[EMBOSS] accessing emboss ftp site
Gabor Toth
tothg at abc.hu
Mon Sep 6 11:01:31 UTC 2010
wget times out after issuing the 'LIST -a' command.
wget 1.11.4 / Linux (openSUSE 11.2 x86_64)
Gabor
On Wed July 28 2010 13:49:17 Chris Dagdigian wrote:
> 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
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>
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