#8 Selenocysteine (U) at position ### replaced by X

[Lee Katz]

The warning
Selenocysteine (U) at position ### replaced by X
appears during some BLAST steps. This is likely due to U appearing in amino acid sequences in at least the COGs and uniprot_sprot databases.

To find U in the amino acid sequences, go to /data and enter the command
grep -m 1 '^[^>].*U' *

Although this is only a warning and does not affect the outcome of CG-Pipeline, it would be nice to avoid these warnings.

Possible solutions:
1. During install, replace any U in the protein database sequences with X to preempt BLAST from sending that warning.
2. Suppress BLAST warnings, especially if it is this warning

[gtg534z@ollie data]$ grep -m 1 '^[^>].*U' *
Binary file cgpipeline.db3 matches
Binary file cgpipeline.evidence.db3 matches
Binary file cogs.phr matches
Binary file cogs.pin matches
formatdb.log:SUCCESS: formatted database vfdb_CP_VFs_aa
myva:ENPESVMFLGSAKLNNEQAYYIRKFAAFFGTNNVDHQARIUHSATVAGVANTFGYGAMTNHLGDIQRSKC
prot2cogid.tsv:UU186 COG0469
uniprot_sprot.fasta:LGLRMGSSDCRVKIATKANPWIGNSLKPDSVRSQLETSLKRLQCPUVDLFYLHAPDHSAP
Binary file uniprot_sprot.pin matches
Binary file uniprot_sprot_trembl.00.phr matches
Binary file uniprot_sprot_trembl.00.pin matches
Binary file uniprot_sprot_trembl.01.phr matches
Binary file uniprot_sprot_trembl.01.pin matches
Binary file uniprot_sprot_trembl.02.phr matches
Binary file uniprot_sprot_trembl.02.pin matches
Binary file uniprot_sprot_trembl.03.phr matches
Binary file uniprot_sprot_trembl.03.pin matches
uniprot_sprot_trembl.fasta:LGLRMGSSDCRVKIATKANPWIGNSLKPDSVRSQLETSLKRLQCPUVDLFYLHAPDHSAP
uniprot_sprot.xml:<?xml version="1.0" encoding="UTF-8"?>
Binary file uniprot_trembl.00.phr matches
Binary file uniprot_trembl.00.pin matches
Binary file uniprot_trembl.01.phr matches
Binary file uniprot_trembl.01.pin matches
Binary file uniprot_trembl.02.phr matches
Binary file uniprot_trembl.02.pin matches
Binary file uniprot_trembl.03.phr matches
Binary file uniprot_trembl.03.pin matches
uniprot_trembl.fasta:MVTLHGUACKLPDTELENLVKGIISEDDLKYAKVGLGDDAAVVIKNGMAIVKTIDVFTPI
uniprot_trembl.xml:<?xml version="1.0" encoding="UTF-8"?>
Binary file vfdb_CP_VFs_aa.pin matches
Binary file vfdb_CP_VFs_nt.nin matches
Binary file vfdb_CP_VFs_nt.nsq matches
Binary file vfdb_VFs_aa.pin matches
Binary file vfdb_VFs_nt.nin matches
Binary file vfdb_VFs_nt.nsq matches
Binary file VFs.xls matches
whog: Buc: BU048