google-deepmind / google-deepmind/alphafold

HHblits error: sequences in fasta file do not all have the same number of columns

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Description

hi, i ran into a similar issue as https://github.com/soedinglab/hh-suite/issues/337 and https://github.com/google-deepmind/alphafold/issues/661. i have also tried -db_preset (as suggested in #661) but seems like it doesn't recognize it as a flag. i am using v3.3.0 hhblits and I downloaded UniRef30_2023_02 database. thank you for your help.

`$ hhblits -i anti_seq/unix_clean_light.fasta -o results.hhr -oa3m results.a3m -d UniRef30/UniRef30_2023_02 -n 2 -e 1e-3 -p 20 -db_preset reduced_dbs -M first
- 12:40:21.205 WARNING: Ignoring unknown option -db_preset

- 12:40:21.205 WARNING: Ignoring unknown option reduced_dbs

- 12:40:28.327 INFO: Searching 36293491 column state sequences.

- 12:40:28.371 INFO: anti_seq/unix_clean_light.fasta is in A2M, A3M or FASTA format

- 12:40:28.376 ERROR: - 12:40:28.376 ERROR: Error in /home/desmond/antibodygpt3/hh-suite/src/hhalignment.cpp:1246: Compress:

- 12:40:28.376 ERROR: sequences in anti_seq/unix_clean_light.fasta do not all have the same number of columns,

- 12:40:28.376 ERROR:
e.g. first sequence and sequence Sequence_2.`

here's how my sequences look like in unix_clean_light.fasta:
>Sequence_1
EIVLVESGGGLVQPGGSLRLSCAASGFTFSSYGMHWVRQAPGKGLEWVSAISSSGGSTYY
ADSVKGRFTISRDNSKNTLYLQMNP
>Sequence_2
EIVLVESGGGLVQPGGSLRLSCAASGFTFSSYAMHWVRQAPGKGLEWVSSISSGGGSTYY
ADSVKGRFTISRDNAKNSLYLP
>Sequence_3
EIVLVESGGGLVQPGGSLRLSCAASGFTFSSYGMHWVRQAPGKGLEWVSAISSDGSTYYA
DSVKGRFTISRDNAKNSLYLQMNP

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