LncPipeReporter (Generating report ...)` terminated with an error exit status (1)

[sateeshperi]

Aug-09 02:25:52.700 [Task monitor] ERROR nextflow.processor.TaskProcessor - Erro
r executing process > 'Run_LncPipeReporter (Generating report ...)'

Caused by:
  Process `Run_ #LncPipeReporter (Generating report ...)` terminated with an error
 exit status (1)

Command executed:

  Rscript -e "library(LncPipeReporter);run_reporter(input='.', output = 'reporte
r.html',output_dir='./LncPipeReports',de.method='deseq2',theme = 'npg',cdf.perce
nt = 10,max.lncrna.len = 10000,min.expressed.sample = 50, ask = FALSE)"

Command exit status:
  1
-----
Oops... Pipeline execution stopped with the following message: 

processing file: reporter.Rmd

processing file: ./Hisat2.Rmd

processing file: ./deseq2.Rmd
converting counts to integer mode
Quitting from lines 9-27 (./deseq2.Rmd) 
Quitting from lines NA-98 (./deseq2.Rmd) 
Error in counts(dds) : could not find function "counts"
Calls: run_reporter ... withVisible -> eval -> eval -> rowSums -> is.data.frame
Execution halted

PFA my nextflow.log. I have a kallisto.count.txt file ~ 4.6MB in my work dir. any thoughts on this?

nextflow.log.txt

nextflow.log.txt

[likelet]

hi，i have never meet this before, but i am sure that the error is from the lncpipereporter. i have contacted the author of the package, he will figure it out soon. can you plz send the count table to me by mail: zhaoqi@sysucc.org.cn ? we are appreciated that you can help us to improve our software

[bioinformatist]

Hi, it's LncPipeReporter's author here. It seems like a problem caused by NAMESPACE of my package. Could you provide us your count table? No matter my bro's email above or mine sun_yu@mail.nankai.edu.cn is ok. Thank you :smile:

[bioinformatist]

This bug has been fixed. If you're using our docker image, pls pull it again about two hours later (it needs time for rebuilding).

[sateeshperi]

After pulling the new docker image, can i '-resume' or will it re-run pipeline again?

[likelet]

yes, you can use -resume option

[sateeshperi]

I ran into the same error even after pulling the latest docker image. I sent you the nextflow.log_0810.txt by e-mail. Do let me know if I am doing something wrong. @bioinformatist @likelet

[likelet]

that is weird, we will check the log ASAP

[bioinformatist]

Please pull the latest doker image then try again. Sorry for inconvenience.

[sateeshperi]

ok

[sateeshperi]

Have a new error running LncPipeReporter, I sent the 081418_nextflow.log to your e-mails. let me know if you are able to find the bug. Thanks

[likelet]

get

[likelet]

@sateeshperi hi, can you plz also send the design.file to me to reproduce the errors? You can just paste it in reply. Thanks~

[bioinformatist]

@sateeshperi It seems you're using LncPipe of old version. Its output data had some problems. You may get latest LncPipe using git pull and then pull the latest docker image again. Thanks.

[sateeshperi]

Here is my design.file:

Fertile:AAhu-FFfer-TTsp-SS1,AAhu-FFfer-TTsp-SS2,AAhu-FFfer-TTsp-SS3,AAhu-FFfer-TTsp-SS4
Infertile:AAhu-FFinfer-TTsp-SS2,AAhu-FFinfer-TTsp-SS3,AAhu-FFinfer-TTsp-SS5,AAhu-FFinfer-TTsp-SS6,AAhu-FFinfer-TTsp-SS7,AAhu-FFinfer-TTsp-SS8,AAhu-FFinfer-TTsp-SS9,AAhu-FFinfer-TTsp-SS10

[sateeshperi]

The latest build on Docker hub from 4hrs ago has an Error status, can i use this?

[sateeshperi]

$ docker pull bioinformatist/lncpipe Using default tag: latest latest: Pulling from bioinformatist/lncpipe Digest: sha256:8c544ec868749550a9eb4c6dc5e14bbb882a3866a0f996c995265bf4a7e13dc4 Status: Image is up to date for bioinformatist/lncpipe:latest

[likelet]

@sateeshperi not that version, the latest build did not success, plz wait few fours, we will rebuilt ASAP.

[bioinformatist]

@sateeshperi We're sorry that the last docker image building is failed due to the poor network between docker hub and hisat2 (one of the dependencies of our pipeline) archive server. It's my carelessness that missed this status. I've re-triggered the building, and it do finish successfully now. You could pull it and try again.

[likelet]

plz also pull the latest lncPipe to rerun your analysis by -resume function

[sateeshperi]

Getting this new error:

$ nextflow -c docker.config run LncRNAanalysisPipe.nf -resume
N E X T F L O W  ~  version 0.31.0
Launching `LncRNAanalysisPipe.nf` [voluminous_lamport] - revision: 003a48066e
ERROR ~ expecting '}', found 'else' @ line 1164, column 6.
       }else if (params.species=="mouse"){
        ^

1 error

 -- Check '.nextflow.log' file for details

[likelet]

sorry... a mistake of missing letter i in https://github.com/likelet/LncPipe/blob/f6810b54ea145fe7eafadc976be4716e86636b56/LncRNAanalysisPipe.nf#L1157 you can fix it in nf file (add an i letter) or try pull again,

[sateeshperi]

Also the .nf file seems to be missing a '}' at line 1601. I added it and was able to launch the workflow

[sateeshperi]

I had to change some reference files so, I am running the pipeline from the beginning. Will update you on how it goes.

[sateeshperi]

ERROR ~ Error executing process > 'Rerun_CPAT_to_evaluate_lncRNA (1)'

Caused by:
  No such property: design for class: nextflow.script.FileInParam

Source block:
      if(params.species=="human"){
          '''
          cpat.py -g !{lncRNA_final_cpat_fasta} \
                                         -x !{params.cpatpath}/dat/Human_Hexamer.tsv \
                                         -d !{params.cpatpath}/dat/Human_logitModel.RData \
                                         -o lncRNA.final.CPAT.out
          '''
      }else if (params.species=="mouse"){
          '''
          cpat.py -g !{lncRNA_final_cpat_fasta} \
                                         -x !{params.cpatpath}/dat/Mouse_Hexamer.tsv \
                                         -d !{params.cpatpath}/dat/Mouse_logitModel.RData \
                                         -o lncRNA.final.CPAT.out
          '''

      }else if (params.species=="zebrafish"){
          '''
          cpat.py -g !{lncRNA_final_cpat_fasta} \
                                         -x !{params.cpatpath}/dat/zebrafish_Hexamer.tsv \
                                         -d !{params.cpatpath}/dat/zebrafish_logitModel.RData \
                                         -o lncRNA.final.CPAT.out
          '''
      }else {
          '''
          cpat.py -g !{lncRNA_final_cpat_fasta} \
                                         -x !{params.cpatpath}/dat/fly_Hexamer.tsv \
                                         -d !{params.cpatpath}/dat/fly_logitModel.RData \
                                         -o lncRNA.final.CPAT.out
          '''

  }

[likelet]

i can not reproduce this error, but i came accrocess another error in the same line , also fixed this. BTW, i added a new feature to help to skip the alignment and assembly proces, which take too much time. if you have this error, means you have alread run the assemble step, plz mv the merged.gtf from you result folder like

     ln -s Result/Merged_assemblies/merged.gtf .

and then rerun the pipe by

nextflow -c docker.config run LncRNAanalysisPipe.nf --merged_gtf merged.gtf -resume --qctools none

--qctools none means you will skip you qc process in quantification step.

sorry again for my mistake, try git pull lncPipe again.

Qi

[brunohhomem]

Hi, how are you guys? I'm having the same problem like @sateeshperi . I'm running mouse data, with the latest docker image, nextflow version and lncpipe git. Someone can help me? pipe.txt I'm running two samples at a time, more than two samples we can't run because my server is weak. I've tried with other samples and with new ref files.

Can I use the generated files without the lncPipeReporter step? If I can't fix this issue, maybe there is another way to work with the generated data? I'm assuming that the data was generated because my issue is on reporter step.