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plagnollab / RNASeq_pipeline

Set of scripts for RNA-Seq data processing
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cannot find bundle/human_hg38/biomart/biomart_annotations_human.tab #7

Closed pontikos closed 8 years ago

pontikos commented 8 years ago

Is this file not meant to be stored in the repo?

> annotations <- read.table(annotation.file, header = TRUE, sep = '\t', quote = "")
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file '/home/rmhanpo/bin/RNASeq_pipeline/bundle/human_hg38/biomart/biomart_annotations_human.tab': No such file or directory
Execution halted
vplagnol commented 8 years ago

Are you using the version 7 or 8 of the pipeline? I am trying to rationalize the locations:

/scratch2/vyp-scratch2/reference_datasets/RNASeq/Human_hg38/

On Thu, Nov 26, 2015 at 1:47 PM, Nikolas Pontikos notifications@github.com wrote:

Is this file not meant to be stored in the repo?

annotations <- read.table(annotation.file, header = TRUE, sep = '\t', quote = "") Error in file(file, "rt") : cannot open the connection Calls: read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file '/home/rmhanpo/bin/RNASeq_pipeline/bundle/human_hg38/biomart/biomart_annotations_human.tab': No such file or directory Execution halted

— Reply to this email directly or view it on GitHub https://github.com/plagnollab/RNASeq_pipeline/issues/7.

Vincent Plagnol University College London Genetics Institute Darwin building, office 210 Gower Street, London, WC1E 6BT Cell: +44-(0)7946-546923 Office: +44-(0) 2031-084002 Website: http://www.ucl.ac.uk/ugi/research/vincentplagnol Lab blog: http://plagnol-lab.blogspot.co.uk/

pontikos commented 8 years ago

version 8

On 26 November 2015 at 13:53, Vincent Plagnol notifications@github.com wrote:

Are you using the version 7 or 8 of the pipeline? I am trying to rationalize the locations:

/scratch2/vyp-scratch2/reference_datasets/RNASeq/Human_hg38/

On Thu, Nov 26, 2015 at 1:47 PM, Nikolas Pontikos < notifications@github.com> wrote:

Is this file not meant to be stored in the repo?

annotations <- read.table(annotation.file, header = TRUE, sep = '\t', quote = "") Error in file(file, "rt") : cannot open the connection Calls: read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file '/home/rmhanpo/bin/RNASeq_pipeline/bundle/human_hg38/biomart/biomart_annotations_human.tab': No such file or directory Execution halted

— Reply to this email directly or view it on GitHub https://github.com/plagnollab/RNASeq_pipeline/issues/7.

Vincent Plagnol University College London Genetics Institute Darwin building, office 210 Gower Street, London, WC1E 6BT Cell: +44-(0)7946-546923 Office: +44-(0) 2031-084002 Website: http://www.ucl.ac.uk/ugi/research/vincentplagnol Lab blog: http://plagnol-lab.blogspot.co.uk/

— Reply to this email directly or view it on GitHub https://github.com/plagnollab/RNASeq_pipeline/issues/7#issuecomment-159921361 .

vplagnol commented 8 years ago

So version 8 should find all of these files, I am surprised you still have links pointing to some other location. I need to figure out what links are causing the pbm.

On Thu, Nov 26, 2015 at 2:12 PM, Nikolas Pontikos notifications@github.com wrote:

version 8

On 26 November 2015 at 13:53, Vincent Plagnol notifications@github.com wrote:

Are you using the version 7 or 8 of the pipeline? I am trying to rationalize the locations:

/scratch2/vyp-scratch2/reference_datasets/RNASeq/Human_hg38/

On Thu, Nov 26, 2015 at 1:47 PM, Nikolas Pontikos < notifications@github.com> wrote:

Is this file not meant to be stored in the repo?

annotations <- read.table(annotation.file, header = TRUE, sep = '\t', quote = "") Error in file(file, "rt") : cannot open the connection Calls: read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file

'/home/rmhanpo/bin/RNASeq_pipeline/bundle/human_hg38/biomart/biomart_annotations_human.tab': No such file or directory

Execution halted

— Reply to this email directly or view it on GitHub https://github.com/plagnollab/RNASeq_pipeline/issues/7.

Vincent Plagnol University College London Genetics Institute Darwin building, office 210 Gower Street, London, WC1E 6BT Cell: +44-(0)7946-546923 Office: +44-(0) 2031-084002 Website: http://www.ucl.ac.uk/ugi/research/vincentplagnol Lab blog: http://plagnol-lab.blogspot.co.uk/

— Reply to this email directly or view it on GitHub < https://github.com/plagnollab/RNASeq_pipeline/issues/7#issuecomment-159921361

.

— Reply to this email directly or view it on GitHub https://github.com/plagnollab/RNASeq_pipeline/issues/7#issuecomment-159924796 .

Vincent Plagnol University College London Genetics Institute Darwin building, office 210 Gower Street, London, WC1E 6BT Cell: +44-(0)7946-546923 Office: +44-(0) 2031-084002 Website: http://www.ucl.ac.uk/ugi/research/vincentplagnol

pontikos commented 8 years ago

so the problem i think is the generating script is passing these files on the command line see:

/cluster/project8/vyp/pontikos/People/JessicaGardner/output/cluster/submission/starSubmissionStep3.sh
#!/bin/bash
#$ -S /bin/bash
#$ -o /cluster/project8/vyp/pontikos/People/JessicaGardner/output/cluster/out
#$ -e /cluster/project8/vyp/pontikos/People/JessicaGardner/output/cluster/error
#$ -cwd
#$ -pe smp 4
#$ -l tmem=5.9G,h_vmem=5.9G
#$ -V
#$ -R y
#$ -l h_rt=21:50:00

/cluster/project8/vyp/vincent/Software/R-3.2.2/bin/R CMD BATCH --no-save --no-restore --gff=/scratch2/vyp-scratch2/reference_datasets/RNASeq/Human_hg38/Homo_sapiens.GRCh38.82_fixed.gff --annotation.file=/home/rmhanpo/bin/RNASeq_pipeline/bundle/human_hg38/biomart/biomart_annotations_human.tab --keep.dups=FALSE --support.frame=input-trimmed.txt --code=JessicaGardner_X --iFolder=/cluster/project8/vyp/pontikos/People/JessicaGardner/output /home/rmhanpo/bin/RNASeq_pipeline//counts_prepare_pipeline.R /cluster/project8/vyp/pontikos/People/JessicaGardner/output/cluster/R/count_prepare.out

/cluster/project8/vyp/vincent/Software/R-3.2.2/bin/R CMD BATCH --no-save --no-restore --keep.sex=FALSE --support.frame=input-trimmed.txt --keep.dups=FALSE --code=JessicaGardner_X --annotation.file=/home/rmhanpo/bin/RNASeq_pipeline/bundle/human_hg38/biomart/biomart_annotations_human.tab --iFolder=/cluster/project8/vyp/pontikos/People/JessicaGardner/output /home/rmhanpo/bin/RNASeq_pipeline//deseq2_pipeline.R /cluster/project8/vyp/pontikos/People/JessicaGardner/output/cluster/R/deseq_JessicaGardner_X.out

/cluster/project8/vyp/vincent/Software/R-3.2.2/bin/R CMD BATCH --no-save --no-restore --gff=/scratch2/vyp-scratch2/reference_datasets/RNASeq/Human_hg38/Homo_sapiens.GRCh38.82_fixed.gff --keep.sex=FALSE --keep.dups=FALSE --support.frame=input-trimmed.txt --code=JessicaGardner_X --annotation.file=/home/rmhanpo/bin/RNASeq_pipeline/bundle/human_hg38/biomart/biomart_annotations_human.tab --iFolder=/cluster/project8/vyp/pontikos/People/JessicaGardner/output /home/rmhanpo/bin/RNASeq_pipeline//dexseq_pipeline_v2.R /cluster/project8/vyp/pontikos/People/JessicaGardner/output/cluster/R/dexseq_JessicaGardner_X.out
pontikos commented 8 years ago

ok so it's obvious, the culprit is this line: https://github.com/plagnollab/RNASeq_pipeline/blob/master/RNAseq_pipeline_v8.sh#L266

So just hardcode the correct path there?

pontikos commented 8 years ago

Fixed it myself.

https://github.com/plagnollab/RNASeq_pipeline/commit/6ab78d67bcf525b17e67fbe51bcac3bda2c758bb