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Posted to commits@airavata.apache.org by ma...@apache.org on 2019/06/02 17:22:49 UTC
[airavata-php-gateway] 02/14: adding explanation for job failure
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a commit to branch dreg-gateway
in repository https://gitbox.apache.org/repos/asf/airavata-php-gateway.git
commit c678d7caa6af3c716e1b0aa34bdfca6c1da3d95c
Author: root <ro...@dreg-gateway-instance1.jetstreamlocal>
AuthorDate: Mon Jun 18 19:04:07 2018 +0000
adding explanation for job failure
---
public/themes/dreg/assets/img/failure1.png | Bin 0 -> 53330 bytes
public/themes/dreg/assets/img/failure2.png | Bin 0 -> 29925 bytes
public/themes/dreg/assets/img/failure3-reason.png | Bin 0 -> 15519 bytes
public/themes/dreg/assets/img/failure3.png | Bin 0 -> 31908 bytes
public/themes/dreg/assets/img/failure4-reason.png | Bin 0 -> 17034 bytes
public/themes/dreg/partials/doc.blade.php | 39 ++++++++++++++++++++++
public/themes/dreg/partials/faq.blade.php | 12 +++++--
7 files changed, 49 insertions(+), 2 deletions(-)
diff --git a/public/themes/dreg/assets/img/failure1.png b/public/themes/dreg/assets/img/failure1.png
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diff --git a/public/themes/dreg/assets/img/failure2.png b/public/themes/dreg/assets/img/failure2.png
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diff --git a/public/themes/dreg/assets/img/failure3-reason.png b/public/themes/dreg/assets/img/failure3-reason.png
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diff --git a/public/themes/dreg/assets/img/failure3.png b/public/themes/dreg/assets/img/failure3.png
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diff --git a/public/themes/dreg/assets/img/failure4-reason.png b/public/themes/dreg/assets/img/failure4-reason.png
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diff --git a/public/themes/dreg/partials/doc.blade.php b/public/themes/dreg/partials/doc.blade.php
index ae77e01..74c54ce 100755
--- a/public/themes/dreg/partials/doc.blade.php
+++ b/public/themes/dreg/partials/doc.blade.php
@@ -71,6 +71,45 @@ the user can click <b>'Open Folder'</b> link in the experiment summary page to c
<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment summary" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.exp.folder.png"></img></div>
+<a name="failure"></a>
+ <p class="description" style="padding:16px">
+ 10) <b>When you meet failure</b><br>
+
+Currently when you run the dREG jobs, there are two types of errors you may have. One error may come from the system, called a system error, such as no computing time on specific GPU nodes or an internal errors in Apache Airavata. The other type of error is caused by the users' bigwig, called bigwig error, which can occur when read counts are normalized, each read is mapped to a region, or read counts in minus strand are positive values. The following figures show how to identify the err [...]
+
+
+ <p class="description" style="padding:16px">
+ a) <b>System error</b><br>
+When users submit the experiment, the failure will be shown in the experiment summary page soon as figure 10-S1 or 10-S2. The <b>experiment status</b> is "Failed" and many java errors are shown in the <b>"Errors"</b> item. Users can't solve this problem and should report this error the web master.</p>
+
+<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="System error(1)" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/failure1.png"></img></div>
+<div style="clear:both;text-align:center;"><center>Figure 10-S1</center></div>
+
+<br>
+
+<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="System error(2)" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/failure2.png"></img></div>
+<div style="clear:both;text-align:center;"><center>Figure 10-S2</center></div>
+
+<br>
+ <p class="description" style="padding:16px">
+ b) <b>Bigwig error</b><br>
+After the experiment is complete, no results can be downloaded and job status shows a failure (see Figure 10-S3). Users can find the dREG log file or task log file to identify the problem. Enter into <b>"storage directory"</b> by clicking the <b>"open"</b> link. The users can find <b>"ARCHIVE"</b> folder where Apache Airavata copy back all files from the computing node. Check the dREG log file (<b>out.dREG.log</b>) to see the bigwig problem or check the task log file ("slurm-tasknoxxx.ou [...]
+
+<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="Bigwig error" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/failure3.png"></img></div>
+<div style="clear:both;text-align:center;"><center>Figure 10-S3</center></div>
+<BR>
+
+<p>This figure shows the bigWig problems in the dREG log file.</p>
+
+<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="Bigwig error(1)" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/failure3-reason.png"></img></div>
+<div style="clear:both;text-align:center;"><center>Figure 10-S4</center></div>
+<BR>
+
+<p>This figure shows the task log file in which explains the task was killed due to time limit.</p>
+
+<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="Bigwig error(2)" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/failure4-reason.png"></img></div>
+<div style="clear:both;text-align:center;"><center>Figure 10-S5</center></div>
+<BR>
</div>
</div>
diff --git a/public/themes/dreg/partials/faq.blade.php b/public/themes/dreg/partials/faq.blade.php
index e92be49..ea4b3a9 100755
--- a/public/themes/dreg/partials/faq.blade.php
+++ b/public/themes/dreg/partials/faq.blade.php
@@ -8,6 +8,10 @@
<p><b>Q: How should I prepare bigWig files for use with the dREG gateway?</b></p>
<p>A: Information about how to prepare files can be found <A href="https://github.com/Danko-Lab/tutorials/blob/master/PRO-seq.md#read-mapping"> here </A>.</p>
+
+<p><b>Q: How should I do when I meet the computational failure in the dREG gateway?</b></p>
+<p>A: There are two types of error you may have, we explain how to identify your error and how to handle it <A href="https://dreg.dnasequence.org/pages/doc#failure"> here</A>.</p>
+
<p><b>Q: What types of enhancers and promoters can be identified using the dREG gateway?</b></p>
<p>A: As a general rule of thumb, high-quality datasets provide very similar groups of enhancers and promoters as ChIP-seq for H3K27ac. This suggests that dREG identifies the location of all of the so-called ‘active’ class of enhancers and promoters. </p>
<p><b>Q: Will the dREG gateway work with my data type?</b></p>
@@ -18,8 +22,12 @@
<p>A: Sensitivity is reasonable at ~40 million mapped reads and saturates at ~100 million mapped reads. See our analysis here: <A href="http://www.nature.com/nmeth/journal/v12/n5/fig_tab/nmeth.3329_SF3.html">supplementary figure 3 in dREG paper</A>.</p>
<p><b>Q: How to I cite the dREG gateway?</b></p>
<p>A: Please cite one of our papers if you use dREG results in your publication:<BR/>
-<A href="http://www.nature.com/nmeth/journal/v12/n5/full/nmeth.3329.html">
-Danko, C. G., Hyland, S. L., Core, L. J., Martins, A. L., Waters, C. T., Lee, H. W., ... & Siepel, A. (2015). Identification of active transcriptional regulatory elements from GRO-seq data. Nature methods, 12(5), 433-438. </A></p>
+<A target="_blank" href="http://www.nature.com/nmeth/journal/v12/n5/full/nmeth.3329.html">
+(1) Danko, C. G., Hyland, S. L., Core, L. J., Martins, A. L., Waters, C. T., Lee, H. W., ... & Siepel, A. (2015). Identification of active transcriptional regulatory elements from GRO-seq data. Nature methods, 12(5), 433-438. </A></p>
+<A target="_blank" href="https://www.biorxiv.org/content/early/2018/05/14/321539.abstract">
+(2) Wang, Z., Chu, T., Choate, L. A., & Danko, C. G. (2018). Identification of regulatory elements from nascent transcription using dREG. bioRxiv, 321539. </A></P>
+
+
<p><b>Q: Do I have to create account before using this service?</b></p>
<p>A: Yes, this system is supported by an NSF funded supercomputing resource known as <A title="XSEDE" href="http://www.xsede.org">XSEDE</A>, who regularly needs to report bulk usage statistics to NSF. Nevertheless, data that you provide are completely safe.</p>
<p><b>Q: How do I know the status of the computational nodes? </b></p>