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Published 20 hours ago • verified publisher icon katholt

configuration

Open adrianmu opened this issue 9 years ago • 12 comments

Hello, i must admit that i am a novice at this, but bear with me, i am trying to configure this pipe line, it is not so clear where these configurations should be made.

In the manual you say that all can be done in RedDog_config.py , i have tried editing this file to include the directory to my reference and reads by i have no permission. i have tried "chmod u+x" this does not work either, could you please help

Adrian

adrianmu avatar Aug 18 '15 17:08 adrianmu

Hi Adrian, RedDog is loaded to Github with permissions set to 770 (i.e. user and group can read, write or execute) - so it sounds like permision problems at your end...

Try making a copy of the config file and use that: e.g change directory to the RedDog folder, and then: cp RedDog_config.py ./my_config.py you should then be able to edit or change permissions on the copy you make. If not, seek out your nearest IT administrator... hope this helps, David

d-j-e avatar Aug 18 '15 23:08 d-j-e

Many thanks...

Sent from my iPad

On 19 Aug 2015, at 00:36, d-j-e [email protected] wrote:

Hi Adrian, RedDog is loaded to Github with permissions set to 770 (i.e. user and group can read, write or execute) - so it sounds like permision problems at your end...

Try making a copy of the config file and use that: e.g change directory to the RedDog folder, and then: cp RedDog_config.py ./my_config.py you should then be able to edit or change permissions on the copy you make. If not, seek out your nearest IT administrator... hope this helps, David

— Reply to this email directly or view it on GitHub.

adrianmu avatar Aug 19 '15 13:08 adrianmu

Hello David, i am stuck again, here is the error message i get.. i managed to configure the pipelines but something is amiss as it aborts ...

RedDog V1beta.4 - phylogeny run

Copyright (c) 2015, David Edwards, Bernie Pope, Kat Holt

All rights reserved. (see README.txt for more details)

Mapping: Bowtie2 V2.2.3

Preset Option: --sensitive-local

1 replicon(s) in FASTA reference NC_002945

1 replicon(s) to be reported

0 sequence pair(s) to be mapped

Output folder:

/groups2/bronsvoort_grp/SOFTWARE/test1_output/

Start Pipeline? (y/n) y

Starting pipeline...

17 jobs to be executed in total

Tasks which will be run:

Task = RedDog.makeDir

   Job = [False

         ->dir.makeDir.Success]

     Job needs update: Missing file

/groups2/bronsvoort_grp/SOFTWARE/test1_output/temp/success/dir.makeDir.Success

Task = RedDog.copyRef

   Job = [NC_002945.fna

         ->[NC_002945.fna, NC_002945.copyRef.Success]]

     Job needs update: Missing file

/groups2/bronsvoort_grp/SOFTWARE/test1_output/temp/NC_002945.fna

Task = RedDog.buildBowtieIndex

   Job = [NC_002945.fna

         ->[NC_002945.1.bt2, NC_002945.buildBowtieIndex.Success]]

     Job needs update: Missing file

/groups2/bronsvoort_grp/SOFTWARE/test1_output/temp/NC_002945.fna

Task = RedDog.alignBowtiePE

   !!! No jobs for this task. Are you sure there is not a error in your

code / regular expression?

Task = RedDog.checkBam

   !!! No jobs for this task. Are you sure there is not a error in your

code / regular expression?

Task = RedDog.indexBam

   !!! No jobs for this task. Are you sure there is not a error in your

code / regular expression?

Task = RedDog.getSamStats

   !!! No jobs for this task. Are you sure there is not a error in your

code / regular expression?

Task = RedDog.checkpoint_getSamStats

   Job = [[]

         ->[checkpoint.txt, getSamStats.checkpoint.Success]]

     Job needs update: Missing file

/groups2/bronsvoort_grp/SOFTWARE/test1_output/temp/checkpoint.txt

Task = RedDog.filterUnmapped

   !!! No jobs for this task. Are you sure there is not a error in your

code / regular expression?

On Wed, Aug 19, 2015 at 2:15 PM, Adrian Muwonge [email protected] wrote:

Many thanks...

Sent from my iPad

On 19 Aug 2015, at 00:36, d-j-e [email protected] wrote:

Hi Adrian, RedDog is loaded to Github with permissions set to 770 (i.e. user and group can read, write or execute) - so it sounds like permision problems at your end...

Try making a copy of the config file and use that: e.g change directory to the RedDog folder, and then: cp RedDog_config.py ./my_config.py you should then be able to edit or change permissions on the copy you make. If not, seek out your nearest IT administrator... hope this helps, David

— Reply to this email directly or view it on GitHub https://github.com/katholt/RedDog/issues/39#issuecomment-132391097.

adrianmu avatar Aug 20 '15 08:08 adrianmu

What is your entry for 'sequences' in the config file?

d-j-e avatar Aug 20 '15 08:08 d-j-e

Hello David, this is how i have edited the RedDog_config.py file

Essential pipeline variables.

'''

reference = "/groups2/bronsvoort_grp/SOFTWARE/NC_002945.fna"

#reference = "/full_path_to/pipeline_test_sets/reference/NC_007384_with_plasmid.gbk"

sequences = "/groups2/bronsvoort_grp/SOFTWARE/trial/*.fastq.gz"

#sequences = "/full_path_to/pipeline_test_sets/*.fastq.gz"

#sequences = "/full_path_to/pipeline_test_sets/*.fastq.gz"

output = "/groups2/bronsvoort_grp/SOFTWARE/test1_output"

#output = "/full_path_to/<your_directory>/RedDog_output//"

out_merge_target = ""

#out_merge_target = "/full_path_to/<your_directory>/RedDog_output//"

On Thu, Aug 20, 2015 at 9:45 AM, d-j-e [email protected] wrote:

What is your entry for 'sequences' in the config file?

— Reply to this email directly or view it on GitHub https://github.com/katholt/RedDog/issues/39#issuecomment-132941141.

adrianmu avatar Aug 20 '15 13:08 adrianmu

Okay, I think I know what is going on - but just to check could you run the following: cd /groups2/bronsvoort_grp/SOFTWARE/trial/ ls -lh

and send me the list of files it should generate...

The pipeline currently only accepts reads with the one pattern - for paired end reads this is _1.fastq.gz and _2.fastq.gz

d-j-e avatar Aug 20 '15 23:08 d-j-e

hello David here are the contents of that file

[amuwonge@ris-lx02 trial]$ ls -lh

total 393M

-rwxr-xr-x 1 amuwonge bronsvoort_grp 83M Aug 18 17:10 BBB01315ME_1.fastq.gz

-rwxr-xr-x 1 amuwonge bronsvoort_grp 88M Aug 18 17:11 BBB01315ME_2.fastq.gz

-rwxr-xr-x 1 amuwonge bronsvoort_grp 64M Aug 18 17:11 BBB01533ME_1.fastq.gz

-rwxr-xr-x 1 amuwonge bronsvoort_grp 68M Aug 18 17:12 BBB01533ME_2.fastq.gz

-rwxr-xr-x 1 amuwonge bronsvoort_grp 43M Aug 18 17:11 DDD00321ME_1.fastq.gz

-rwxr-xr-x 1 amuwonge bronsvoort_grp 48M Aug 18 17:11 DDD00321ME_2.fastq.gz

On Fri, Aug 21, 2015 at 12:43 AM, d-j-e [email protected] wrote:

Okay, I think I know what is going on - but just to check could you run the following: cd /groups2/bronsvoort_grp/SOFTWARE/trial/ ls -lh

and send me the list of files it should generate...

The pipeline currently only accepts reads with the one pattern - for paired end reads this is _1.fastq.gz and _2.fastq.gz

— Reply to this email directly or view it on GitHub https://github.com/katholt/RedDog/issues/39#issuecomment-133212309.

adrianmu avatar Aug 24 '15 08:08 adrianmu

Those names should work - the only thing I can think of is that you haven't given the full path.

Can you try the following? cd /groups2/bronsvoort_grp/SOFTWARE/trial/ pwd

and check the path it returns - this is the full path. If this is the same as you are using in the config file let me know asap - I have a bug to find. Otherwise, edit the paths in your config to match.

d-j-e avatar Aug 24 '15 11:08 d-j-e

hello David, it is the correct path i am using.. see below

[amuwonge@ris-lx02 trial]$ pwd

/groups2/bronsvoort_grp/SOFTWARE/trial

On Mon, Aug 24, 2015 at 12:26 PM, d-j-e [email protected] wrote:

Those names should work - the only thing I can think of is that you haven't given the full path.

Can you try the following? cd /groups2/bronsvoort_grp/SOFTWARE/trial/ pwd

and check the path it returns - this is the full path. If this is the same as you are using in the config file let me know asap - I have a bug to find. Otherwise, edit the paths in your config to match.

— Reply to this email directly or view it on GitHub https://github.com/katholt/RedDog/issues/39#issuecomment-134158309.

adrianmu avatar Aug 24 '15 13:08 adrianmu

Hi Adrian,

sorry for the delay in getting onto this - have another project on the go...

At the moment I'm flummoxed, especially as I can't replicate the error. Can you open up the main RedDog.py file and find the following line: # print "\nRAxML output ext: " + raxExt

Then add the three following lines immediately after this line and save: print sequencePatterns print sequences print sequence_list

Then rerun RedDog and post screen output from number of sequences to be mapped to when asked if you want to start the pipeline run.

David

d-j-e avatar Aug 27 '15 03:08 d-j-e

errorlog.txt Dear David,

Please have a look at error log file to find the possible reason for the error and suggest the solution.

Thanks and Happy New Year.

Mohd Wasif Khan Kuwait University

wasifkhan88 avatar Dec 31 '15 12:12 wasifkhan88

Hi Mohd Wasif Khan, first of apologies for not getting back to you sooner, was on holiday...

I have seen something like this before... It looks as though there is no python available for the job to run properly - check the version of python on your system (it needs to be 2.5+ with Biopython installed..) then make sure exactly the same version is in the list of modules in the config file.

cheers, David

d-j-e avatar Jan 10 '16 21:01 d-j-e