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...
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 : firstname.lastname@example.org
Objet : [galaxy-dev] ustacks - bad interpreter
I have a user attempting to run ustacks. They are receiving the following error
Fatal error: Exit code 126 (Error in Stacks execution)
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
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
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
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.
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