<div dir="ltr">It's a Java heap space error. How much memory is available to Docker? You also might need to configure how much bfconvert can use: <a href="https://docs.openmicroscopy.org/bio-formats/5.9.1/users/comlinetools/index.html#command-line-environment">https://docs.openmicroscopy.org/bio-formats/5.9.1/users/comlinetools/index.html#command-line-environment</a><div><br></div><div>Cheers,</div><div><br></div><div>Douglas</div></div><br><div class="gmail_quote"><div dir="ltr">On Thu, 23 Aug 2018 at 13:32 Narapareddy, Mohanapriya <<a href="mailto:mohanapriya.narapareddy@emory.edu">mohanapriya.narapareddy@emory.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div id="m_6997727838363348083divtagdefaultwrapper" style="font-size:12pt;color:#000000;font-family:Calibri,Helvetica,sans-serif" dir="ltr">
<p style="margin-top:0;margin-bottom:0">Hello when i am trying to run the bftools dockerfile on a alpine base image i am getting the below error.</p>
<p style="margin-top:0;margin-bottom:0"></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures">CellSensReader initializing OS-1.vsi</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures">[CellSens VSI] -> sample-%s.tif [Tagged Image File Format]</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures">Tile size = 512 x 512</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"></span>Series 0: converted 1/1 planes (100%)</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures">Tile size = 512 x 512</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures">Exception in thread "main" java.lang.OutOfMemoryError: Java heap space</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"></span>at java.util.Arrays.copyOf(Arrays.java:3236)</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"></span>at java.io.ByteArrayOutputStream.toByteArray(ByteArrayOutputStream.java:191)</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"></span>at loci.formats.tiff.TiffSaver.writeImage(TiffSaver.java:384)</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"></span>at loci.formats.tiff.TiffSaver.writeImage(TiffSaver.java:277)</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"></span>at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:270)</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"></span>at loci.formats.tools.ImageConverter.convertTilePlane(ImageConverter.java:748)</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"></span>at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:634)</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"></span>at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:563)</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"></span>at loci.formats.tools.ImageConverter.main(ImageConverter.java:884)</span></p>
<br>
<p></p>
<p style="margin-top:0;margin-bottom:0">Below is my docker file. </p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0"></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures">FROM alpine:3.5</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255);min-height:13px">
<span style="font-variant-ligatures:no-common-ligatures"><span class="m_6997727838363348083Apple-converted-space"> </span></span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures">RUN apk -Uuv add bash openjdk8-jre \</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"><span class="m_6997727838363348083Apple-converted-space">
</span>&& mkdir /opt \</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"><span class="m_6997727838363348083Apple-converted-space">
</span>&& wget <a href="http://downloads.openmicroscopy.org/latest/bio-formats5.6/artifacts/bftools.zip" target="_blank">http://downloads.openmicroscopy.org/latest/bio-formats5.6/artifacts/bftools.zip</a> \</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"><span class="m_6997727838363348083Apple-converted-space">
</span>&& unzip bftools.zip -x '*.bat' -d /opt/ \</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"><span class="m_6997727838363348083Apple-converted-space">
</span>&& rm /var/cache/apk/*</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255);min-height:13px">
<span style="font-variant-ligatures:no-common-ligatures"></span><br>
</p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures">ENV PATH $PATH:/opt/bftools/</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255);min-height:13px">
<span style="font-variant-ligatures:no-common-ligatures"></span><br>
</p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures">WORKDIR /tmp</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(94,52,255);background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures">~ <span class="m_6997727838363348083Apple-converted-space">
</span></span></p>
<br>
<p></p>
<p style="margin-top:0;margin-bottom:0"></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"></span></p>
Please resolve this issue. Look forward to hear from you.
<p></p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<div id="m_6997727838363348083Signature">
<p>Thanks,</p>
<p>Mohanapriya</p>
</div>
</div>
<hr style="display:inline-block;width:98%">
<div id="m_6997727838363348083divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> ome-users <<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" target="_blank">ome-users-bounces@lists.openmicroscopy.org.uk</a>> on behalf of Manuel Stritt <<a href="mailto:manuel.stritt@idorsia.com" target="_blank">manuel.stritt@idorsia.com</a>><br>
<b>Sent:</b> Thursday, August 16, 2018 10:17:29 AM</font></div></div><div dir="ltr"><div id="m_6997727838363348083divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><br>
<b>To:</b> OME User Support List<br>
</font></div></div><div dir="ltr"><div id="m_6997727838363348083divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>Subject:</b> Re: [ome-users] Fw: bfconvert command</font></div></div><div dir="ltr">
<div>
<div dir="ltr"><span style="font-size:14.6667px;float:none;display:inline">Dear Mohanapriya,</span>
<br>
<div class="m_6997727838363348083x_gmail_extra"><br>
</div>
<div class="m_6997727838363348083x_gmail_extra">an VSI file contains one or several scenes. Each scene /series is stored in a ets file.</div>
<div class="m_6997727838363348083x_gmail_extra">For that reason you should have a subdirectory at the location of your VSI file which is</div>
<div class="m_6997727838363348083x_gmail_extra">names like the VSI file (with a "_" at the start and end). Probably you moved/copied the</div>
<div class="m_6997727838363348083x_gmail_extra">VSI file but not the corresponding ets subdirectory.</div>
<div class="m_6997727838363348083x_gmail_extra"><br>
</div>
<div class="m_6997727838363348083x_gmail_extra">Regards,</div>
<div class="m_6997727838363348083x_gmail_extra">Manuel</div>
<div class="m_6997727838363348083x_gmail_extra"><br>
</div>
<div class="m_6997727838363348083x_gmail_extra"><br>
<div class="m_6997727838363348083x_gmail_quote">
<blockquote class="m_6997727838363348083x_gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div id="m_6997727838363348083x_m_4816580915808717552divtagdefaultwrapper" dir="ltr" style="font-size:12pt;color:#000000;font-family:Calibri,Helvetica,sans-serif">
<p style="margin-top:0;margin-bottom:0">Hello Josh,</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">i have done the change to "%s" and executed again but i still getting the same result.</p>
<p style="margin-top:0;margin-bottom:0"></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span>bf@fc435e6036f7:~/data$ bfconvert -bigtiff -compression LZW OS-1.vsi sample1-%s.tif</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span>OS-1.vsi</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span>CellSensReader initializing OS-1.vsi</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span style="background-color:rgb(255,255,0)">Missing expected .ets files in /home/bf/data/_OS-1_</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span>[CellSens VSI] -> sample1-%s.tif [Tagged Image File Format]</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span><span style="white-space:pre-wrap"></span>Converted 1/1 planes (100%)</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span>[done]</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span>5.339s elapsed (35.0+4022.0ms per plane, 1267ms overhead)</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span><br>
</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span><br>
</span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span><span style="font-size:12pt">can u please let me know </span></span></p>
<p style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<span><span style="font-size:12pt">"</span><span style="font-family:Menlo;font-size:12pt">Missing expected .ets files in /home/bf/data/_OS-1_" what does this mean</span></span></p>
<br>
<p></p>
<p style="margin-top:0;margin-bottom:0">Look forward to hear from you.</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">Thanks,</p>
<div id="m_6997727838363348083x_m_4816580915808717552Signature">
<p>Mohanapriya</p>
</div>
</div>
<hr style="display:inline-block;width:98%">
<div id="m_6997727838363348083x_m_4816580915808717552divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> ome-users <<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" target="_blank">ome-users-bounces@lists.openmicroscopy.org.uk</a>>
on behalf of Josh Moore <<a href="mailto:josh@glencoesoftware.com" target="_blank">josh@glencoesoftware.com</a>><br>
<b>Sent:</b> Thursday, August 16, 2018 4:04:22 AM<br>
<b>To:</b> OME User Support List<br>
<b>Cc:</b> Narapareddy, Mohanapriya<br>
<b>Subject:</b> Re: [ome-users] Fw: bfconvert command</font>
<div> </div>
</div>
<div class="m_6997727838363348083x_m_4816580915808717552BodyFragment"><font size="2"><span style="font-size:11pt">
<div class="m_6997727838363348083x_m_4816580915808717552PlainText">Hi Mohan,<br>
<br>
Thanks for the details. It looks like there is a typo in the command<br>
line you are using in docker:<br>
<br>
bfconvert -bigtiff -compression LZW OS-1.vsi sample1-s%.tif<br>
<br>
Here "s%" should be "%s".<br>
<br>
All the best,<br>
~Josh<br>
<br>
<br>
---------- Forwarded message ----------<br>
From: Narapareddy, Mohanapriya <<a href="mailto:mohanapriya.narapareddy@emory.edu" target="_blank">mohanapriya.narapareddy@emory.edu</a>><br>
Date: Wed, Aug 15, 2018 at 8:12 PM<br>
Subject: Re: ome-users mailing list email<br>
To: Josh Moore <<a href="mailto:j.a.moore@dundee.ac.uk" target="_blank">j.a.moore@dundee.ac.uk</a>><br>
<br>
<br>
Hello Josh Moore,<br>
<br>
Thanks for your reply.<br>
<br>
i have used java version 7 and bio formats version 5.8.2 .<br>
docker run -it -v ~/Desktop/dir:/home/bf/data test<br>
]This is my docker run<br>
command. and inside the container i am executing the following<br>
command.<br>
bfconvert<br>
-bigtiff -compression LZW OS-1.vsi sample1-s%.tif<br>
FROM java:7 MAINTAINER <a href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank">
ome-devel@lists.openmicroscopy.org.uk</a> RUN<br>
apt-get install -y curl RUN curl -o bftools.zip $(curl -Ls -o<br>
/dev/null -w %{url_effective}<br>
<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__downloads.openmicroscopy.org_latest_bio-2Dformats-29_artifacts_bftools.zip&d=DwMFAg&c=WO-RGvefibhHBZq3fL85hQ&r=hG980ESxUhpWXeq9BOrnOv3CUpq5lW8uGu7OdRUzoVI&m=voky8_dW4UwOtkK0WpmWnZzp7BaSnvyFxatV-lr3kbQ&s=4ETZLRNOcMDE7VxI5PFQsud3HfmoF9cG0Bnp2yPu36w&e=" target="_blank">http://downloads.openmicroscopy.org/latest/bio-formats)/artifacts/bftools.zip</a><br>
RUN apt-get install -y unzip RUN unzip -d /opt bftools.zip && rm<br>
bftools.zip RUN chmod a+rx /opt/bftools/* RUN useradd -m bf USER bf<br>
RUN echo 'export PATH=/opt/bftools:$PATH' >> /home/bf/.bashrc ENV HOME<br>
/home/bf WORKDIR /home/bf CMD bash<br>
<br>
<br>
<br>
The above is my docker file.<br>
<br>
<br>
4. I dont see any error messages but i am getting the following out put.<br>
<br>
<br>
bf@935e7d25059c:~/data$ bfconvert -bigtiff -compression LZW OS-1.vsi<br>
sample1-s%.tif<br>
<br>
OS-1.vsi<br>
<br>
CellSensReader initializing OS-1.vsi<br>
<br>
Missing expected .ets files in /home/bf/data/_OS-1_<br>
<br>
[CellSens VSI] -> sample1-s%.tif [Tagged Image File Format]<br>
<br>
Converted 1/1 planes (100%)<br>
<br>
[done]<br>
<br>
6.95s elapsed (69.0+5815.0ms per plane, 1053ms overhead)<br>
<br>
<br>
<br>
<br>
look forward to hear from you.<br>
<br>
Thanks,<br>
<br>
Mohanapriya<br>
<br>
On Tue, Aug 14, 2018 at 10:59 PM, Narapareddy, Mohanapriya<br>
<<a href="mailto:mohanapriya.narapareddy@emory.edu" target="_blank">mohanapriya.narapareddy@emory.edu</a>> wrote:<br>
><br>
><br>
> mohanapriya<br>
><br>
><br>
><br>
> ________________________________<br>
> From: Narapareddy, Mohanapriya<br>
> Sent: Tuesday, August 14, 2018 4:39 PM<br>
> To: <a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" target="_blank">
ome-users-bounces@lists.openmicroscopy.org.uk</a><br>
> Subject: bfconvert command<br>
><br>
><br>
> I am trying to execute this command<br>
> bfconvert -bigtiff -compression LZW <input file.vsi> <outfile>-%s.tif<br>
><br>
> its working fine in centOs , i am getting multiple image planes,<br>
> but when i am trying to execute in docker container i am getting only a<br>
> single image plane. Please resolve this issue.<br>
><br>
><br>
> Thanks,<br>
><br>
> Mohanapriya<br>
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