Is it reasonable to use diamond(blastx) instead of blast(blastx) in the ARG-OAP？

[jiangyoufeng]

Hi,

When my data volume is large, I want to accelerate the alignment process. So I want to ask is it reasonable to use diamond(blastx) instead of blast(blastx) in ARG-OAP ？For example, is it reasonable if I change the codes in the .py to make the alignment done by diamond?

Thanks!

[xinehc]

yes, you can replace blastx with diamond's blastx in stage_two. the results should not be largely different if you use the same cutoff.

[jiangyoufeng]

Thanks for your reply!

[diego00012138]

Hi! I am interested in this replacememt, but unfortunately I am not familiar with python, I would appreciate it if you could give me a specific modification Sincerely

[diego00012138]

Hi! Am I right to edit the code like below 1)only change the corresponding parameters in this area and do nothing to the else.

2)exchange the stage_two.py of these directions 3)install the diamond to the environment Sincerely

[xinehc]

Yes you only need to replace subprocess.run([...]) with your diamond arguments. Please note the name of arguments may not be exactly identical, e.g. -mt_mode is not used by diamond.

[diego00012138]

Hi After some attempts, it didn't work. First,I changed subprocess.run([...]) to this:

__def extract_seqs(self): ''' Extract target sequences using more stringent cutoffs & blast. ''' logger.info(f'Processing <{self.setting.extracted}> ...') nbps, nlines = simple_count(self.setting.extracted) blast_mode = 'blastx' if self.dbtype == 'prot' else 'blastn'

    logger.info('Extracting target sequences using BLAST ...')
    logger.info(f'BLAST settings: {nbps} bps, {nlines} reads, {self.thread} threads')

    subprocess.run([
        'diamond',
        blast_mode,
        '--db', self.db,
        '-q', self.setting.extracted,
        '-o', self.setting.blastout,
        '--outfmt', ' '.join(['6'] + self.setting.columns),
        '-e', str(self.e),
        '--max-target-seqs', '5',
        '-p', str(self.thread)])

but I get this error:"Error: Invalid output format: 6 qseqid sseqid pident length qlen slen evalue bitscore"

I can not figure it out SO I just delete the"'--outfmt', ' '.join(['6'] + self.setting.columns)," to find out could it run.

But I get another error :"Opening the database... Error: This executable was not compiled with support for BLAST databases.

[xinehc]

try this one:

subprocess.run([
    'diamond',
    blast_mode,
    '--db', self.db + '.dmnd',
    '-q', self.setting.extracted,
    '-o', self.setting.blastout,
    '--outfmt', '6'] + self.setting.columns + [
    '-e', str(self.e),
    '--max-target-seqs', '5',
    '-p', str(self.thread)])