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qsub command failed with exit status: 172

4

Hello, I am running the pipeline and I am getting this error, could you help me? Thanks! Starting pipeline... 155 jobs to be executed in total Traceback (most recent call...

vealvarez

Error at first stage of pipeline

14

Hi, We are having a bit of trouble getting Red dog to run on our cluster. At this stage we can't seem to get past the first step. We keep...

jasonshiller

Pipeline not progressing past checkBam

8

Hi there, I'm having problems getting RedDog to progress any further than Task=RedDog.checkBam. All tasks up to this point are classified as "up-to-date". I have run ‘errorcheck.txt’ but it did...

RMann24

configuration

12

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...

adrianmu


d-j-e

amendment to large_RedDog_config

1

Add option to up memory for collateRepAlleleMatrix step. Default fails with latest TB dataset

prmcadam

Would be nice if it ran a check at the start to make sure all dependencies were installed and of the right version (like SRST2 does) - and refused to...

jhawkey

At the moment the pipe only takes Illumina paired-end with the endings _1.fastq.gz, _2.fastq.gz. This currently means the user has to rename the reads to match the pattern before running...

d-j-e

merging reads

1

katholt

Bowtie Error "mkfifo"

1

Hi David, I can't remember what this error means and it isn't linked to a particular strain... [lraven@barcoo RedDog_v052]$ cat log/alignBowtiePE.3390684.stderr (ERR): mkfifo(/tmp/26318.inpipe1) failed. Exiting now ... Working directory is...

lesleygray