Hi David,

You may want to have a look at the first line of:

/home/big_galaxy/galaxy/tool_dependencies/_conda/envs/mulled-v1-8e6d35eac718a13db6458b9361ca87c93be9feed656f9938ebcc435642f3a0a3/bin/stacks_summary.py

The shell is claiming it is:

#!/home/big_galaxy/galaxy/tool_dependencies/_conda/envs/mulled-v1-8e6d35eac718a1

When it should be:

#!/home/big_galaxy/galaxy/tool_dependencies/_conda/envs/mulled-v1-8e6d35eac718a13db6458b9361ca87c93be9feed656f9938ebcc435642f3a0a3/bin/python

However, it could be that the line is correct and the output was truncated, or the shell has a length limit for the shebang (although the truncated string is only 79 characters, I'd be surprised if the limit for your shell was that short).

--nate

On Fri, Jul 7, 2017 at 8:21 AM, David Meltzer <David.Meltzer@glasgow.ac.uk> wrote:

Good afternoon,

 

I will do my best!


Best Regards,
David

 

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


To: David Meltzer <David.Meltzer@glasgow.ac.uk>, "galaxy-dev@lists.galaxyproject.org" <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>
Date : 07/07/2017 13:47 (GMT+01:00)
À : Yvan Le Bras <yvan.le-bras@mnhn.fr>, 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> on behalf of David Meltzer <David.Meltzer@glasgow.ac.uk>
Date: Friday, July 7, 2017 at 12:31 PM
To: Yvan Le Bras <yvan.le-bras@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-bras@mnhn.fr>
Date: Friday, July 7, 2017 at 12:08 PM
To: David Meltzer <David.Meltzer@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.Meltzer@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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