Test suite fails when running PGAP

[SJohnsonMayo]

Hi all,

I'm trying to run RAPT on a HPC system running CentOS8 with singularity version 3.5.3 (Docker is not an option for me). I'm able to run the first 5 tests, but a failure on the 6th test.

This is the output I get in concise.log for that test:

[2021-02-17 15:47:54] Starting test #6: Contigs with matching SRA run and taxonomy information in submol file
[2021-02-17 15:47:54] No submol yaml provided. Try to make one from acxn ERR3938362
[2021-02-17 15:47:59] Acquired genus_species=Mycoplasma feriruminatoris
[2021-02-17 15:59:01] Pipeline pgap failed on FASTA file /dkm_output_dir/ERR3938362_sk_out.fa and submol file /dkm_output_dir/.rapt_scratch/ERR3938362_Mycoplasma_feriruminatoris.yaml
[2021-02-17 15:59:01] **FAILED**


[2021-02-17 15:59:01] Test cycle complete, total tests run: 6, total succeeded: 5.
[2021-02-17 15:59:01] Sending PINGER url https://www.ncbi.nlm.nih.gov/stat?ncbi_app=raptdocker&version=2021-01-11.build5132&uuid=fddd345e-7160-11eb-83d6-1866daee9238&evt=test_end
[2021-02-17 15:59:06] status=21
[2021-02-17 15:59:06] Sending PINGER url https://www.ncbi.nlm.nih.gov/stat?ncbi_app=raptdocker&version=2021-01-11.build5132&uuid=fddd345e-7160-11eb-83d6-1866daee9238&evt=rapt_exit

I'm really not sure why this is failing, is there any other information I can provide?