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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