Error in checkForRemoteErrors(val) : QuasR: can't pass alignment parameters
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@amer-ghalawinji-14376
Last seen 4.2 years ago

Hey :)

I am trying to do a bisulfite alignment with qAlign function. This is my command:

align <- qAlign("/analysis/SampleFile.txt","/analysis/refgenome.fa",aligner="Rbowtie",bisulfite="dir",alignmentParameter=" -m 3 -v 5 --best --strata")

I always get the following error whenever i try to pass alignment parameters no matter what the parameters are:

Error in checkForRemoteErrors(val) :
one node produced an error: Error on server.whorke.de processing sample /testread.fasta : bowtie (CtoT) failed to perform the alignments.

Any suggestion?

Best,

Amer

quasR quasr error alignmentparameters quasr • 869 views
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As Hans-Rudolf already mentioned, changing the QuasR alignment parameters for bisulfite data is not recommended. Regarding the error, what other parameter combinations did you try to conclude that you "always get the following error [...] no matter what the parameters are"? I can reproduce this error on the example data with your provided parameters, but from the bowtie manual (http://bowtie-bio.sourceforge.net/manual.shtml#the--v-alignment-mode) you can read that

In -v mode, alignments may have no more than V mismatches, where V may be a number from 0 through 3 set using the -v option.

If I set -v to e.g. 2 or 3 rather than 5 (i.e., compliant with the bowtie instructions), I do not get an error (again, of course, even if it "works" it does not mean that it's a recommended thing to do).

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Hi Amer

Why do you want to provide "alignment parameters"? Have you read the help text for qAlign?

 If ‘alignmentParameter’ is ‘NULL’ (recommended), ‘qAlign’ will
select default parameters that are suitable for the experiment
type. Please note that for bisulfite or allele-specific
experiments, each read is aligned multiple times, and resulting
alignments need to be combined. This requires special settings for
the alignment parameters that are not recommended to be changed.


Regards, Hans-Rudolf