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<p class="MsoNormal">Hello,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am downloading lots of (wonderful) ensembl data this morning (EDT), running commands like:<o:p></o:p></p>
<p class="p1">wget -r -l 10 -c --retry-connrefused --tries=0 --timeout=5 -A bed.gz ftp://ftp.ensembl.org/pub/release-$ENSEMBL/regulation/homo_sapiens/Peaks/ &<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Where $ENSEMBL is the version.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">During this process I often get a few refused requests, I assume because ensembl limits bandwidth, example:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="background:black"><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2">--2022-10-26 13:54:19-- ftp://ftp.ensembl.org/pub/release-107/regulation/mus_musculus/Peaks/MEL_cell_line/EP300/mus_musculus.GRCm39.MEL_cell_line.EP300.SWEmbl_R0005.peaks.20201021.bed.gz<o:p></o:p></span></p>
<p class="MsoNormal" style="background:black"><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2"> (try: 4) => 'ftp.ensembl.org/pub/release-107/regulation/mus_musculus/Peaks/MEL_cell_line/EP300/mus_musculus.GRCm39.MEL_cell_line.EP300.SWEmbl_R0005.peaks.20201021.bed.gz'<o:p></o:p></span></p>
<p class="MsoNormal" style="background:black"><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2">Connecting to ftp.ensembl.org (ftp.ensembl.org)|193.62.193.139|:21... connected.<o:p></o:p></span></p>
<p class="MsoNormal" style="background:black"><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2">Logging in as anonymous ... Logged in!<o:p></o:p></span></p>
<p class="MsoNormal" style="background:black"><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2">==> SYST ... done. ==> PWD ... done.<o:p></o:p></span></p>
<p class="MsoNormal" style="background:black"><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2">==> TYPE I ... done. ==> CWD (1) /pub/release-107/regulation/mus_musculus/Peaks/MEL_cell_line/EP300 ... done.<o:p></o:p></span></p>
<p class="MsoNormal" style="background:black"><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2">==> PASV ... couldn't connect to 193.62.193.139 port 37209:
</span><span style="font-size:12.0pt;font-family:Monaco;color:#C00000">Connection refused</span><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:black"><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2">Retrying.<o:p></o:p></span></p>
<p class="MsoNormal" style="background:black"><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:black"><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2">--2022-10-26 13:54:24-- ftp://ftp.ensembl.org/pub/release-107/regulation/mus_musculus/Peaks/MEL_cell_line/EP300/mus_musculus.GRCm39.MEL_cell_line.EP300.SWEmbl_R0005.peaks.20201021.bed.gz<o:p></o:p></span></p>
<p class="MsoNormal" style="background:black"><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2"> (try: 5) => 'ftp.ensembl.org/pub/release-107/regulation/mus_musculus/Peaks/MEL_cell_line/EP300/mus_musculus.GRCm39.MEL_cell_line.EP300.SWEmbl_R0005.peaks.20201021.bed.gz'<o:p></o:p></span></p>
<p class="MsoNormal" style="background:black"><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2">Connecting to ftp.ensembl.org (ftp.ensembl.org)|193.62.193.139|:21... connected.<o:p></o:p></span></p>
<p class="MsoNormal" style="background:black"><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2">Logging in as anonymous ... Logged in!<o:p></o:p></span></p>
<p class="MsoNormal" style="background:black"><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2">==> SYST ... done. ==> PWD ... done.<o:p></o:p></span></p>
<p class="MsoNormal" style="background:black"><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2">==> TYPE I ... done. ==> CWD (1) /pub/release-107/regulation/mus_musculus/Peaks/MEL_cell_line/EP300 ... done.<o:p></o:p></span></p>
<p class="MsoNormal" style="background:black"><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2">==> PASV ... couldn't connect to 193.62.193.139 port 64353:
</span><span style="font-size:12.0pt;font-family:Monaco;color:#C00000">Connection refused</span><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:black"><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2">Retrying.<o:p></o:p></span></p>
<p class="MsoNormal" style="background:black"><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:black"><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2">--2022-10-26 13:54:31-- ftp://ftp.ensembl.org/pub/release-107/regulation/mus_musculus/Peaks/MEL_cell_line/EP300/mus_musculus.GRCm39.MEL_cell_line.EP300.SWEmbl_R0005.peaks.20201021.bed.gz<o:p></o:p></span></p>
<p class="MsoNormal" style="background:black"><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2"> (try: 6) => 'ftp.ensembl.org/pub/release-107/regulation/mus_musculus/Peaks/MEL_cell_line/EP300/mus_musculus.GRCm39.MEL_cell_line.EP300.SWEmbl_R0005.peaks.20201021.bed.gz'<o:p></o:p></span></p>
<p class="MsoNormal" style="background:black"><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2">Connecting to ftp.ensembl.org (ftp.ensembl.org)|193.62.193.139|:21... connected.<o:p></o:p></span></p>
<p class="MsoNormal" style="background:black"><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2">Logging in as anonymous ... Logged in!<o:p></o:p></span></p>
<p class="MsoNormal" style="background:black"><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2">==> SYST ... done. ==> PWD ... done.<o:p></o:p></span></p>
<p class="MsoNormal" style="background:black"><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2">==> TYPE I ... done. ==> CWD (1) /pub/release-107/regulation/mus_musculus/Peaks/MEL_cell_line/EP300 ... done.<o:p></o:p></span></p>
<p class="MsoNormal" style="background:black"><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2">==> PASV ... done. ==> RETR mus_musculus.GRCm39.MEL_cell_line.EP300.SWEmbl_R0005.peaks.20201021.bed.gz ... done.<o:p></o:p></span></p>
<p class="MsoNormal" style="background:black"><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2">Length: 262591 (256K)<o:p></o:p></span></p>
<p class="MsoNormal" style="background:black"><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:black"><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2">ftp.ensembl.org/pub/release-107/regulati 100%[</span><span style="font-size:12.0pt;font-family:Monaco;color:#00B050">===============================================================================></span><span style="font-size:12.0pt;font-family:Monaco;color:#F2F2F2">]
256.44K 651KB/s in 0.4s <o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Is my doing this <i>unfriendly</i> to the ensembl ftp server(s)? Should I be reducing requests? (How?) Can I get the data over without all the “Connection refused” in between each request? If this is okay and just how it works then you
need take no action I think, just confirming it is okay to transfer data. In this case regulation peak files.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Matt Gerring<o:p></o:p></p>
<p class="MsoNormal">Jackson Laboratory<o:p></o:p></p>
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