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input file issue with pipeline_rnaseqtranscripts.py #94

Closed csandorfr closed 7 years ago

csandorfr commented 9 years ago

Hi

pipeline_rnaseqtranscripts.py have some issue to find the file geneset_all.gtf.gz used by buildReferenceGeneSet.

when I configure the following parameters in pipeline.ini

like this (1) directory with annotation information dir=/net/isi-scratch/cynthia/DATA/Parkinson/RNAseq/bsg-ftp.well.ox.ac.uk/ANNOTATIONS

I have this error:

No way to run job: Input file '/net/isi-scratch/cynthia/DATA/Parkinson/RNAseq/bsg-ftp.well.ox.ac.uk/ANNOTATIONS/geneset_all.gtf.gz' does not exist

like this (2)

directory with annotation information dir=/net/isi-scratch/cynthia/DATA/Parkinson/RNAseq/bsg-ftp.well.ox.ac.uk/ANNOTATIONS/ensembl.dir

I have this error: No way to run job: Input file '/net/isi-scratch/cynthia/DATA/Parkinson/RNAseq/bsg-ftp.well.ox.ac.uk/ANNOTATIONS/ensembl.dir/ensembl.dir/geneset_all.gtf.gz' does not exist

I updated the pipeline.

Cynthia

AndreasHeger commented 9 years ago

@csandorfr , thanks. Recently the layout of the annotations pipeline has changed. The configuration should be (1):

dir=/net/isi-scratch/cynthia/DATA/Parkinson/RNAseq/bsg-ftp.well.ox.ac.uk/ANNOTATIONS

but you might need to re-run the annotations pipeline to create the correct files.

csandorfr commented 9 years ago

Thanks

OK it doesn't work with dir=/net/isi-scratch/cynthia/DATA/Parkinson/RNAseq/bsg-ftp.well.ox.ac.uk/ANNOTATIONS

I have this error: No way to run job: Input file '/net/isi-scratch/cynthia/DATA/Parkinson/RNAseq/bsg-ftp.well.ox.ac.uk/ANNOTATIONS/geneset_all.gtf.gz' does not exist

I'm updating the pipelines and I will re run pipeline_annotations.py

csandorfr commented 9 years ago

I updated my version of CGAT pipelines (with git, the date of file changed). I re-ran the pipeline_annotations. However I have still the same error:

check_input_files_exist (*param) File "/net/isi-scratch/cynthia/CGAT-DEPS/virtualenv-1.11.6/cgat-venv/lib/python2.7/site-packages/ruffus/file_name_parameters.py", line 381, in check_input_files_exist "Input file '%s' does not exist" % f) MissingInputFileError: 

                                                     No way to run job: Input file '/net/isi-scratch/cynthia/DATA/Parkinson/RNAseq/bsg-ftp.well.ox.ac.uk/ANNOTATIONS2/geneset_all.gtf.gz' does not exist