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blaxterlab / blobology

Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a QC step (NO LONGER MANTAINED)
MIT License
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Contig-taxid file does not seem to have two cols with the seqid in the first col and taxid in the second col #8

Closed pkfsantos closed 2 years ago

pkfsantos commented 7 years ago

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

RJBeng commented 7 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

DRL commented 7 years ago

Hi both,

the blobology pipeline is no longer maintained and its use is not encouraged...

You might want to check out BlobTools:

cheers,

dom

kalonji08 commented 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 @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 :)