Cannot give sequence using the --sequence option of check_structure

[PabloNA97]

I'm trying to build a workflow using fix_backbone from biobb_model.

However we noticed that the gaps were not modelled using Modeller. fix_backbone was just adding caps to the fist and last residues of the gap.

I took a look at the output file of fix_backbone and modeller was called through check_structure but it was not finding any canonical sequence. See below:

...
Found 1 Backbone breaks
 ALA A843   - CYS A852
...
Modeller v10.5 detected
...
Fixing chain/model A/0
No canonical sequence found for chain A/0
Capping terminal ends
...

fixbackbone_out_1.txt
fixbackbone_err_1.txt

I took a closer look at the call to check_structure in fix_backbone. I see that you are providing the fasta sequence as a stdin file in line 101. Since it seems like Modeller is not reading the canonical sequence, I tried to provide the fasta seq using the --sequence option of check_structure, but I obtain an error. See

fixbackbone_out_2.txt
fixbackbone_err_2.txt

I suspect there may be something broken in check_structure, but haven't been able to figure out what. I am very unfamiliar with this biobb.

It would be amazing if you could take a look into this. Thank you for your time! :)

Versions:

biobb_amber               4.2.0              pyhdfd78af_0    bioconda
biobb_analysis            4.2.0              pyhdfd78af_0    bioconda
biobb_common              4.2.0              pyhdfd78af_0    bioconda
biobb_gromacs             4.2.0              pyhdfd78af_0    bioconda
biobb_io                  4.2.0              pyhdfd78af_0    bioconda
biobb_model               4.2.3              pyhdfd78af_0    bioconda
biobb_pdb_tools           4.2.0              pyhdfd78af_0    bioconda
biobb_structure_checking  3.13.4             pyhca03a8a_0    bioconda
biobb_structure_utils     4.2.0              pyhdfd78af_0    bioconda