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