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cougarlj / COMPSRA

COMPSRA: a COMprehensive Platform for Small RNA-Seq data Analysis
https://regepi.bwh.harvard.edu/circurna/
GNU General Public License v3.0
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Running Microbe Module #25

Open 84AP opened 2 years ago

84AP commented 2 years ago

Hello,

I am trying to use the microbe module, however it does not work.

I noticed that the command:

"~ / COMPSRA $ java -jar COMPSRA.jar -tk -dr -ck blast_archaea" "~ / COMPSRA $ java -jar COMPSRA.jar -tk -dr -ck blast_virus" "~ / COMPSRA $ java -jar COMPSRA.jar -tk -dr -ck blast_bacteria" "~ / COMPSRA $ java -jar COMPSRA.jar -tk -dr -ck blast_fungi"

does not download the pre-built full microbial databases.

Could you help me? Thanks

cougarlj commented 2 years ago

Dear 84AP,

Thank you for using COMPSRA. Our server is not robust, so sometimes it's difficult to download the database. Maybe you can download (save as ... ) the resource by hand through https://regepi.bwh.harvard.edu/circurna/ .

Thanks!

amyhiteBISR commented 2 years ago

I am having the same problem. I'm assuming server connection problems. I was able to download the archaea manually, but get errors on virus, bacteria, and fungi. Is there another source for these?

Here is the error when downloading through COMPSRA: 13:09:40.756 [main] INFO edu.harvard.channing.compass.utility.Download - Start to download the resource: https://regepi.bwh.harvard.edu/circurna/bundle_v1/db/nt/nt_fungi.fasta.gz 13:09:41.339 [main] INFO edu.harvard.channing.compass.utility.Download - Fail to download the resource: https://regepi.bwh.harvard.edu/circurna/bundle_v1/db/nt/nt_fungi.fasta.gz java.io.IOException: Server returned HTTP response code: 500 for URL: https://regepi.bwh.harvard.edu/circurna/bundle_v1/db/nt/nt_fungi.fasta.gz at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1900) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1498) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:268) at org.apache.commons.io.FileUtils.copyURLToFile(FileUtils.java:1484) at edu.harvard.channing.compass.utility.Download.download(Download.java:58) at edu.harvard.channing.compass.toolkit.DownloadResource.downloadResource(DownloadResource.java:211) at edu.harvard.channing.compass.toolkit.DownloadResource.runKit(DownloadResource.java:45) at edu.harvard.channing.compass.toolkit.ProduceTK.Dispatch(ProduceTK.java:41) at edu.harvard.channing.compass.core.COMPSRA.main(COMPSRA.java:54) 13:09:41.340 [main] INFO edu.harvard.channing.compass.core.Produce - ToolKit module was completed.

84AP commented 2 years ago

I am trying to download from https://regepi.bwh.harvard.edu/circurna/ however the site is protected and I cannot download the files. Could you share a compressed folder?

Il mer 10 nov 2021, 19:19 amyhiteBISR @.***> ha scritto:

I am having the same problem. I'm assuming server connection problems. I was able to download the archaea manually, but get errors on virus, bacteria, and fungi. Is there another source for these?

Here is the error when downloading through COMPSRA: 13:09:40.756 [main] INFO edu.harvard.channing.compass.utility.Download - Start to download the resource: https://regepi.bwh.harvard.edu/circurna/bundle_v1/db/nt/nt_fungi.fasta.gz 13:09:41.339 [main] INFO edu.harvard.channing.compass.utility.Download - Fail to download the resource: https://regepi.bwh.harvard.edu/circurna/bundle_v1/db/nt/nt_fungi.fasta.gz java.io.IOException: Server returned HTTP response code: 500 for URL: https://regepi.bwh.harvard.edu/circurna/bundle_v1/db/nt/nt_fungi.fasta.gz at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1900) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1498) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:268) at org.apache.commons.io.FileUtils.copyURLToFile(FileUtils.java:1484) at edu.harvard.channing.compass.utility.Download.download(Download.java:58) at edu.harvard.channing.compass.toolkit.DownloadResource.downloadResource(DownloadResource.java:211) at edu.harvard.channing.compass.toolkit.DownloadResource.runKit(DownloadResource.java:45) at edu.harvard.channing.compass.toolkit.ProduceTK.Dispatch(ProduceTK.java:41) at edu.harvard.channing.compass.core.COMPSRA.main(COMPSRA.java:54) 13:09:41.340 [main] INFO edu.harvard.channing.compass.core.Produce - ToolKit module was completed.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/cougarlj/COMPSRA/issues/25#issuecomment-965615954, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFTJ5PS5DQB76HVNC5VN7T3ULKZUNANCNFSM5HCENOGA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

cougarlj commented 2 years ago

Dear amyhiteBISR,

Our server doesn't support file download well and we are trying to transfer the resource to other servers. However, this still needs some time. It should be finished early next year.

Best regards, Jiang Li

On Thu, Nov 11, 2021 at 2:19 AM amyhiteBISR @.***> wrote:

I am having the same problem. I'm assuming server connection problems. I was able to download the archaea manually, but get errors on virus, bacteria, and fungi. Is there another source for these?

Here is the error when downloading through COMPSRA: 13:09:40.756 [main] INFO edu.harvard.channing.compass.utility.Download - Start to download the resource: https://regepi.bwh.harvard.edu/circurna/bundle_v1/db/nt/nt_fungi.fasta.gz 13:09:41.339 [main] INFO edu.harvard.channing.compass.utility.Download - Fail to download the resource: https://regepi.bwh.harvard.edu/circurna/bundle_v1/db/nt/nt_fungi.fasta.gz java.io.IOException: Server returned HTTP response code: 500 for URL: https://regepi.bwh.harvard.edu/circurna/bundle_v1/db/nt/nt_fungi.fasta.gz at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1900) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1498) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:268) at org.apache.commons.io.FileUtils.copyURLToFile(FileUtils.java:1484) at edu.harvard.channing.compass.utility.Download.download(Download.java:58) at edu.harvard.channing.compass.toolkit.DownloadResource.downloadResource(DownloadResource.java:211) at edu.harvard.channing.compass.toolkit.DownloadResource.runKit(DownloadResource.java:45) at edu.harvard.channing.compass.toolkit.ProduceTK.Dispatch(ProduceTK.java:41) at edu.harvard.channing.compass.core.COMPSRA.main(COMPSRA.java:54) 13:09:41.340 [main] INFO edu.harvard.channing.compass.core.Produce - ToolKit module was completed.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/cougarlj/COMPSRA/issues/25#issuecomment-965615954, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABGMADY6T3KSW5E6AZ76HOLULKZUNANCNFSM5HCENOGA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

cougarlj commented 2 years ago

Dear 84AP,

Our server doesn't support file download well and we are trying to transfer the resource to other servers. However, this still needs some time. It should be finished early next year.

Best regards, Jiang Li

On Thu, Nov 11, 2021 at 5:00 AM 84AP @.***> wrote:

I am trying to download from https://regepi.bwh.harvard.edu/circurna/ however the site is protected and I cannot download the files. Could you share a compressed folder?

Il mer 10 nov 2021, 19:19 amyhiteBISR @.***> ha scritto:

I am having the same problem. I'm assuming server connection problems. I was able to download the archaea manually, but get errors on virus, bacteria, and fungi. Is there another source for these?

Here is the error when downloading through COMPSRA: 13:09:40.756 [main] INFO edu.harvard.channing.compass.utility.Download - Start to download the resource:

https://regepi.bwh.harvard.edu/circurna/bundle_v1/db/nt/nt_fungi.fasta.gz 13:09:41.339 [main] INFO edu.harvard.channing.compass.utility.Download - Fail to download the resource:

https://regepi.bwh.harvard.edu/circurna/bundle_v1/db/nt/nt_fungi.fasta.gz java.io.IOException: Server returned HTTP response code: 500 for URL:

https://regepi.bwh.harvard.edu/circurna/bundle_v1/db/nt/nt_fungi.fasta.gz at

sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1900) at

sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1498) at

sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:268) at org.apache.commons.io.FileUtils.copyURLToFile(FileUtils.java:1484) at edu.harvard.channing.compass.utility.Download.download(Download.java:58) at

edu.harvard.channing.compass.toolkit.DownloadResource.downloadResource(DownloadResource.java:211) at

edu.harvard.channing.compass.toolkit.DownloadResource.runKit(DownloadResource.java:45) at

edu.harvard.channing.compass.toolkit.ProduceTK.Dispatch(ProduceTK.java:41) at edu.harvard.channing.compass.core.COMPSRA.main(COMPSRA.java:54) 13:09:41.340 [main] INFO edu.harvard.channing.compass.core.Produce - ToolKit module was completed.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/cougarlj/COMPSRA/issues/25#issuecomment-965615954, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AFTJ5PS5DQB76HVNC5VN7T3ULKZUNANCNFSM5HCENOGA

. Triage notifications on the go with GitHub Mobile for iOS < https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675

or Android < https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/cougarlj/COMPSRA/issues/25#issuecomment-965741715, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABGMAD6XEOQK2HQR7MJY5CLULLMPLANCNFSM5HCENOGA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.