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Hello! I have some troubles using Sirius #21

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llbbhh112233 opened this issue Dec 17, 2020 · 10 comments
Closed

Hello! I have some troubles using Sirius #21

llbbhh112233 opened this issue Dec 17, 2020 · 10 comments

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@llbbhh112233
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Hello!
When using "Sirius", I got the warning message below. How can I solve this problem.

Connection error
org.apache.http.conn.ConnectTimeoutException: Connect to www.google.com:443 [www.google.com/157.240.3.50] failed: connect timed out
at org.apache.http.impl.conn.DefaultHttpClientConnectionOperator.connect(DefaultHttpClientConnectionOperator.java:143)
at org.apache.http.impl.conn.PoolingHttpClientConnectionManager.connect(PoolingHttpClientConnectionManager.java:353)
at org.apache.http.impl.execchain.MainClientExec.establishRoute(MainClientExec.java:380)
at org.apache.http.impl.execchain.MainClientExec.execute(MainClientExec.java:236)
at org.apache.http.impl.execchain.ProtocolExec.execute(ProtocolExec.java:184)
at org.apache.http.impl.execchain.RetryExec.execute(RetryExec.java:88)
at org.apache.http.impl.execchain.RedirectExec.execute(RedirectExec.java:110)
at org.apache.http.impl.client.InternalHttpClient.doExecute(InternalHttpClient.java:184)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:82)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:107)
at de.unijena.bioinf.webapi.ProxyManager$LockedClosableHttpClient.execute(ProxyManager.java:344)
at de.unijena.bioinf.webapi.ProxyManager$LockedClosableHttpClient.execute(ProxyManager.java:313)
at de.unijena.bioinf.webapi.ProxyManager.checkConnectionToUrl(ProxyManager.java:224)
at de.unijena.bioinf.webapi.ProxyManager.checkExternal(ProxyManager.java:211)
at de.unijena.bioinf.webapi.ProxyManager.checkInternetConnection(ProxyManager.java:135)
at de.unijena.bioinf.webapi.WebAPI.lambda$checkConnection$0(WebAPI.java:134)
at de.unijena.bioinf.webapi.ProxyManager.doWithClient(ProxyManager.java:279)
at de.unijena.bioinf.webapi.WebAPI.checkConnection(WebAPI.java:130)
at de.unijena.bioinf.ms.gui.net.ConnectionMonitor$CheckJob.compute(ConnectionMonitor.java:121)
at de.unijena.bioinf.ms.gui.net.ConnectionMonitor$CheckJob.compute(ConnectionMonitor.java:117)
at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:95)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)
Caused by: java.net.SocketTimeoutException: connect timed out
at java.base/java.net.PlainSocketImpl.waitForConnect(Native Method)
at java.base/java.net.PlainSocketImpl.socketConnect(Unknown Source)
at java.base/java.net.AbstractPlainSocketImpl.doConnect(Unknown Source)
at java.base/java.net.AbstractPlainSocketImpl.connectToAddress(Unknown Source)
at java.base/java.net.AbstractPlainSocketImpl.connect(Unknown Source)
at java.base/java.net.SocksSocketImpl.connect(Unknown Source)
at java.base/java.net.Socket.connect(Unknown Source)
at org.apache.http.conn.ssl.SSLConnectionSocketFactory.connectSocket(SSLConnectionSocketFactory.java:337)
at org.apache.http.impl.conn.DefaultHttpClientConnectionOperator.connect(DefaultHttpClientConnectionOperator.java:134)
... 24 more

Dec 17, 2020 4:19:25 PM de.unijena.bioinf.ms.rest.client.info.InfoClient getVersionInfo
警告: Could not reach fingerid version specific URL for version verification. Try to reach root url. Cause:Connect to www.csi-fingerid.uni-jena.de:443 [www.csi-fingerid.uni-jena.de/141.35.12.31] failed: Read timed out
Dec 17, 2020 4:19:25 PM de.unijena.bioinf.ms.rest.client.info.InfoClient getVersionInfo
警告: Could not reach fingerid version specific URL for version verification. Try to reach root url. Cause:Connect to www.csi-fingerid.uni-jena.de:443 [www.csi-fingerid.uni-jena.de/141.35.12.31] failed: Read timed out
Dec 17, 2020 4:19:57 PM de.unijena.bioinf.ms.rest.client.info.InfoClient getVersionInfo
警告: Could not reach fingerid version specific URL for version verification. Try to reach root url. Cause:Read timed out
Dec 17, 2020 4:19:57 PM de.unijena.bioinf.ms.rest.client.info.InfoClient getVersionInfo
警告: Could not reach fingerid version specific URL for version verification. Try to reach root url. Cause:Read timed out
@mfleisch
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Hey,
is this issue reproducible/persistent? The most likely reason for this problem is that your internet connection was temporarily unavailable.

@llbbhh112233
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llbbhh112233 commented Dec 17, 2020 via email

@mfleisch
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mfleisch commented Dec 17, 2020 •
edited
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Please have a look at this issue: #17 (comment)

Try deleting 'sirius_rosmarin' or using an output directory that is either empty or does not exist.

Best.

@llbbhh112233
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llbbhh112233 commented Dec 18, 2020 via email

@kaibioinfo
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Your mzml files seem to contain only very few MS/MS spectra (around 10). I think there is no meaning in aligning ten features. If you just want to extract the MS/MS run the tool without the lcms-align subtool.

@llbbhh112233
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llbbhh112233 commented Dec 18, 2020 via email

@kaibioinfo
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Hi,

I checked your mzml file and it seems that you have DIA data. We do not support this kind of data: mass spectra in DIA are highly multiplexed and have to be deconvoluted first. You can try MSFinder which is one of the few software methods that can deal with such kind of data.

@llbbhh112233
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llbbhh112233 commented Dec 21, 2020 via email

@mfleisch
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SIRIUS writes results to disk as soon as they are available but summary files are written as very last step of a analysis.
So if the analysis was stopped forcefully or crashed it is likely that summary files have not been written.

However summaries can be created from an existing project separately by reading the project-space without doing anything.

sirius -i <my-project> project-space

@mfleisch
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I am closing this issue because it is not focused on a specific topic.
If there are further issues please open a new issue (per topic) with a descriptive title.

mfleisch added a commit that referenced this issue Nov 3, 2023
@mfleisch
Closes #21. Increased max page size to integer max value
a8c8164
mfleisch pushed a commit that referenced this issue Aug 2, 2024
Merge branch '21-database-filter-is-filtering-everything-out-if-there…
f3897a4 
…-is-an-index' into 'master'

Filtering over indexed field

Closes #21

See merge request bright-giant/sirius/sirius-libs!5
mfleisch pushed a commit that referenced this issue Aug 2, 2024
Merge branch '300-merge-sirius-libs-into-sirius-frontend-to-create-a-…
b2ff245 
…mono-repo' into 'master'

Resolve "Merge sirius-libs into sirius-frontend to create a mono repo."

Closes #300, #132, #126, #123, #128, #125, #127, #124, #122, #121, #120, #109, #115, #106, #99, #112, #111, #61, #110, #103, #108, #107, #104, #221, #102, #98, #198, #92, #94, #93, #85, #84, #87, #76, #56, #73, #32, #70, #65, #43, #63, #33, #53, #58, #59, #57, #54, #52, #41, #47, #50, #49, #48, #39, #46, #37, #38, #27, #34, #22, #31, #28, #18, #23, #21, #19, #9, #240, #280, #254, #242, #246, #238, #156, #25, #155, #189, #172, #154, #11, #6, #16, and #4

See merge request bright-giant/sirius/sirius-frontend!106
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@kaibioinfo @mfleisch @llbbhh112233