I have some trouble to run taxa_counts.r
here is the error message.
[1] "Started extracting barcode data from fastq files for T117"
Error in validObject(.Object) :
invalid class “SRFilterResult” object: superclass "Mnumeric" not defined in the environment of the object's class
Calls: [ ... SRFilterResult -> new -> initialize -> initialize -> validObject
Execution halted
I'm not sure if it's due to the format of the sequencing file. So the first a few lines of the fa file are listed below.
I have some trouble to run taxa_counts.r here is the error message.
I'm not sure if it's due to the format of the sequencing file. So the first a few lines of the fa file are listed below.
For the same concern of the sequencing file, I tried another sample, listed here.
while I got error message again, but not the same one as the first try.
there is no sample taxa file. I'm not sure if the taxa file I used for --taxa is correct. So the first couple of lines are listed here, just in case.
<link id=Main-File rel=Main-File href="file:////Users/rwang10/Library/Group%20Containers/UBF8T346G9.Office/TemporaryItems/msohtmlclip/clip.htm"> <link rel=File-List href="file:////Users/rwang10/Library/Group%20Containers/UBF8T346G9.Office/TemporaryItems/msohtmlclip/clip_filelist.xml">
taxid.x | r | p | name | r1 | r2 | r3 | p1 | p2 | p3 | rank | CLrpmm | taxid.y | rpmm -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- 27291 | 1 | 0 | Saccharomyces paradoxus | 0.8 | 0.6 | 0.8 | 0.33333333 | 0.41666667 | 0.33333333 | S | 939.562791 | 27291 | 6.67252069 28985 | 0.99998343 | 0 | Kluyveromyces lactis | 0.82857143 | 0.82857143 | 1 | 0.05833333 | 0.05833333 | 0.00277778 | S | 5744.24666 | 28985 | 218.858679 76775 | 0.8665019 | 1.02E-103 | Malassezia restricta | 0.57142857 | 0.89285714 | 0.53571429 | 0.2 | 0.01230159 | 0.23571429 | S | 14610.0636 | 76775 | 1698.82377