Question: How to decompress the nr database from NCBI
0
gravatar for albagg1396
4 months ago by
albagg13960
albagg13960 wrote:

Hi everyone,

I've downloaded the NR database from NCBI databases to perform a local alignment using the update_blastdb.pl script and trying at the same time to decompress the files generated during the downloaded. This is the output:

perl update_blastdb.pl --decompress nr 
Connected to NCBI
Downloading nr (39 volumes) ...
Downloading nr.01.tar.gz... [OK]
Downloading nr.02.tar.gz... [OK]
Downloading nr.03.tar.gz... [OK]
Downloading nr.04.tar.gz... [OK]
Downloading nr.05.tar.gz... [OK]
Downloading nr.06.tar.gz... [OK]
Downloading nr.07.tar.gz... [OK]
Downloading nr.08.tar.gz... [OK]
Downloading nr.09.tar.gz... [OK]
Downloading nr.10.tar.gz... [OK]
Downloading nr.11.tar.gz... [OK]
Downloading nr.12.tar.gz... [OK]
Downloading nr.13.tar.gz... [OK]
Downloading nr.14.tar.gz... [OK]
Downloading nr.15.tar.gz... [OK]
Downloading nr.16.tar.gz... [OK]
Downloading nr.17.tar.gz... [OK]
Downloading nr.18.tar.gz... [OK]
Downloading nr.19.tar.gz... [OK]
Downloading nr.20.tar.gz... [OK]
Downloading nr.21.tar.gz... [OK]
Downloading nr.22.tar.gz... [OK]
Downloading nr.23.tar.gz... [OK]
Downloading nr.24.tar.gz... [OK]
Downloading nr.25.tar.gz... [OK]
Downloading nr.26.tar.gz... [OK]
Downloading nr.27.tar.gz... [OK]
Downloading nr.28.tar.gz... [OK]
Downloading nr.29.tar.gz... [OK]
Downloading nr.30.tar.gz... [OK]
Downloading nr.31.tar.gz... [OK]
Downloading nr.32.tar.gz... [OK]
Downloading nr.33.tar.gz... [OK]
Downloading nr.34.tar.gz... [OK]
Downloading nr.35.tar.gz... [OK]
Downloading nr.36.tar.gz... [OK]
Downloading nr.37.tar.gz... [OK]
Downloading nr.38.tar.gz... [OK]
Decompressing nr.00.tar.gz ...Read error on tarfile (missing data) 'nr.pdb' at offset unknown at update_blastdb.pl line 412.
 [OK]
Decompressing nr.01.tar.gz ... [OK]
Decompressing nr.02.tar.gz ... [OK]
Decompressing nr.03.tar.gz ... [OK]
Decompressing nr.04.tar.gz ... [OK]
Decompressing nr.05.tar.gz ... [OK]
Decompressing nr.06.tar.gz ... [OK]
Decompressing nr.07.tar.gz ... [OK]
Decompressing nr.08.tar.gz ... [OK]
Decompressing nr.09.tar.gz ... [OK]
Decompressing nr.10.tar.gz ... [OK]
Decompressing nr.11.tar.gz ... [OK]
Decompressing nr.12.tar.gz ... [OK]
Decompressing nr.13.tar.gz ... [OK]
Decompressing nr.14.tar.gz ... [OK]
Decompressing nr.15.tar.gz ... [OK]
Decompressing nr.16.tar.gz ... [OK]
Decompressing nr.17.tar.gz ... [OK]
Decompressing nr.18.tar.gz ... [OK]
Decompressing nr.19.tar.gz ... [OK]
Decompressing nr.20.tar.gz ... [OK]
Decompressing nr.21.tar.gz ... [OK]
Decompressing nr.22.tar.gz ... [OK]
Decompressing nr.23.tar.gz ... [OK]
Decompressing nr.24.tar.gz ... [OK]
Decompressing nr.25.tar.gz ...Could not write data to '/home/i2sysbio/ncbi-blast-2.10.1+/bin/nr.25.ppi' at update_blastdb.pl line 412.
Failed to decompress nr.25.tar.gz (Could not write data to '/home/i2sysbio/ncbi-blast-2.10.1+/bin/nr.25.ppi'), please do so manually.
Decompressing nr.26.tar.gz ...Could not write data to '/home/i2sysbio/ncbi-blast-2.10.1+/bin/nr.26.pin' at update_blastdb.pl line 412.
Failed to decompress nr.26.tar.gz (Could not write data to '/home/i2sysbio/ncbi-blast-2.10.1+/bin/nr.26.pin'), please do so manually.
Decompressing nr.27.tar.gz ...Could not write data to '/home/i2sysbio/ncbi-blast-2.10.1+/bin/nr.27.pin' at update_blastdb.pl line 412.
Failed to decompress nr.27.tar.gz (Could not write data to '/home/i2sysbio/ncbi-blast-2.10.1+/bin/nr.27.pin'), please do so manually.
Decompressing nr.28.tar.gz ...Could not write data to '/home/i2sysbio/ncbi-blast-2.10.1+/bin/nr.28.pin' at update_blastdb.pl line 412.
Failed to decompress nr.28.tar.gz (Could not write data to '/home/i2sysbio/ncbi-blast-2.10.1+/bin/nr.28.pin'), please do so manually.
Decompressing nr.29.tar.gz ...Could not write data to '/home/i2sysbio/ncbi-blast-2.10.1+/bin/nr.29.pin' at update_blastdb.pl line 412.
Failed to decompress nr.29.tar.gz (Could not write data to '/home/i2sysbio/ncbi-blast-2.10.1+/bin/nr.29.pin'), please do so manually.
Decompressing nr.30.tar.gz ...Could not write data to '/home/i2sysbio/ncbi-blast-2.10.1+/bin/nr.30.pin' at update_blastdb.pl line 412.
Failed to decompress nr.30.tar.gz (Could not write data to '/home/i2sysbio/ncbi-blast-2.10.1+/bin/nr.30.pin'), please do so manually.
Decompressing nr.31.tar.gz ...Could not write data to '/home/i2sysbio/ncbi-blast-2.10.1+/bin/nr.31.pin' at update_blastdb.pl line 412.
Failed to decompress nr.31.tar.gz (Could not write data to '/home/i2sysbio/ncbi-blast-2.10.1+/bin/nr.31.pin'), please do so manually.
Decompressing nr.32.tar.gz ...Could not write data to '/home/i2sysbio/ncbi-blast-2.10.1+/bin/nr.32.pin' at update_blastdb.pl line 412.
Failed to decompress nr.32.tar.gz (Could not write data to '/home/i2sysbio/ncbi-blast-2.10.1+/bin/nr.32.pin'), please do so manually.
Decompressing nr.33.tar.gz ...Could not write data to '/home/i2sysbio/ncbi-blast-2.10.1+/bin/nr.33.pin' at update_blastdb.pl line 412.
Failed to decompress nr.33.tar.gz (Could not write data to '/home/i2sysbio/ncbi-blast-2.10.1+/bin/nr.33.pin'), please do so manually.
Decompressing nr.34.tar.gz ...Could not write data to '/home/i2sysbio/ncbi-blast-2.10.1+/bin/nr.34.pin' at update_blastdb.pl line 412.
Failed to decompress nr.34.tar.gz (Could not write data to '/home/i2sysbio/ncbi-blast-2.10.1+/bin/nr.34.pin'), please do so manually.
Decompressing nr.35.tar.gz ...Could not write data to '/home/i2sysbio/ncbi-blast-2.10.1+/bin/nr.35.pin' at update_blastdb.pl line 412.
Failed to decompress nr.35.tar.gz (Could not write data to '/home/i2sysbio/ncbi-blast-2.10.1+/bin/nr.35.pin'), please do so manually.
Decompressing nr.36.tar.gz ...Could not write data to '/home/i2sysbio/ncbi-blast-2.10.1+/bin/nr.36.pin' at update_blastdb.pl line 412.
Failed to decompress nr.36.tar.gz (Could not write data to '/home/i2sysbio/ncbi-blast-2.10.1+/bin/nr.36.pin'), please do so manually.
Decompressing nr.37.tar.gz ...Could not write data to '/home/i2sysbio/ncbi-blast-2.10.1+/bin/nr.37.pin' at update_blastdb.pl line 412.
Failed to decompress nr.37.tar.gz (Could not write data to '/home/i2sysbio/ncbi-blast-2.10.1+/bin/nr.37.pin'), please do so manually.
Decompressing nr.38.tar.gz ...Could not write data to '/home/i2sysbio/ncbi-blast-2.10.1+/bin/nr.38.pin' at update_blastdb.pl line 412.
Failed to decompress nr.38.tar.gz (Could not write data to '/home/i2sysbio/ncbi-blast-2.10.1+/bin/nr.38.pin'), please do so manually.

The problem is that during the decompression process I've obtained several errors related to the line 412 of the script, but I don't know indeed which is the mistake.

Thank you. Alba

genbank blast local ncbi • 237 views
ADD COMMENTlink modified 4 months ago by GenoMax95k • written 4 months ago by albagg13960

Do you have enough local disk space available? nr requires 300G+ as I recall. Since the first 24 files decompressed fine most likely cause is related to storage.

ADD REPLYlink modified 4 months ago • written 4 months ago by GenoMax95k
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