Open AJTDaedalus opened 2 years ago
I got a similar error message
$ krakenuniq-download --db SOMEWHERE/db/ --dust microbial-nt
Storing taxonomy timestamp [date > SOMEWHERE ] ... done (took 0s)
Extracting nodes file [tar -C SOMWHERE/db//taxonomy -zxvf SOMEWHERE/db//taxonomy/taxdump.tar.gz nodes.dmp 1>&2] ...nodes.dmp
done (took 6s)
SOMEWHERE/db//taxonomy/nodes.dmp check [163.80 MB]
Extracting names file [tar -C SOMEWHERE/db//taxonomy -zxvf SOMEWHERE/db//taxonomy/taxdump.tar.gz names.dmp 1>&2] ...names.dmp
done (took 4s)
SOMEWHERE/db//taxonomy/names.dmp check [219.76 MB]
: downloading ...Content-length mismatch: expected 279998465077 bytes, got 280000205317
Redid with --verbose
option, the download URL is ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nt.gz
, the size is indeed 279998465077. My colleagues and I tried this a few times and got the same message (but the "got" sizes slight different).
In my case, I think the problem was due to downloading the ftp* URL by using the perl module. The following change downloaded correct size and get into GUNZIPPING step.
$ diff krakenuniq-download krakenuniq-download.bck
344c344
< if ($url =~ /^http/ || $url =~ /^ftp/) {
---
> if ($url =~ /^http/) {
$ krakenuniq-download --verbose --db SOMEWHERE/db --dust microbial-nt
Fetching ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz to SOMEWHERE/db/taxonomy/taxdump.tar.gz ... % Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 57.9M 100 57.9M 0 0 6476k 0 0:00:09 0:00:09 --:--:-- 11.2M
SUCCESS
Storing taxonomy timestamp [date > SOMEWHERE/db/taxonomy/timestamp] ... done (took 0s)
Extracting nodes file [tar -C SOMEWHERE/db/taxonomy -zxvf SOMEWHERE/db/taxonomy/taxdump.tar.gz nodes.dmp 1>&2] ...nodes.dmp
done (took 3s)
SOMEWHERE/db/taxonomy/nodes.dmp check [163.81 MB]
Extracting names file [tar -C SOMEWHERE/db/taxonomy -zxvf SOMEWHERE/db/taxonomy/taxdump.tar.gz names.dmp 1>&2] ...names.dmp
done (took 4s)
SOMEWHERE/db/taxonomy/names.dmp check [219.79 MB]
Fetching ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nt.gz to SOMEWHERE/db/nt.fna.gz ... % Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 260G 100 260G 0 0 13.7M 0 5:24:08 5:24:08 --:--:-- 13.6M
GUNZIPPING
When running krakenuniq-download I get the error below. I've also included my arguments for context. It seems like I'm getting more from NCBI than the program expects.