017 at 12:08 PM
To: David Meltzer <david.melt...@glasgow.ac.uk>, 
"galaxy-dev@lists.galaxyproject.org" <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.melt...@glasgow.ac.uk>
Date : 07/07/2017 12:38 (GMT+01:00)
À : 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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