Database for Blastn

[xichuan Zhai]

Looks like everything is now set up, we will first clean up the input file, and then we will start the host prediction steps themselves
[1/1/Run] Running blastn against genomes...
[1/3/Run] Get relevant blast matches...
The blastn output file was empty, this may be ok, but is still unusual, so you may want to check the blastn log (Wdir/blastgenomes.tsv.log)
[2/1/Run] Running blastn against CRISPR...
[2/2/Run] Get relevant crispr matches...
The blastn output file for the CRISPR spacers was empty, this may be ok, but is still unusual, so you may want to check the blastn log (Wdir/blastcrispr.tsv.log)
[3/1/Run] Running (recoded)WIsH...

Welcome to iPHoP

I am not sure if this is normal or not, when I check the blastgenomes.tsv.log and blastcrispr.tsv.log, it showed like this: BLAST Database error: Error: Not a valid version 4 database.

The blast command from the log file is:

blastn -task megablast -query /media/server/95d691e7-0d78-417e-b796-a49c36203e5e/virome_host_2200/h_qual_clean_contigs_2200_clean.fna -db /media/server/95d691e7-0d78-417e-b796-a49c36203e5e/iphop_db/Sept_2021_pub_rw/db/Host_Genomes/Host_Genomes -out /media/server/95d691e7-0d78-417e-b796-a49c36203e5e/cow_virome_tax/virome_host_2200/Wdir/blastgenomes.tsv -num_threads 20 -evalue 1e-3 -outfmt '6 std qlen slen nident positive' -max_target_seqs 25000 -perc_identity 80 > /media/server/95d691e7-0d78-417e-b796-a49c36203e5e/cow_virome_tax/virome_host_2200/Wdir/blastgenomes.tsv.log 2>&1

The database was completed with command: iphop download --db_dir ./

Is there something wrong with the iphop database?

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Best,

XC-Zhai

[Simon Roux]

Hi XC-Zhai,

This seems like an incompatibility between the version of blastn you run and iPHoP database. Could you check the output of >blastn -version ?

Best,

Simon

[xichuan Zhai]

Here is the blastn that I am using:

blastn -version
blastn: 2.2.31+
Package: blast 2.2.31, build Jan 7 2016 23:17:17

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Can I put an updated version of blast under iphop conda environment?

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Best,

Xichuan

[Simon Roux]

Right, so the current requirement for iPHoP is blast 2.12.* , and it seems like you are running an older version of blast. I would recommend trying to update your blast to 2.12 and try again (probably on a new output folder so that iPHoP does not try to re-use some of these files).

[xichuan Zhai]

Thanks, this works for me.

[Simon Roux]

User reported that the problem was solved