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Novartis / EQP-cluster

Unix-based RNA-seq quantification pipeline
Apache License 2.0
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Unable to run process-samples.sh Split on demo data or my own #5

Closed hmgill closed 3 years ago

hmgill commented 3 years ago

Hello,

I installed the EQP-cluster as per the instructions & it seems to have installed without any problems (creation of Bowtie2 indices completed).

When I attempt to use Split though (./process-samples.sh split), I get the message below:

Samples: sample1 sample2 Sample sample1 Split job SP-sample1-209 is still in job queue ... skipping sample sample1 Sample sample2 Split job SP-sample2-209 is still in job queue ... skipping sample sample2

This also happens when I try the -noqsub 1 option. I also tried using my own data but the same message appears. There is also no data in the log and fastq files subdirectories in the sample 1, 2 directories.

Wasn't able to find anything online about this. I was wondering what I should try? Please let me know if there is something I can clarify

Thanks in advance! Hunter

sven0schuierer commented 3 years ago

Hi Hunter,

As you have probably seen this repository has not been maintained for a couple of years, mainly due to lack of interest and I am also working on other projects now. I am sorry.

I would suggest to use the rail pipeline of recount2 (https://github.com/leekgroup/recount-contributions) which also delivers gene, exon, and junction counts and which is still maintained.

Best regards,

Sven