User: Tom

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Tom10
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Posts by Tom

<prev • 32 results • page 2 of 4 • next >
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Answer: A: CopywriteR error: "Error in .Method"
... I looked inside the Copywriter.log file and it ended with: INFO [2016-07-12 14:35:29] remote-error in value[[3L]](cond): failed to open BamFile: file(s) do not exist:   ‘XXX(one of my bam files).bam’ I corrected the wrong path and then CopywriteR() ended successfully.   ...
written 3.4 years ago by Tom10
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Comment: C: CopywriteR error: "Error in .Method"
... Keith, Thank you for your reply. The head (n=5) of BAMlist.txt is: /home/tom/ngs/data/output/barcode/160405_Target/bam/s_TA_C001D/s_TA_C001D.markdup.bam /home/tom/ngs/data/output/barcode/160405_Target/bam/s_TA_C002D/s_TA_C002D.markdup.bam /home/tom/ngs/data/output/barcode/160405_Target/bam/s_TA_C ...
written 3.4 years ago by Tom10
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CopywriteR error: "Error in .Method"
... Dear all, I have used CopywriteR package with sequencing data and got an error. Because I previously got a successful result with a different set of bam files, I think the problem would be the bam list (or some of the bam files), but I don't figure out what exactly is the problem. My script, erro ...
copywriter written 3.4 years ago by Tom10
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Comment: C: UCSC web service API
... Make sure you are actually loading the rtracklayer 1.33.9 by sessionInfo() ...
written 3.4 years ago by Tom10
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Answer: A: Gviz error 'Expectation Failed'
... *Summary: The error messages below seem to occur when you are in outside of the region of a UCSC mirror which you try to use. Using rtracklayer 1.33.9 (now in devel) solved my problem.   *Error messages: > library(rtracklayer) > session <- browserSession() > genome(session) <- " ...
written 3.4 years ago by Tom10
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Comment: C: Gviz error 'Expectation Failed'
... Dear all, I tried the development version of rtracklayer and it worked perfectly. Because I have been working on this problem from Japan, that error seems to appear, as Michael mentioned, when we try to access UCSC (mirror) using the package from outside of their region. Many thanks for all your a ...
written 3.4 years ago by Tom10
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Comment: C: Gviz error 'Expectation Failed'
... How can I set redirect=manual for rtracklayer? ...
written 3.4 years ago by Tom10
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Comment: C: Gviz error 'Expectation Failed'
... Hmmm... Do you think we can solve it on our end? or should I make an inquiry at UCSC genome browser web page? ...
written 3.5 years ago by Tom10
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Comment: C: Gviz error 'Expectation Failed'
... Martin, I tried your test codes. The outputs with genome(session)="hg19" were: > genome(session)="hg19" * Adding handle: conn: 0x111004800 * Adding handle: send: 0 * Adding handle: recv: 0 * Curl_addHandleToPipeline: length: 1 * - Conn 2 (0x111004800) send_pipe: 1, recv_pipe: 0 * About to con ...
written 3.5 years ago by Tom10
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Comment: C: Gviz error 'Expectation Failed'
... Yes, absolutely frustrating...  and I really appreciate Martin's and your help. As Asma wrote on C: Error when using Gviz, IdeogramTrack() and library(rtracklayer) session <- browserSession() genome(session) <- "hg38" passed w/ "genome" set to the latest hg38. Seems like the problem is som ...
written 3.5 years ago by Tom10

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Popular Question 2.8 years ago, created a question with more than 1,000 views. For Gviz error 'Expectation Failed'

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