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Question: (QuasR Error) Error in checkForRemoteErrors(val) : one node produced an error: bowtie failed to perform the alignments
0
gravatar for tarek.mohamed
14 months ago by
tarek.mohamed0 wrote:

My name is Tarek , I am using QuasR package for RNAseq analysis ( I have 12 samples of paired end reads). I

did alignment using

sampleFile <- "2_DOX_RNAseq.txt"
genomeFile<-"BSgenome.Hsapiens.NCBI.GRCh38"
proj <- qAlign(sampleFile, genomeFile)

It was successful for 8 samples , then I got an error message 

" one node produced an error: Error on FSMMJ02UCX1 processing sample C:\Users\tmm447\AppData\Local\Temp\RtmpkLS7LW\CON3_0uM_1.fastq.gz1ae8210858ab.fastq : bowtie failed to perform the alignments"  

 

I re-did the analysis and I got the same errorr again. 

How can I solve this issue and why it worked successfully for 8 samples then it was stuck.

 

Thanks

Tarek

ADD COMMENTlink modified 14 months ago • written 14 months ago by tarek.mohamed0
0
gravatar for Hotz, Hans-Rudolf
14 months ago by
Switzerland
Hotz, Hans-Rudolf370 wrote:

Hi Tarek

Maybe there is something wrong with the two fastq files of the 9th sample. What happened if you create a new sampleFile with just the 10th, eleventh, and twelfth sample?

If this also fails, you might have run out of 'tmp' space. Check C:\Users\tmm447\AppData\Local\Temp\ . You might need to set an alternative location (see chapter 4.1 "File storage locations") in the QuasR vignette.

Hope this helps

Hans-Rudolf

 

 

ADD COMMENTlink written 14 months ago by Hotz, Hans-Rudolf370

Hi Hans,

Thanks for you reply, I think the last problem was because of space issue in tempdir. I deleted some files to be able to continue. could you please tell me how can I change the temporary directory?

Now I have a new problem ,I have updated both R and R studio to the latest versions.I tried to complete the analysis and now I got an error before It did not even align a single file

alignment files missing - need to:
    create alignment index for the genome
    create 12 genomic alignment(s)
will start in ..9s..8s..7s..6s..5s..4s..3s..2s..1s
Creating an Rbowtie index for C:\Users\tmm447\AppData\Local\Temp\Rtmp46j2ry\fileb884215693f.fa
Finished creating index
Installing package into ‘C:/Users/tmm447/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
* installing *source* package 'BSgenome.Hsapiens.NCBI.GRCh38.Rbowtie' ...
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* DONE (BSgenome.Hsapiens.NCBI.GRCh38.Rbowtie)

Testing the compute nodes...OK
Loading QuasR on the compute nodes...Error in checkForRemoteErrors(lapply(cl, recvResult)) : 
 one node produced an error: package or namespace load failed for 'QuasR
'

Thanks 

Tarek

ADD REPLYlink written 14 months ago by tarek.mohamed0
0
gravatar for tarek.mohamed
14 months ago by
tarek.mohamed0 wrote:

Hi Hans,

Thanks for you reply, I think the last problem was because of space issue in tempdir. I deleted some files to be able to continue. could you please tell me how can I change the temporary directory?

Now I have a new problem ,I have updated both R and R studio to the latest versions.I tried to complete the analysis and now I got an error before It did not even align a single file

alignment files missing - need to:
    create alignment index for the genome
    create 12 genomic alignment(s)
will start in ..9s..8s..7s..6s..5s..4s..3s..2s..1s
Creating an Rbowtie index for C:\Users\tmm447\AppData\Local\Temp\Rtmp46j2ry\fileb884215693f.fa
Finished creating index
Installing package into ‘C:/Users/tmm447/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
* installing *source* package 'BSgenome.Hsapiens.NCBI.GRCh38.Rbowtie' ...
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* DONE (BSgenome.Hsapiens.NCBI.GRCh38.Rbowtie)

Testing the compute nodes...OK
Loading QuasR on the compute nodes...Error in checkForRemoteErrors(lapply(cl, recvResult)) : 
 one node produced an error: package or namespace load failed for 'QuasR
'

Thanks 

Tarek

ADD COMMENTlink written 14 months ago by tarek.mohamed0
0
gravatar for tarek.mohamed
14 months ago by
tarek.mohamed0 wrote:

Hi Hans,

Thanks for you reply, I think the last problem was because of space issue in tempdir. I deleted some files to be able to continue. could you please tell me how can I change the temporary directory?

Now I have a new problem ,I have updated both R and R studio to the latest versions.I tried to complete the analysis and now I got an error before It did not even align a single file

alignment files missing - need to:
    create alignment index for the genome
    create 12 genomic alignment(s)
will start in ..9s..8s..7s..6s..5s..4s..3s..2s..1s
Creating an Rbowtie index for C:\Users\tmm447\AppData\Local\Temp\Rtmp46j2ry\fileb884215693f.fa
Finished creating index
Installing package into ‘C:/Users/tmm447/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
* installing *source* package 'BSgenome.Hsapiens.NCBI.GRCh38.Rbowtie' ...
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* DONE (BSgenome.Hsapiens.NCBI.GRCh38.Rbowtie)

Testing the compute nodes...OK
Loading QuasR on the compute nodes...Error in checkForRemoteErrors(lapply(cl, recvResult)) : 
 one node produced an error: package or namespace load failed for 'QuasR
'

Thanks 

Tarek

ADD COMMENTlink written 14 months ago by tarek.mohamed0

Hi Tarek

 

I am glad to hear, you manage to solve your problem by cleaning up the tempdir.

As I wrote in my first answer, you can change the temdir to an alternative location (see chapter 4.1 "File storage locations" in the QuasR vignette.)

WRT you new problem, I recommend you start a new thread, with a new subject line. Also, include the output of 'sessionInfo()'

 

Regards, Hans-Rudolf

ADD REPLYlink written 14 months ago by Hotz, Hans-Rudolf370
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