snandiDS
commented
2 years ago ---------- Forwarded message --------- From: Firoj Mahmud @.> Date: Fri, May 6, 2022 at 4:26 PM Subject: Re: [snandiDS/prokseq-v2.0] RUVg / RUVseq - execution halted (Issue #9) To: Soumyadeep Nandi @.>
It seems, there was no set of control genes predicted. So either, the control genes file should be added or RUVseq parameter should be switched off to see if this is the reason. If there is a variation in biological replicate, control set of genes may be not predicted by RUVseq
/Firoj
From: Soumyadeep Nandi @.**> Sent: Friday, May 6, 2022 9:48:11 AM To: Firoj Mahmud Subject:* Fwd: [snandiDS/prokseq-v2.0] RUVg / RUVseq - execution halted (Issue #9)
Hi Firoj,
Any idea regarding the error?
Best, Soumyadeep
---------- Forwarded message --------- From: criskzimpel @.> Date: Thu, May 5, 2022 at 2:43 AM Subject: [snandiDS/prokseq-v2.0] RUVg / RUVseq - execution halted (Issue #9) To: snandiDS/prokseq-v2.0 @.> Cc: Subscribed @.***>
I was able to run most of the pipeline; But after NOISeq I am getting an error with RUVseq as follow:
Rscript --vanilla /root/prokseq/depend/RUVSeq_pe.r samples.bowtie.PEsample param.bowtie.yaml 0 testFile.bgl Status : FAIL 1 Loading required package: Biobase .... Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
null device 1 null device 1 Error in svd(Ycenter[, cIdx]) : a dimension is zero Calls: RUVg -> RUVg -> RUVg -> RUVg -> svd Execution halted
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I was able to run most of the pipeline; But after NOISeq I am getting an error with RUVseq as follow:
Rscript --vanilla /root/prokseq/depend/RUVSeq_pe.r samples.bowtie.PEsample param.bowtie.yaml 0 testFile.bgl Status : FAIL 1 Loading required package: Biobase .... Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
null device 1 null device 1 Error in svd(Ycenter[, cIdx]) : a dimension is zero Calls: RUVg -> RUVg -> RUVg -> RUVg -> svd Execution halted