[vecscreen] WARNING: readdb: wrong version of formatdb was used to make database

[mollydawson]

Hi there,

I am running removecScreen as the individual commands, and I am running into an error that is outside my control in section two, adapter screen. I have vecscreen installed and the adaptor contamination files downloaded, and per the instruction, I made a makeblastdb of the adaptors_for_screening_euks.fa file as follows:

# BLAST v2.12.0

makeblastdb -dbtype nucl \
-in adaptors_for_screening_euks.fa \
-out adaptors_for_screening_euks_BLAST_v2.12.0_nucl_db

This resulted in these db files:
adaptors_for_screening_euks_BLAST_v2.12.0_nucl_db.ndb
adaptors_for_screening_euks_BLAST_v2.12.0_nucl_db.nhr
adaptors_for_screening_euks_BLAST_v2.12.0_nucl_db.nin
adaptors_for_screening_euks_BLAST_v2.12.0_nucl_db.not
adaptors_for_screening_euks_BLAST_v2.12.0_nucl_db.nsq
adaptors_for_screening_euks_BLAST_v2.12.0_nucl_db.ntf
adaptors_for_screening_euks_BLAST_v2.12.0_nucl_db.nto

I then run vecscreen as follows:

vecscreen \
-d adaptors_for_screening_euks_BLAST_v2.12.0_nucl_db \
-f3 \
-i input.fasta \
-o output.txt 

I get the error message:
[vecscreen] WARNING: readdb: wrong version of formatdb was used to make database adaptors_for_screening_euks_BLAST_v2.12.0_nucl_db.
[vecscreen] WARNING: readdb: wrong version of formatdb was used to make database adaptors_for_screening_euks_BLAST_v2.12.0_nucl_db.
[vecscreen] WARNING: readdb: wrong version of formatdb was used to make database adaptors_for_screening_euks_BLAST_v2.12.0_nucl_db.
[vecscreen] FATAL ERROR: Database adaptors_for_screening_euks_BLAST_v2.12.0_nucl_db was not found or does not exist

Why is my database not compatible with vecscreen? It was made with BLAST v2.12.0, is this version not compatible with vecscreen? How should the vecscreen databse be built?

Thanks!

[htafer]

Hi Molly I am not maintaining this package. Please have a look at another tool Thank you

…

On Fri, Aug 27, 2021 at 9:53 PM mollydawson ***@***.***> wrote: Hi there, I am running removecScreen as the individual commands, and I am running into an error that is outside my control in section two, adapter screen. I have vecscreen installed and the adaptor contamination files downloaded, and per the instruction, I made a makeblastdb of the adaptors_for_screening_euks.fa file as follows: *# BLAST v2.12.0* makeblastdb ---dbtype nucl \ -in adaptors_for_screening_euks.fa \ -out adaptors_for_screening_euks_BLAST_v2.12.0_nucl_db *This resulted in these db files:* adaptors_for_screening_euks_BLAST_v2.12.0_nucl_db.ndb adaptors_for_screening_euks_BLAST_v2.12.0_nucl_db.nhr adaptors_for_screening_euks_BLAST_v2.12.0_nucl_db.nin adaptors_for_screening_euks_BLAST_v2.12.0_nucl_db.not adaptors_for_screening_euks_BLAST_v2.12.0_nucl_db.nsq adaptors_for_screening_euks_BLAST_v2.12.0_nucl_db.ntf adaptors_for_screening_euks_BLAST_v2.12.0_nucl_db.nto *I then run vecscreen as follows:* vecscreen \ -db adaptors_for_screening_euks_BLAST_v2.12.0_nucl_db \ -f3 \ -i input.fasta \ -o output.txt *I get the error message:* [vecscreen] WARNING: readdb: wrong version of formatdb was used to make database adaptors_for_screening_euks_BLAST_v2.12.0_nucl_db. [vecscreen] WARNING: readdb: wrong version of formatdb was used to make database adaptors_for_screening_euks_BLAST_v2.12.0_nucl_db. [vecscreen] WARNING: readdb: wrong version of formatdb was used to make database adaptors_for_screening_euks_BLAST_v2.12.0_nucl_db. [vecscreen] FATAL ERROR: Database adaptors_for_screening_euks_BLAST_v2.12.0_nucl_db was not found or does not exist Why is my database not compatible with vecscreen? It was made with BLAST v2.12.0, is this version not compatible with vecscreen? How should the vecscreen databse be built? Thanks! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AACWIBMMEZEAMCBNBM3XGP3T67UMLANCNFSM5C6F4UEA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.