Question: I use update_blastdb.pl to update nr database, and problem come out
0
gravatar for zoukai3412085
16 days ago by
zoukai34120850 wrote:

when I use update_blastdb.pl to update the latest version of nr database, it always reports an error:

#

nr.69.tar.gz is up to date.

nr.70.tar.gz is up to date.

nr.71.tar.gz is up to date.

nr.72.tar.gz is up to date.

nr.73.tar.gz is up to date.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 307.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 309.

nr.74.tar.gz is up to date.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 307.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 309.

nr.75.tar.gz is up to date.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 307.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 309.

nr.76.tar.gz is up to date.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 307.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 309.

nr.77.tar.gz is up to date.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 307.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 309.

nr.78.tar.gz is up to date.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 307.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 309.

nr.79.tar.gz is up to date.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 307.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 309.

nr.80.tar.gz is up to date.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 307.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 309.

nr.81.tar.gz is up to date.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 307.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 309.

nr.82.tar.gz is up to date.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 307.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 309.

nr.83.tar.gz is up to date.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 307.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 309.

nr.84.tar.gz is up to date.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 307.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 309.

nr.85.tar.gz is up to date.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 307.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 309.

nr.86.tar.gz is up to date.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 307.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 309.

nr.87.tar.gz is up to date.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 307.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 309.

nr.88.tar.gz is up to date.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 307.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 309.

nr.89.tar.gz is up to date.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 307.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 309.

nr.90.tar.gz is up to date.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 307.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 309.

nr.91.tar.gz is up to date.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 307.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 309.

nr.92.tar.gz is up to date.

Use of uninitialized value in numeric lt (<) at /home/zoukai/miniconda3/bin/update_blastdb.pl line 309.

Downloading nr.93.tar.gz...Failed to download nr.93.tar.gz.md5!

#

I tried all the methods I know to solve, but I failed. Can anyone help me to solve this problem? Thank you!

blast • 90 views
ADD COMMENTlink modified 16 days ago • written 16 days ago by zoukai34120850

did you have a look at what it tries to do at the lines it reports (in the update_blastdb.pl script)?

ADD REPLYlink written 16 days ago by lieven.sterck6.4k

Please provide command-line used, and version of BLAST+ used.

As a side note, the PATH to the update_blastdb.pl script suggests you installed BLAST+ at the root of your conda install, you should seriously consider creating separate conda environments to install different programs.

ADD REPLYlink written 16 days ago by h.mon28k

yes, I use conda install to install blast at the root account. but I have not creat new conda environment, and install it at the defult environment, always like that.

ADD REPLYlink written 10 days ago by zoukai34120850

few things to check:

  • Has it been a while since you last updated the DB?
  • Does it reports this from the very first files or only after a while?
  • Does it run for a long time? (might be your connection is disrupted, cfr previous question) ?

you can also try to run it with the option -force, to force it to download all files again

ADD REPLYlink written 10 days ago by lieven.sterck6.4k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1892 users visited in the last hour