Apptainer - [FATAL ERROR] Error executing /dbgwas/bin/DBGWAS_lib///makeblastdb -dbtype nucl -in output/step3/nucl_db_fixed. Exit status: 256
Hello there,
We are trying to run DGBWAS using singularity/apptainer. During execution of the container on a small dataset we receive the following error with regard to makeblastdb.
`$ apptainer run /local/scratch/jbury/apptainer/dbgwas-0.5.4.sif -strains /local/scratch/jbury/appdata/dbgwas-strains/manifest_pheno.txt -nc-db /local/scratch/jbury/appdata/dbgwas-fasta/coptr_index.1.bt2 -SFF q500 -skip2 -nb-cores 4
Step 1. Building DBG and mapping strains on the DBG...
Skipping Step 1!
build_dbg
map_reads
Done!
Step 2. Running statistical test (bugwas + gemma)...
Skipping Step 2!
statistical_test
Done!
Step 3. Building visualisation around significant unitigs...
Executing /dbgwas/bin/DBGWAS_lib///makeblastdb -dbtype nucl -in output/step3/nucl_db_fixed...
Building a new DB, current time: 04/12/2023 22:39:50 New DB name: /local/scratch/jbury/appdata/output/step3/nucl_db_fixed New DB title: output/step3/nucl_db_fixed Sequence type: Nucleotide Keep MBits: T Maximum file size: 1000000000B
[FATAL ERROR] Error executing /dbgwas/bin/DBGWAS_lib///makeblastdb -dbtype nucl -in output/step3/nucl_db_fixed. Exit status: 256 `
Note: We have also tried running the command using a local copy makebastdb in from our shared software area. I receive the following error below.
`$ apptainer run /local/scratch/jbury/apptainer/dbgwas-0.5.4.sif -Blast-path /usr/local/packages/ncbi-blast+-2.13.0/bin -strains /local/scratch/jbury/appdata/dbgwas-strains/manifest_pheno.txt -nc-db /local/scratch/jbury/appdata/dbgwas-fasta/coptr_index.1.bt2 -output outlocal -SFF q500 -skip2 -nb-cores 4
Step 1. Building DBG and mapping strains on the DBG...
Skipping Step 1!
build_dbg
map_reads
Done!
Step 2. Running statistical test (bugwas + gemma)...
Skipping Step 2!
statistical_test
Done!
Step 3. Building visualisation around significant unitigs...
[FATAL ERROR] Error executing /usr/local/packages/ncbi-blast+-2.13.0/bin/makeblastdb -version. Exit status: 32512 Message: You want to annotate the output subgraphs with -nc-db , but /usr/local/packages/ncbi-blast+-2.13.0/bin/makeblastdb does not work. You can install a version of the Blast suite that works on your system and tell DBGWAS to use it through the parameter -Blast-path . `
Any help would be very appreciated.
Thanks - John