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HIT-ImmunologyLab / DBSCAN-SWA

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ERROR: nhmmer failed to run - Error: Invalid alphabet type in target for nhmmer. Expect DNA or RNA #21

Open zhaocx314 opened 1 year ago

zhaocx314 commented 1 year ago

I have followed all the instruction mentioned in your readme installed all the necessary dependencies and added the DBSCAN_SWA in my .bashrc but still I am getting error as follows, [23:55:09] Re-using existing --outdir /home/denovo/result_1002/dbscan/results/1002_10971/protein_annotation [23:55:09] Using filename prefix: 1002_10971.XXX [23:55:09] Setting HMMER_NCPU=1 [23:55:09] Writing log to: /home/denovo/result_1002/dbscan/results/1002_10971/protein_annotation/1002_10971.log [23:55:09] Determined tbl2asn version is 25.8 [23:55:09] Looking for 'less' - found /bin/less [23:55:09] Looking for 'sed' - found /bin/sed [23:55:09] Looking for 'tbl2asn' - found /share/soft/miniconda3/envs/prokka/bin/tbl2asn [23:55:09] Loading and checking input file: /home/denovo/result_1002/dbscan/results/1002_10917/1002_10917.fna [barrnap] ERROR: nhmmer failed to run - Error: Invalid alphabet type in target for nhmmer. Expect DNA or RNA.

fengxiaZhou commented 1 year ago

I have followed all the instruction mentioned in your readme installed all the necessary dependencies and added the DBSCAN_SWA in my .bashrc but still I am getting error as follows, [23:55:09] Re-using existing --outdir /home/denovo/result_1002/dbscan/results/1002_10971/protein_annotation [23:55:09] Using filename prefix: 1002_10971.XXX [23:55:09] Setting HMMER_NCPU=1 [23:55:09] Writing log to: /home/denovo/result_1002/dbscan/results/1002_10971/protein_annotation/1002_10971.log [23:55:09] Determined tbl2asn version is 25.8 [23:55:09] Looking for 'less' - found /bin/less [23:55:09] Looking for 'sed' - found /bin/sed [23:55:09] Looking for 'tbl2asn' - found /share/soft/miniconda3/envs/prokka/bin/tbl2asn [23:55:09] Loading and checking input file: /home/denovo/result_1002/dbscan/results/1002_10917/1002_10917.fna [barrnap] ERROR: nhmmer failed to run - Error: Invalid alphabet type in target for nhmmer. Expect DNA or RNA.

Whether there are other alphabets in the fasta sequence except A/T/C/G？

zhaocx314 commented 1 year ago

There are no alphabets in the fasta sequence except ATCG.

zhaocx314 commented 1 year ago

Sorry, I just noticed that several sequences contain N bases, so how can I correct this? Thanks for your time!