The -i paremeter doesn't work should be -incomplete

[timothyjlaurent]

This confused someone in the lab (including me)

Thanks for the software

[mlangill]

Could you specify what script this is failing with?

I have just tested:
./download_load_and_delete_old_version.pl -d ~/tmp/ -s '-i'

and

./download_version.pl -d /home/mlangill/tmp/ -s Escherichia_coli -i

and they were both successful (note the -i has to be in quotes in the first case).

Glad MicrobeDB is working for you!

[timothyjlaurent]

On Wed, Nov 6, 2013 at 11:26 AM, Morgan Langille
[email protected]:

./download_version.pl

-d /home/mlangill/tmp/ -s Escherichia_coli -i

ok so I guess it does work --- well almost.

laurentt@shattuck:~/MicrobeDB/scripts$ ./download_version.pl -d ~/tmp/ -s
Escherichia_coli -o
2013/11/06 12:11:13> Using FTP to download since --search,--incomplete,
and/or --only_incomplete option(s) selected.
2013/11/06 12:11:13> Downloading files to directory:
/mnt/data/home/laurentt/tmp/
2013/11/06 12:11:13> Note: NCBI has removed their metadata files. We are
looking for another source of metadata information, but until then we can
only use metadata for genomes fr
om before June, 2012.
2013/11/06 12:11:13> Downloading file:
/mnt/data/home/laurentt/tmp/NCBI_orginfo.txt from Dropbox at:
http://dl.dropbox.com/u/5329340/NCBI_orginfo.txt
2013/11/06 12:11:15> Downloading file:
/mnt/data/home/laurentt/tmp/NCBI_completegenomes.txt from Dropbox at:
http://dl.dropbox.com/u/5329340/NCBI_completegenomes.txt
2013/11/06 12:11:17> Downloading genomes using FTP option
2013/11/06 12:11:17> Downloading draft genomes now.
2013/11/06 12:11:22> Found 683 draft genomes that matched the search:
Escherichia_coli
2013/11/06 12:11:22> Downloading genome: Escherichia_coli_07798_uid181911
2013/11/06 12:11:23> Downloading genome:
Escherichia_coli_09BKT078844_uid188354
2013/11/06 12:11:24> Downloading genome: Escherichia_coli_0_1288_uid181931
2013/11/06 12:11:26> Downloading genome: Escherichia_coli_0_1304_uid181932
2013/11/06 12:11:27> Downloading genome: Escherichia_coli_101_1_uid54363
2013/11/06 12:11:28> Downloading genome: Escherichia_coli_10_0821_uid180960
2013/11/06 12:11:30> Downloading genome: Escherichia_coli_10_0833_uid181884

So this looks promising ( I did the entire set of almost 7k last night)
however in the directory there aren't any files :

laurentt@shattuck:/tmp$ cd Escherichia_coli_07798_uid181911
laurentt@shattuck:/tmp/Escherichia_coli_07798_uid181911$ ll
total 28K
drwxr-xr-x 2 laurentt lsd 4.0K Nov 6 12:11 ./
drwxr-xr-x 251 laurentt lsd 20K Nov 6 12:16 ../
-rw-r--r-- 1 laurentt lsd 1.4K Nov 6 12:11 .listing
laurentt@shattuck:~/tmp/Escherichia_coli_07798_uid181911$ cat .listing
-r--r--r-- 1 ftp anonymous 11422 Nov 29 2012 NZ_AMUP00000000.asn
-r--r--r-- 1 ftp anonymous 2675 Dec 11 2012 NZ_AMUP00000000.gbk
-r--r--r-- 1 ftp anonymous 261 Dec 29 2012 NZ_AMUP00000000.rpt
-r--r--r-- 1 ftp anonymous 1600657 Apr 29 2013
NZ_AMUP00000000.scaffold.asn.tgz
-r--r--r-- 1 ftp anonymous 986551 Apr 29 2013
NZ_AMUP00000000.scaffold.faa.tgz
-r--r--r-- 1 ftp anonymous 1411297 Apr 29 2013
NZ_AMUP00000000.scaffold.ffn.tgz
-r--r--r-- 1 ftp anonymous 1537698 Apr 29 2013
NZ_AMUP00000000.scaffold.fna.tgz
-r--r--r-- 1 ftp anonymous 5473 Apr 29 2013
NZ_AMUP00000000.scaffold.frn.tgz
-r--r--r-- 1 ftp anonymous 4373167 Apr 29 2013
NZ_AMUP00000000.scaffold.gbk.tgz
-r--r--r-- 1 ftp anonymous 17831 Apr 29 2013
NZ_AMUP00000000.scaffold.gbs.tgz
-r--r--r-- 1 ftp anonymous 275197 Apr 29 2013
NZ_AMUP00000000.scaffold.gff.tgz
-r--r--r-- 1 ftp anonymous 140729 Apr 29 2013
NZ_AMUP00000000.scaffold.ptt.tgz
-r--r--r-- 1 ftp anonymous 2608 Apr 29 2013
NZ_AMUP00000000.scaffold.rnt.tgz
-r--r--r-- 1 ftp anonymous 7096 Apr 29 2013
NZ_AMUP00000000.scaffold.rpt.tgz
-r--r--r-- 1 ftp anonymous 1445811 Apr 29 2013
NZ_AMUP00000000.scaffold.val.tgz
-r--r--r-- 1 ftp anonymous 4372 Nov 29 2012 NZ_AMUP00000000.val

Do you have any idea why this is happening?

Thanks for your help, we' love to get this up and running.

BTW, Morgan, this is for Katie Pollard's Lab. I understand that you are a
former iSEEM member -- We previously had an updater pipeline to mirror the
JGI's IMG database, but they have since restricted headless access to the
database.

One more thing of note -- below is the terminal output after lastnight's
run, before I know that I didn't have the genomes.
Notice that it says: "Downloading REFSEQ genomes now" and then there is no
listing of the individual genomes before going on the the draft genomes.

aurentt@shattuck:~/MicrobeDB/scripts$ ./
download_load_and_delete_old_version.pl -d
/mnt/data/work/pollardlab/MicrobeDB_test/ -s '-incomplete -t
faa,fna,gbk,ffn'
2013/11/06 11:16:33> Making download directory:
/mnt/data/work/pollardlab/MicrobeDB_test/Bacteria_2013-11-06
2013/11/06 11:16:33> Downloading all genomes from NCBI.(Downloading time
will vary depending on your connection and how flaky NCBI is today; (10
minutes to a few hours))
2013/11/06 11:16:34> Using FTP to download since --search,--incomplete,
and/or --only_incomplete option(s) selected.
2013/11/06 11:16:34> Downloading files to directory:
/mnt/data/work/pollardlab/MicrobeDB_test/Bacteria_2013-11-06/
2013/11/06 11:16:34> Note: NCBI has removed their metadata files. We are
looking for another source of metadata information, but until then we can
only use metadata for genomes fr
om before June, 2012.
2013/11/06 11:16:34> Downloading file:
/mnt/data/work/pollardlab/MicrobeDB_test/Bacteria_2013-11-06/NCBI_orginfo.txt
from Dropbox at: http://dl.dropbox.com/u/5329340/NCBI_orginfo.
txt
2013/11/06 11:16:35> Downloading file:
/mnt/data/work/pollardlab/MicrobeDB_test/Bacteria_2013-11-06/NCBI_completegenomes.txt
from Dropbox at: http://dl.dropbox.com/u/5329340/NCBI_
completegenomes.txt
2013/11/06 11:16:37> Downloading genomes using FTP option
2013/11/06 11:16:37> Downloading RefSeq genomes now.
2013/11/06 11:30:26> Downloading draft genomes now.
2013/11/06 11:30:31> Downloading genome:
Acaricomes_phytoseiuli_DSM_14247_uid199097
2013/11/06 11:30:38> Downloading genome: Acaryochloris_CCMEE_5410_uid78283

Anyways I'd be happy to help to fix this in any way I can to get it working
for us.
Please let me know things I could try or parts of the code that could be
altered to get this working.

Best,

Timothy Laurent

[timothyjlaurent]

Oh I think I see now. All the sequences are in the tar.gz files. then I
unpack them and add to database?

Ok that works!

Thanks for indulging me and for your nice software.

-Tim

On Wed, Nov 6, 2013 at 12:30 PM, Timothy Laurent
[email protected]:

On Wed, Nov 6, 2013 at 11:26 AM, Morgan Langille <[email protected]

wrote:

./download_version.pl

-d /home/mlangill/tmp/ -s Escherichia_coli -i

ok so I guess it does work --- well almost.

laurentt@shattuck:~/MicrobeDB/scripts$ ./download_version.pl -d ~/tmp/
-s Escherichia_coli -o
2013/11/06 12:11:13> Using FTP to download since --search,--incomplete,
and/or --only_incomplete option(s) selected.
2013/11/06 12:11:13> Downloading files to directory:
/mnt/data/home/laurentt/tmp/
2013/11/06 12:11:13> Note: NCBI has removed their metadata files. We are
looking for another source of metadata information, but until then we can
only use metadata for genomes fr
om before June, 2012.
2013/11/06 12:11:13> Downloading file:
/mnt/data/home/laurentt/tmp/NCBI_orginfo.txt from Dropbox at:
http://dl.dropbox.com/u/5329340/NCBI_orginfo.txt
2013/11/06 12:11:15> Downloading file:
/mnt/data/home/laurentt/tmp/NCBI_completegenomes.txt from Dropbox at:
http://dl.dropbox.com/u/5329340/NCBI_completegenomes.txt
2013/11/06 12:11:17> Downloading genomes using FTP option
2013/11/06 12:11:17> Downloading draft genomes now.
2013/11/06 12:11:22> Found 683 draft genomes that matched the search:
Escherichia_coli
2013/11/06 12:11:22> Downloading genome: Escherichia_coli_07798_uid181911
2013/11/06 12:11:23> Downloading genome:
Escherichia_coli_09BKT078844_uid188354
2013/11/06 12:11:24> Downloading genome: Escherichia_coli_0_1288_uid181931
2013/11/06 12:11:26> Downloading genome: Escherichia_coli_0_1304_uid181932
2013/11/06 12:11:27> Downloading genome: Escherichia_coli_101_1_uid54363
2013/11/06 12:11:28> Downloading genome: Escherichia_coli_10_0821_uid180960
2013/11/06 12:11:30> Downloading genome: Escherichia_coli_10_0833_uid181884

So this looks promising ( I did the entire set of almost 7k last night)
however in the directory there aren't any files :

laurentt@shattuck:/tmp$ cd Escherichia_coli_07798_uid181911
laurentt@shattuck:/tmp/Escherichia_coli_07798_uid181911$ ll
total 28K
drwxr-xr-x 2 laurentt lsd 4.0K Nov 6 12:11 ./
drwxr-xr-x 251 laurentt lsd 20K Nov 6 12:16 ../
-rw-r--r-- 1 laurentt lsd 1.4K Nov 6 12:11 .listing
laurentt@shattuck:~/tmp/Escherichia_coli_07798_uid181911$ cat .listing
-r--r--r-- 1 ftp anonymous 11422 Nov 29 2012 NZ_AMUP00000000.asn
-r--r--r-- 1 ftp anonymous 2675 Dec 11 2012 NZ_AMUP00000000.gbk
-r--r--r-- 1 ftp anonymous 261 Dec 29 2012 NZ_AMUP00000000.rpt
-r--r--r-- 1 ftp anonymous 1600657 Apr 29 2013
NZ_AMUP00000000.scaffold.asn.tgz
-r--r--r-- 1 ftp anonymous 986551 Apr 29 2013
NZ_AMUP00000000.scaffold.faa.tgz
-r--r--r-- 1 ftp anonymous 1411297 Apr 29 2013
NZ_AMUP00000000.scaffold.ffn.tgz
-r--r--r-- 1 ftp anonymous 1537698 Apr 29 2013
NZ_AMUP00000000.scaffold.fna.tgz
-r--r--r-- 1 ftp anonymous 5473 Apr 29 2013
NZ_AMUP00000000.scaffold.frn.tgz
-r--r--r-- 1 ftp anonymous 4373167 Apr 29 2013
NZ_AMUP00000000.scaffold.gbk.tgz
-r--r--r-- 1 ftp anonymous 17831 Apr 29 2013
NZ_AMUP00000000.scaffold.gbs.tgz
-r--r--r-- 1 ftp anonymous 275197 Apr 29 2013
NZ_AMUP00000000.scaffold.gff.tgz
-r--r--r-- 1 ftp anonymous 140729 Apr 29 2013
NZ_AMUP00000000.scaffold.ptt.tgz
-r--r--r-- 1 ftp anonymous 2608 Apr 29 2013
NZ_AMUP00000000.scaffold.rnt.tgz
-r--r--r-- 1 ftp anonymous 7096 Apr 29 2013
NZ_AMUP00000000.scaffold.rpt.tgz
-r--r--r-- 1 ftp anonymous 1445811 Apr 29 2013
NZ_AMUP00000000.scaffold.val.tgz
-r--r--r-- 1 ftp anonymous 4372 Nov 29 2012 NZ_AMUP00000000.val

Do you have any idea why this is happening?

Thanks for your help, we' love to get this up and running.

BTW, Morgan, this is for Katie Pollard's Lab. I understand that you are a
former iSEEM member -- We previously had an updater pipeline to mirror the
JGI's IMG database, but they have since restricted headless access to the
database.

One more thing of note -- below is the terminal output after lastnight's
run, before I know that I didn't have the genomes.
Notice that it says: "Downloading REFSEQ genomes now" and then there is no
listing of the individual genomes before going on the the draft genomes.

aurentt@shattuck:~/MicrobeDB/scripts$ ./
download_load_and_delete_old_version.pl -d
/mnt/data/work/pollardlab/MicrobeDB_test/ -s '-incomplete -t
faa,fna,gbk,ffn'
2013/11/06 11:16:33> Making download directory:
/mnt/data/work/pollardlab/MicrobeDB_test/Bacteria_2013-11-06
2013/11/06 11:16:33> Downloading all genomes from NCBI.(Downloading time
will vary depending on your connection and how flaky NCBI is today; (10
minutes to a few hours))
2013/11/06 11:16:34> Using FTP to download since --search,--incomplete,
and/or --only_incomplete option(s) selected.
2013/11/06 11:16:34> Downloading files to directory:
/mnt/data/work/pollardlab/MicrobeDB_test/Bacteria_2013-11-06/
2013/11/06 11:16:34> Note: NCBI has removed their metadata files. We are
looking for another source of metadata information, but until then we can
only use metadata for genomes fr
om before June, 2012.
2013/11/06 11:16:34> Downloading file:
/mnt/data/work/pollardlab/MicrobeDB_test/Bacteria_2013-11-06/NCBI_orginfo.txt
from Dropbox at: http://dl.dropbox.com/u/5329340/NCBI_orginfo.
txt
2013/11/06 11:16:35> Downloading file:
/mnt/data/work/pollardlab/MicrobeDB_test/Bacteria_2013-11-06/NCBI_completegenomes.txt
from Dropbox at: http://dl.dropbox.com/u/5329340/NCBI_
completegenomes.txt
2013/11/06 11:16:37> Downloading genomes using FTP option
2013/11/06 11:16:37> Downloading RefSeq genomes now.
2013/11/06 11:30:26> Downloading draft genomes now.
2013/11/06 11:30:31> Downloading genome:
Acaricomes_phytoseiuli_DSM_14247_uid199097
2013/11/06 11:30:38> Downloading genome: Acaryochloris_CCMEE_5410_uid78283

Anyways I'd be happy to help to fix this in any way I can to get it
working for us.
Please let me know things I could try or parts of the code that could be
altered to get this working.

Best,

Timothy Laurent

Timothy Laurent

[timothyjlaurent]

Ok I'm still confused -- I'm not getting the genome files I want in the
directories. I am running some controlled tests now and will report back
when I have results.

On Wed, Nov 6, 2013 at 12:43 PM, Timothy Laurent
[email protected]:

Oh I think I see now. All the sequences are in the tar.gz files. then I
unpack them and add to database?

Ok that works!

Thanks for indulging me and for your nice software.

-Tim

On Wed, Nov 6, 2013 at 12:30 PM, Timothy Laurent <
[email protected]> wrote:

On Wed, Nov 6, 2013 at 11:26 AM, Morgan Langille <
[email protected]> wrote:

./download_version.pl

-d /home/mlangill/tmp/ -s Escherichia_coli -i

ok so I guess it does work --- well almost.

laurentt@shattuck:~/MicrobeDB/scripts$ ./download_version.pl -d ~/tmp/
-s Escherichia_coli -o
2013/11/06 12:11:13> Using FTP to download since --search,--incomplete,
and/or --only_incomplete option(s) selected.
2013/11/06 12:11:13> Downloading files to directory:
/mnt/data/home/laurentt/tmp/
2013/11/06 12:11:13> Note: NCBI has removed their metadata files. We are
looking for another source of metadata information, but until then we can
only use metadata for genomes fr
om before June, 2012.
2013/11/06 12:11:13> Downloading file:
/mnt/data/home/laurentt/tmp/NCBI_orginfo.txt from Dropbox at:
http://dl.dropbox.com/u/5329340/NCBI_orginfo.txt
2013/11/06 12:11:15> Downloading file:
/mnt/data/home/laurentt/tmp/NCBI_completegenomes.txt from Dropbox at:
http://dl.dropbox.com/u/5329340/NCBI_completegenomes.txt
2013/11/06 12:11:17> Downloading genomes using FTP option
2013/11/06 12:11:17> Downloading draft genomes now.
2013/11/06 12:11:22> Found 683 draft genomes that matched the search:
Escherichia_coli
2013/11/06 12:11:22> Downloading genome: Escherichia_coli_07798_uid181911
2013/11/06 12:11:23> Downloading genome:
Escherichia_coli_09BKT078844_uid188354
2013/11/06 12:11:24> Downloading genome: Escherichia_coli_0_1288_uid181931
2013/11/06 12:11:26> Downloading genome: Escherichia_coli_0_1304_uid181932
2013/11/06 12:11:27> Downloading genome: Escherichia_coli_101_1_uid54363
2013/11/06 12:11:28> Downloading genome:
Escherichia_coli_10_0821_uid180960
2013/11/06 12:11:30> Downloading genome:
Escherichia_coli_10_0833_uid181884

So this looks promising ( I did the entire set of almost 7k last night)
however in the directory there aren't any files :

laurentt@shattuck:/tmp$ cd Escherichia_coli_07798_uid181911
laurentt@shattuck:/tmp/Escherichia_coli_07798_uid181911$ ll
total 28K
drwxr-xr-x 2 laurentt lsd 4.0K Nov 6 12:11 ./
drwxr-xr-x 251 laurentt lsd 20K Nov 6 12:16 ../
-rw-r--r-- 1 laurentt lsd 1.4K Nov 6 12:11 .listing
laurentt@shattuck:~/tmp/Escherichia_coli_07798_uid181911$ cat .listing
-r--r--r-- 1 ftp anonymous 11422 Nov 29 2012
NZ_AMUP00000000.asn
-r--r--r-- 1 ftp anonymous 2675 Dec 11 2012
NZ_AMUP00000000.gbk
-r--r--r-- 1 ftp anonymous 261 Dec 29 2012
NZ_AMUP00000000.rpt
-r--r--r-- 1 ftp anonymous 1600657 Apr 29 2013
NZ_AMUP00000000.scaffold.asn.tgz
-r--r--r-- 1 ftp anonymous 986551 Apr 29 2013
NZ_AMUP00000000.scaffold.faa.tgz
-r--r--r-- 1 ftp anonymous 1411297 Apr 29 2013
NZ_AMUP00000000.scaffold.ffn.tgz
-r--r--r-- 1 ftp anonymous 1537698 Apr 29 2013
NZ_AMUP00000000.scaffold.fna.tgz
-r--r--r-- 1 ftp anonymous 5473 Apr 29 2013
NZ_AMUP00000000.scaffold.frn.tgz
-r--r--r-- 1 ftp anonymous 4373167 Apr 29 2013
NZ_AMUP00000000.scaffold.gbk.tgz
-r--r--r-- 1 ftp anonymous 17831 Apr 29 2013
NZ_AMUP00000000.scaffold.gbs.tgz
-r--r--r-- 1 ftp anonymous 275197 Apr 29 2013
NZ_AMUP00000000.scaffold.gff.tgz
-r--r--r-- 1 ftp anonymous 140729 Apr 29 2013
NZ_AMUP00000000.scaffold.ptt.tgz
-r--r--r-- 1 ftp anonymous 2608 Apr 29 2013
NZ_AMUP00000000.scaffold.rnt.tgz
-r--r--r-- 1 ftp anonymous 7096 Apr 29 2013
NZ_AMUP00000000.scaffold.rpt.tgz
-r--r--r-- 1 ftp anonymous 1445811 Apr 29 2013
NZ_AMUP00000000.scaffold.val.tgz
-r--r--r-- 1 ftp anonymous 4372 Nov 29 2012
NZ_AMUP00000000.val

Do you have any idea why this is happening?

Thanks for your help, we' love to get this up and running.

BTW, Morgan, this is for Katie Pollard's Lab. I understand that you are a
former iSEEM member -- We previously had an updater pipeline to mirror the
JGI's IMG database, but they have since restricted headless access to the
database.

One more thing of note -- below is the terminal output after lastnight's
run, before I know that I didn't have the genomes.
Notice that it says: "Downloading REFSEQ genomes now" and then there is
no listing of the individual genomes before going on the the draft genomes.

aurentt@shattuck:~/MicrobeDB/scripts$ ./
download_load_and_delete_old_version.pl -d
/mnt/data/work/pollardlab/MicrobeDB_test/ -s '-incomplete -t
faa,fna,gbk,ffn'
2013/11/06 11:16:33> Making download directory:
/mnt/data/work/pollardlab/MicrobeDB_test/Bacteria_2013-11-06
2013/11/06 11:16:33> Downloading all genomes from NCBI.(Downloading time
will vary depending on your connection and how flaky NCBI is today; (10
minutes to a few hours))
2013/11/06 11:16:34> Using FTP to download since --search,--incomplete,
and/or --only_incomplete option(s) selected.
2013/11/06 11:16:34> Downloading files to directory:
/mnt/data/work/pollardlab/MicrobeDB_test/Bacteria_2013-11-06/
2013/11/06 11:16:34> Note: NCBI has removed their metadata files. We are
looking for another source of metadata information, but until then we can
only use metadata for genomes fr
om before June, 2012.
2013/11/06 11:16:34> Downloading file:
/mnt/data/work/pollardlab/MicrobeDB_test/Bacteria_2013-11-06/NCBI_orginfo.txt
from Dropbox at: http://dl.dropbox.com/u/5329340/NCBI_orginfo.
txt
2013/11/06 11:16:35> Downloading file:
/mnt/data/work/pollardlab/MicrobeDB_test/Bacteria_2013-11-06/NCBI_completegenomes.txt
from Dropbox at: http://dl.dropbox.com/u/5329340/NCBI_
completegenomes.txt
2013/11/06 11:16:37> Downloading genomes using FTP option
2013/11/06 11:16:37> Downloading RefSeq genomes now.
2013/11/06 11:30:26> Downloading draft genomes now.
2013/11/06 11:30:31> Downloading genome:
Acaricomes_phytoseiuli_DSM_14247_uid199097
2013/11/06 11:30:38> Downloading genome: Acaryochloris_CCMEE_5410_uid78283

Anyways I'd be happy to help to fix this in any way I can to get it
working for us.
Please let me know things I could try or parts of the code that could be
altered to get this working.

Best,

Timothy Laurent

Timothy Laurent

Timothy Laurent

[timothyjlaurent]

Ok I have retested the download everything with the following command 👍
$ ./download_load_and_delete_old_version.pl -d /mnt/data/work/pollardlab/MicrobeDBtests/dladov -s '-i -t faa,fna,ffn' 2>&1 | tee -a download_load_and_delete_old_version.log

This makes 9671 folders in my download location.
of these 6946 are empty with only the .listing file.

in the log of the output there were many occasions where "couldn't find the genbank file"

in the database there are only 👍
select count(*) from taxonomy;
2665

So ... is there any way to get the rest of the genomes? What is going wrong here? How can we fix it?