Closed pkfsantos closed 2 years ago
Hello Priscila,
blastn for some reason does not like the configuration of '6 qseqid staxids' from the line
blastn -task megablast -query $RND_ASSEMBLY -db $BLASTDB/nt -evalue 1e-5 -num_threads $NUMPROC -max_target_seqs 1 -outfmt '6 qseqid staxids' -out $RND_ASSEMBLY.nt.1e-5.megablast
I removed the s from staxids so the new configuration is '6 qseqid staxid' and it worked.
Rebecca
Hi both,
the blobology pipeline is no longer maintained and its use is not encouraged...
You might want to check out BlobTools:
cheers,
dom
Hello Priscila,
blastn for some reason does not like the configuration of '6 qseqid staxids' from the line
blastn -task megablast -query $RND_ASSEMBLY -db $BLASTDB/nt -evalue 1e-5 -num_threads $NUMPROC -max_target_seqs 1 -outfmt '6 qseqid staxids' -out $RND_ASSEMBLY.nt.1e-5.megablast
I removed the s from staxids so the new configuration is '6 qseqid staxid' and it worked.
Rebecca
Hi @RJBeng I hope you are well. I have encountered the same issue, would you please expand on how you achieved this ? I'm still new and would really like to get this analysis. Thank you :)
Hello everyone, I am getting the follow error: "Contig-taxid file random10k.example_scaffolds.fa.nt.1e-5.megablast does not seem to have two cols with the seqid in the first col and taxid in the second col at /home/pkfs/blobology/gc_cov_annotate.pl line 58, <$filehandle> line 1. Error in file(file, "rt") : não é possível abrir a conexão Calls: read.delim -> read.table -> file Além disso: Warning message: In file(file, "rt") : não foi possível abrir o arquivo 'blobplot.txt': Arquivo ou diretório não encontrado Execução interrompida " When I open the created file ( "random10k.example_scaffolds.fa.nt.1e-5.megablast"), I have: "372284 N/A 410910 N/A 281600 N/A 3303361 N/A 1790197 N/A 3226893 N/A (...) " Do you have any ideia how can I solve this problem? Best regards,
Priscila