Good afternoon, Thank you for that! I will look in to it!
Best Regards, David Jacob Meltzer From: Nate Coraor <n...@bx.psu.edu> Date: Friday, July 7, 2017 at 5:02 PM To: David Meltzer <david.melt...@glasgow.ac.uk> Cc: 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 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<mailto: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<mailto:yvan.le-b...@mnhn.fr>> Date: Friday, July 7, 2017 at 1:06 PM To: David Meltzer <david.melt...@glasgow.ac.uk<mailto:david.melt...@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.melt...@glasgow.ac.uk<mailto:david.melt...@glasgow.ac.uk>> Date : 07/07/2017 13:47 (GMT+01:00) À : Yvan Le Bras <yvan.le-b...@mnhn.fr<mailto:yvan.le-b...@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-boun...@lists.galaxyproject.org<mailto:galaxy-dev-boun...@lists.galaxyproject.org>> on behalf of David Meltzer <david.melt...@glasgow.ac.uk<mailto:david.melt...@glasgow.ac.uk>> Date: Friday, July 7, 2017 at 12:31 PM To: Yvan Le Bras <yvan.le-b...@mnhn.fr<mailto:yvan.le-b...@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-b...@mnhn.fr<mailto:yvan.le-b...@mnhn.fr>> Date: Friday, July 7, 2017 at 12:08 PM To: David Meltzer <david.melt...@glasgow.ac.uk<mailto:david.melt...@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.melt...@glasgow.ac.uk<mailto:david.melt...@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 ___________________________________________________________ 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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