I use update_blastdb.pl to update nr database, and problem come out

Question

[zoukai3412085]

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

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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!

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

[lieven.sterck]

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

[h.mon]

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.

[zoukai3412085]

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.

[lieven.sterck]

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