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.melt...@glasgow.ac.uk> wrote: > Good afternoon, > > > > I will do my best! > > > Best Regards, > David > > > > *From: *Yvan Le Bras <yvan.le-b...@mnhn.fr> > *Date: *Friday, July 7, 2017 at 1:06 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 > > > > 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.melt...@glasgow.ac.uk> > Date : 07/07/2017 13:47 (GMT+01:00) > À : Yvan Le Bras <yvan.le-b...@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-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 > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ >
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