[EMBOSS] accessing emboss ftp site
Chris Dagdigian
dag at sonsorol.org
Wed Jul 28 11:49:17 UTC 2010
I can't seem to replicate this at all with any of my available FTP
clients or browser-based FTP clients. It works for me from both Mac OS X
clients as well as a CentOS 5.4 based Linux system.
Is there an FTP client / OS combo that seems in particular not to work?
-Chris
Here is one example:
> dag-static:~ dag$ ftp emboss.open-bio.org
> Connected to emboss.open-bio.org.
> 220 (vsFTPd 2.0.1)
> Name (emboss.open-bio.org:dag): anonymous
> 331 Please specify the password.
> Password:
> 230 Login successful.
> Remote system type is UNIX.
> Using binary mode to transfer files.
> ftp> dir
> 229 Entering Extended Passive Mode (|||54472|)
> 150 Here comes the directory listing.
> drwxr-xr-x 8 14 50 4096 May 22 2006 pub
> 226 Directory send OK.
> ftp> cd pub/EMBOSS
> 250 Directory successfully changed.
> ftp> ls
> 229 Entering Extended Passive Mode (|||38343|)
> 150 Here comes the directory listing.
> -rw-rw-r-- 1 501 503 389856 Jul 21 09:25 CBSTOOLS-1.0.0.tar.gz
> -rw-rw-r-- 1 501 503 426218 Jul 21 09:25 DOMAINATRIX-0.1.0.tar.gz
> -rw-rw-r-- 1 501 503 441025 Jul 21 09:25 DOMALIGN-0.1.0.tar.gz
> -rw-rw-r-- 1 501 503 452787 Jul 21 09:25 DOMSEARCH-0.1.0.tar.gz
> -rw-rw-r-- 1 501 503 23572243 Jul 19 13:41 EMBOSS-6.3.1.tar.gz
> lrwxrwxrwx 1 501 503 19 Jul 19 13:42 EMBOSS-latest.tar.gz -> EMBOSS-6.3.1.tar.gz
> -rw-rw-r-- 1 501 503 373798 Jul 21 09:25 EMNU-1.05.tar.gz
> -rw-rw-r-- 1 501 503 415096 Jul 21 09:25 ESIM4-1.0.0.tar.gz
> -rw-rw-r-- 1 501 503 569581 Jul 21 09:25 HMMER-2.3.2.tar.gz
> -rw-rw-r-- 1 501 503 350791 Jul 21 09:25 IPRSCAN-4.3.1.tar.gz
> drwxrwsr-x 7 501 503 4096 Feb 01 2006 Jemboss
> -rw-rw-r-- 1 501 503 513418 Jul 21 09:25 MEMENEW-4.0.0.tar.gz
> -rw-rw-r-- 1 501 503 823636 Jul 21 09:25 MIRA-2.8.2.tar.gz
> -rw-rw-r-- 1 501 503 435315 Jul 21 09:25 MSE-3.0.0.tar.gz
> -rw-rw-r-- 1 501 503 328540 Jul 21 09:25 MYEMBOSS-6.3.0.tar.gz
> -rw-rw-r-- 1 501 503 359488 Jul 21 09:25 MYEMBOSSDEMO-6.3.0.tar.gz
> -rw-rw-r-- 1 501 503 1667760 Jul 21 09:25 PHYLIPNEW-3.69.tar.gz
> -rw-rw-r-- 1 501 503 571008 Jul 21 09:25 SIGNATURE-0.1.0.tar.gz
> -rw-rw-r-- 1 501 503 531604 Jul 21 09:25 STRUCTURE-0.1.0.tar.gz
> -rw-rw-r-- 1 501 503 386287 Jul 21 09:25 TOPO-2.0.0.tar.gz
> -rw-rw-r-- 1 501 503 652433 Jul 21 09:25 VIENNA-1.7.2.tar.gz
> drwxrwsr-x 3 522 503 4096 Aug 21 2006 contrib
> drwxrwsr-x 2 501 503 4096 Nov 11 2005 doc
> drwxrwsr-x 3 501 503 4096 Jul 21 09:25 fixes
> drwxrwsr-x 14 501 503 4096 Jul 19 13:39 old
> drwxrwsr-x 2 501 503 4096 Jul 06 2005 tutorials
> drwxrwsr-x 4 501 503 4096 Jul 19 13:36 windows
> 226 Directory send OK.
> ftp>
Hamish McWilliam wrote:
> Hi Chris,
>
> I'm also seeing problems with the FTP site, but using Mirror rather
> than Transmit, it looks like the server does not like options being
> specified to the LIST command:
>
> Scanning remote directory /pub/EMBOSS
> ---> CWD /pub/EMBOSS
> 250 Directory successfully changed.
> ---> TYPE A
> 200 Switching to ASCII mode.
> ---> PORT 172,21,22,1,171,245
> 200 PORT command successful. Consider using PASV.
> ---> PASV
> 227 Entering Passive Mode (208,94,50,58,104,178)
> ---> LIST -lat
> timed out
> Cannot get remote directory listing because: timed out
> Cannot get remote directory details (/pub/EMBOSS)
> disconnecting from emboss.open-bio.org
>
> Trying it with a command line client I get the response to hang if I
> try using any options to ls or dir, without options they are fine.
>
> All the best,
>
> Hamish
>
> On 29 May 2010 03:44, Koen van der Drift<koenvanderdrift at gmail.com> wrote:
>> Hi Chris,
>>
>> Did you have a chance to look at this? Just tried again, and Transmit still
>> won't let me access the emboss ftp site.
>>
>> Thanks,
>>
>> - Koen.
>>
>>
>> On Apr 23, 2010, at 11:44 AM, Chris Dagdigian wrote:
>>
>>> In the last few months the open-bio.org servers switched datacenters, IP
>>> addresses and firewall/IDS appliances. Lots of juicy things to look at and
>>> debug.
>>>
>>> Koen - if you have a chance can you send me the IP address that you are
>>> using to connect from? I might be able to find some relevant log entries
>>> with that info.
>>>
>>> -Chris
>>>
>>>
>>>
>>> Koen van der Drift wrote:
>>>> Just for the record, it used to work with Transmit, this is only from
>>>> the last few months.
>>>>
>>>> - Koen.
>>>>
>>>> On Thu, Apr 22, 2010 at 7:28 PM, Chris Dagdigian<dag at sonsorol.org>
>>>> wrote:
>>>>> Might be an issue with the Juniper Netscreen firewall/IDS security
>>>>> appliance
>>>>> that sits upstream of the EMBOSS FTP server. I'll take a look at the
>>>>> security logs and alerts.
>>>>>
>>>>> -Chris
>>>>>
>>>>>
>>>>> Koen van der Drift wrote:
>>>>>> Hi,
>>>>>>
>>>>>> For a while now I am unable to access the emboss ftp site using the OS
>>>>>> X
>>>>>> client Transmit. Loggin in works fine, but it chokes on the LIST
>>>>>> command. I have no problems accessing it from the command line. I have
>>>>>> added the output from Transmit below. I don't know if this is a
>>>>>> Transmit
>>>>>> or emboss issue, but just wanted to let you know.
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> - Koen.
>>>>>>
>>>>>>
>>>>>> Transmit 3.6.9 Session Transcript
>>>>>> LibNcFTP 3.2.1 (August 13, 2007) compiled for UNIX
>>>>>> Uname: Darwin|exile.local|9.8.0|Darwin Kernel Version 9.8.0: Wed Jul 15
>>>>>> 16:57:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_PPC|Power Macintosh
>>>>>> 220: (vsFTPd 2.0.1)
>>>>>> Connected to emboss.open-bio.org.
>>>>>> Cmd: USER anonymous
>>>>>> 331: Please specify the password.
>>>>>> Cmd: PASS NcFTP@
>>>>>> 230: Login successful.
>>>>>> Cmd: TYPE A
>>>>>> 200: Switching to ASCII mode.
>>>>>> Logged in to emboss.open-bio.org as anonymous.
>>>>>> Cmd: SYST
>>>>>> 215: UNIX Type: L8
>>>>>> Cmd: PWD
>>>>>> 257: "/"
>>>>>> Cmd: CWD /pub/EMBOSS/fixes
>>>>>> 250: Directory successfully changed.
>>>>>> Cmd: PWD
>>>>>> 257: "/pub/EMBOSS/fixes"
>>>>>> Cmd: PASV
>>>>>> 227: Entering Passive Mode (208,94,50,58,83,232)
>>>>>> Cmd: LIST -a
>>>>>> Could not read reply from control connection -- timed out. (SReadline
>>>>>> 1)
>>>>>> 220: (vsFTPd 2.0.1)
>>>>>> Connected to emboss.open-bio.org.
>>>>>> Cmd: USER anonymous
>>>>>> 331: Please specify the password.
>>>>>> Cmd: PASS NcFTP@
>>>>>> 230: Login successful.
>>>>>> Logged in to emboss.open-bio.org as anonymous.
>>>>>> Cmd: SYST
>>>>>> 215: UNIX Type: L8
>>>>>> Cmd: PWD
>>>>>> 257: "/"
>>>>>> Cmd: CWD /pub/EMBOSS/fixes
>>>>>> 250: Directory successfully changed.
>>>>>> Cmd: PWD
>>>>>> 257: "/pub/EMBOSS/fixes"
>>>>>> Cmd: PASV
>>>>>> 227: Entering Passive Mode (208,94,50,58,222,100)
>>>>>> Cmd: LIST -a
>>>>>> Could not read reply from control connection -- timed out. (SReadline
>>>>>> 1)
>>>>>>
>>>>>> _______________________________________________
>>>>>> EMBOSS mailing list
>>>>>> EMBOSS at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/emboss
>> _______________________________________________
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/emboss
>>
>
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