speedup searching fastas

[andrewjpage]

No description provided.

[jananiravi]

Hi @andrewjpage
I see a series of errors that look similar to the following. I'm running roary on the 'fixed' gff files (roary -f roary_mbov_fixed fixed_input_files/*.gff). These are on sequences directly downloaded from refseq. I've, therefore, not run prokka, yet. Any suggestions on how to avert this issue? Thanks!
I'm posting the Q here since this was the most meaningful hit for this error from the roary issues page.

sh: line 1: 72283 Abort trap: 6 bedtools getfasta -s -fi /Users/janani/mbov-genomes/refseq/bacteria/roary_mbov_fixed/QCDhdn_OVo/GCF_000009445.1_ASM944v1_genomic.gff.proteome.faa.intermediate.fa -bed /Users/janani/mbov-genomes/refseq/bacteria/roary_mbov_fixed/QCDhdn_OVo/GCF_000009445.1_ASM944v1_genomic.gff.proteome.faa.intermediate.bed -fo /Users/janani/mbov-genomes/refseq/bacteria/roary_mbov_fixed/QCDhdn_OVo/GCF_000009445.1_ASM944v1_genomic.gff.proteome.faa.intermediate.extracted.fa -name > /dev/null 2>&1
2018/12/19 17:07:32 Could not extract any protein sequences from /Users/janani/mbov-genomes/refseq/bacteria/fixed_input_files/GCF_000009445.1_ASM944v1_genomic.gff. Does the file contain the assembly as well as the annotation?

... for each of the files ... finally followed by:

BLAST Database error: No alias or index file found for protein database [/Users/janani/mbov-genomes/refseq/bacteria/roary_mbov_fixed/inX1E__4Yy/output_contigs] in search path [/Users/janani/mbov-genomes/refseq/bacteria/roary_mbov_fixed::] Use of uninitialized value in require at /anaconda2/lib/site_perl/5.26.2/darwin-thread-multi-2level/Encode.pm line 61.