ustacks - bad interpreter

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ustacks - bad interpreter

David Meltzer

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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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: ustacks - bad interpreter

Yvan Le Bras-2
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 <[hidden email]>
Date : 07/07/2017 12:38 (GMT+01:00)
À : [hidden email]
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


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/
___________________________________________________________
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:
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Re: ustacks - bad interpreter

David Meltzer

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 <[hidden email]>
Date: Friday, July 7, 2017 at 12:08 PM
To: David Meltzer <[hidden email]>, "[hidden email]" <[hidden email]>
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 <[hidden email]>
Date : 07/07/2017 12:38 (GMT+01:00)
À : [hidden email]
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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|

Re: ustacks - bad interpreter

David Meltzer

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 <[hidden email]> on behalf of David Meltzer <[hidden email]>
Date: Friday, July 7, 2017 at 12:31 PM
To: Yvan Le Bras <[hidden email]>, "[hidden email]" <[hidden email]>
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 <[hidden email]>
Date: Friday, July 7, 2017 at 12:08 PM
To: David Meltzer <[hidden email]>, "[hidden email]" <[hidden email]>
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 <[hidden email]>
Date : 07/07/2017 12:38 (GMT+01:00)
À : [hidden email]
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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Re: ustacks - bad interpreter

Yvan Le Bras-2
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 <[hidden email]>
Date : 07/07/2017 13:47 (GMT+01:00)
À : Yvan Le Bras <[hidden email]>, [hidden email]
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 <[hidden email]> on behalf of David Meltzer <[hidden email]>
Date: Friday, July 7, 2017 at 12:31 PM
To: Yvan Le Bras <[hidden email]>, "[hidden email]" <[hidden email]>
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 <[hidden email]>
Date: Friday, July 7, 2017 at 12:08 PM
To: David Meltzer <[hidden email]>, "[hidden email]" <[hidden email]>
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 <[hidden email]>
Date : 07/07/2017 12:38 (GMT+01:00)
À : [hidden email]
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


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 <[hidden email]> on behalf of David Meltzer <[hidden email]>
Date: Friday, July 7, 2017 at 12:31 PM
To: Yvan Le Bras <[hidden email]>, "[hidden email]" <[hidden email]>
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 <[hidden email]>
Date: Friday, July 7, 2017 at 12:08 PM
To: David Meltzer <[hidden email]>, "[hidden email]" <[hidden email]>
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 <[hidden email]>
Date : 07/07/2017 12:38 (GMT+01:00)
À : [hidden email]
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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Re: ustacks - bad interpreter

David Meltzer

Good afternoon,

 

I will do my best!


Best Regards,
David

 

From: Yvan Le Bras <[hidden email]>
Date: Friday, July 7, 2017 at 1:06 PM
To: David Meltzer <[hidden email]>, "[hidden email]" <[hidden email]>
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 <[hidden email]>
Date : 07/07/2017 13:47 (GMT+01:00)
À : Yvan Le Bras <[hidden email]>, [hidden email]
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 <[hidden email]> on behalf of David Meltzer <[hidden email]>
Date: Friday, July 7, 2017 at 12:31 PM
To: Yvan Le Bras <[hidden email]>, "[hidden email]" <[hidden email]>
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 <[hidden email]>
Date: Friday, July 7, 2017 at 12:08 PM
To: David Meltzer <[hidden email]>, "[hidden email]" <[hidden email]>
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 <[hidden email]>
Date : 07/07/2017 12:38 (GMT+01:00)
À : [hidden email]
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:
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Re: ustacks - bad interpreter

Nate Coraor (nate@bx.psu.edu)
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 <[hidden email]> wrote:

Good afternoon,

 

I will do my best!


Best Regards,
David

 

From: Yvan Le Bras <[hidden email]>
Date: Friday, July 7, 2017 at 1:06 PM


To: David Meltzer <[hidden email]>, "[hidden email]" <[hidden email]>
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 <[hidden email]>
Date : 07/07/2017 13:47 (GMT+01:00)
À : Yvan Le Bras <[hidden email]>, [hidden email]
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 <[hidden email]> on behalf of David Meltzer <[hidden email]>
Date: Friday, July 7, 2017 at 12:31 PM
To: Yvan Le Bras <[hidden email]>, "[hidden email]" <[hidden email]>
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 <[hidden email]>
Date: Friday, July 7, 2017 at 12:08 PM
To: David Meltzer <[hidden email]>, "[hidden email]" <[hidden email]>
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 <[hidden email]>
Date : 07/07/2017 12:38 (GMT+01:00)
À : [hidden email]
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/


___________________________________________________________
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:
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Re: ustacks - bad interpreter

David Meltzer

Good afternoon,

 

Thank you for that! I will look in to it!

 

Best Regards,

David Jacob Meltzer

 

From: Nate Coraor <[hidden email]>
Date: Friday, July 7, 2017 at 5:02 PM
To: David Meltzer <[hidden email]>
Cc: Yvan Le Bras <[hidden email]>, "[hidden email]" <[hidden email]>
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 <[hidden email]> wrote:

Good afternoon,

 

I will do my best!


Best Regards,
David

 

From: Yvan Le Bras <[hidden email]>
Date: Friday, July 7, 2017 at 1:06 PM


To: David Meltzer <[hidden email]>, "[hidden email]" <[hidden email]>
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 <[hidden email]>
Date : 07/07/2017 13:47 (GMT+01:00)
À : Yvan Le Bras <[hidden email]>, [hidden email]
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 <[hidden email]> on behalf of David Meltzer <[hidden email]>
Date: Friday, July 7, 2017 at 12:31 PM
To: Yvan Le Bras <[hidden email]>, "[hidden email]" <[hidden email]>
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 <[hidden email]>
Date: Friday, July 7, 2017 at 12:08 PM
To: David Meltzer <[hidden email]>, "[hidden email]" <[hidden email]>
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 <[hidden email]>
Date : 07/07/2017 12:38 (GMT+01:00)
À : [hidden email]
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/

 


___________________________________________________________
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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Open this post in threaded view
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Re: ustacks - bad interpreter

Björn Grüning-3
Hi,

please also make sure you have a recent conda version. This 80 character
length smalls a lot like an old conda restriction.

Cheers,
Bjoern

Am 07.07.2017 um 18:09 schrieb David Meltzer:

> Good afternoon,
>
>  
>
> Thank you for that! I will look in to it!
>
>  
>
> Best Regards,
>
> David Jacob Meltzer
>
>  
>
> *From: *Nate Coraor <[hidden email]>
> *Date: *Friday, July 7, 2017 at 5:02 PM
> *To: *David Meltzer <[hidden email]>
> *Cc: *Yvan Le Bras <[hidden email]>,
> "[hidden email]" <[hidden email]>
> *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
> <[hidden email] <mailto:[hidden email]>> wrote:
>
>     Good afternoon,
>
>      
>
>     I will do my best!
>
>
>     Best Regards,
>     David
>
>      
>
>     *From: *Yvan Le Bras <[hidden email]
>     <mailto:[hidden email]>>
>     *Date: *Friday, July 7, 2017 at 1:06 PM
>
>
>     *To: *David Meltzer <[hidden email]
>     <mailto:[hidden email]>>,
>     "[hidden email]
>     <mailto:[hidden email]>"
>     <[hidden email]
>     <mailto:[hidden email]>>
>     *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 <[hidden email]
>     <mailto:[hidden email]>>
>     Date : 07/07/2017 13:47 (GMT+01:00)
>     À : Yvan Le Bras <[hidden email]
>     <mailto:[hidden email]>>, [hidden email]
>     <mailto:[hidden email]>
>     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 <[hidden email]
>     <mailto:[hidden email]>> on behalf of
>     David Meltzer <[hidden email]
>     <mailto:[hidden email]>>
>     *Date: *Friday, July 7, 2017 at 12:31 PM
>     *To: *Yvan Le Bras <[hidden email]
>     <mailto:[hidden email]>>, "[hidden email]
>     <mailto:[hidden email]>"
>     <[hidden email]
>     <mailto:[hidden email]>>
>     *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 <[hidden email]
>     <mailto:[hidden email]>>
>     *Date: *Friday, July 7, 2017 at 12:08 PM
>     *To: *David Meltzer <[hidden email]
>     <mailto:[hidden email]>>,
>     "[hidden email]
>     <mailto:[hidden email]>"
>     <[hidden email]
>     <mailto:[hidden email]>>
>     *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 <[hidden email]
>     <mailto:[hidden email]>>
>     Date : 07/07/2017 12:38 (GMT+01:00)
>     À : [hidden email]
>     <mailto:[hidden email]>
>     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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>
>
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