[Debian-med-packaging] Bug#1117994: vecscreen: UniVec is not packaged, UniVec_Core should be default + default path issue

Mon Oct 13 13:57:03 BST 2025

Package: ncbi-tools-bin
Version: 6.1.20170106+dfsg2-6
Severity: wishlist

Dear Maintainer,

Running vecscreen without the -d option fails, as does using -d UniVec_Core.
The only is to use then -d /usr/share/ncbi/data/UniVec_Core.

Thanks!
Patrice

$ vecscreen -i tmp/test.fna
<HTML>
<TITLE>VecScreen Search Results</TITLE>
<BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
<PRE><b>BLASTN 2.2.26 [Sep-21-2011]</b>

<a
href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids
=9254694&dopt=Citation">Reference</a>:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.

<b>Query=</b> test
         (22 letters)

<B> ****** No hits found ******</B>

[vecscreen] FATAL ERROR: Database UniVec was not found or does not exist

$ vecscreen -d UniVec_Core -i tmp/test.fna
<HTML>
<TITLE>VecScreen Search Results</TITLE>
<BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
<PRE><b>BLASTN 2.2.26 [Sep-21-2011]</b>

<a
href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids
=9254694&dopt=Citation">Reference</a>:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.

<b>Query=</b> test
         (22 letters)

<B> ****** No hits found ******</B>

[vecscreen] FATAL ERROR: Database UniVec_Core was not found or does not exist

$ vecscreen -d /usr/share/ncbi/data/UniVec_Core -i tmp/test.fna
<HTML>
<TITLE>VecScreen Search Results</TITLE>
<BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
<PRE><b>BLASTN 2.2.26 [Sep-21-2011]</b>

<a
href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids
=9254694&dopt=Citation">Reference</a>:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.

<b>Query=</b> test
         (22 letters)

<b>Database:</b> UniVec_Core (build 9.0)
           2822 sequences; 536,102 total letters

<B> ****** No hits found ******</B>

</PRE>
<PRE>
  Database: UniVec_Core (build 9.0)
    Posted date:  Mar 9, 2015  3:05 PM
  Number of letters in database: 536,102
  Number of sequences in database:  2822

Lambda     K      H
    1.39    0.747     1.38

Gapped
Lambda     K      H
    1.39    0.747     1.38

Matrix: blastn matrix:1 -5
Gap Penalties: Existence: 3, Extension: 3
Number of Hits to DB: 2
Number of Sequences: 2822
Number of extensions: 2
Number of successful extensions: 2
Number of sequences better than 700.0: 0
Number of HSP's better than 700.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1
Number of HSP's gapped (non-prelim): 0
length of query: 22
length of database: 536,102
effective HSP length: 10
effective length of query: 12
effective length of database: 507,882
effective search space:  6094584
effective search space used: 1750000000000
T: 0
A: 0
X1: 11 (22.0 bits)
X2: 15 (30.0 bits)
S1: 12 (24.4 bits)
S2: 7 (14.5 bits)
</PRE>

</BODY>
</HTML>

-- System Information:
Debian Release: 13.1
  APT prefers stable-updates
  APT policy: (500, 'stable-updates'), (500, 'stable-security'), (500, 'proposed-updates'), (500, 'oldstable-updates'), (500, 'oldstable-security'), (500, 'oldstable-proposed-updates'), (500, 'stable'), (500, 'oldstable')
Architecture: amd64 (x86_64)

Kernel: Linux 6.16.3+deb13-amd64 (SMP w/128 CPU threads; PREEMPT)
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages ncbi-tools-bin depends on:
ii  libc6        2.41-12
ii  libncbi6t64  6.1.20170106+dfsg2-6

ncbi-tools-bin recommends no packages.

Versions of packages ncbi-tools-bin suggests:
ii  libvibrant6t64  6.1.20170106+dfsg2-6
ii  ncbi-blast+     2.16.0+ds-7
ii  ncbi-cn3d       3.0.20170106+dfsg2-6
ii  ncbi-tools-x11  6.1.20170106+dfsg2-6

-- no debconf information