Error running
Jake
My name is Jake, and I am trying to use your juicer software. I seem to have been running in a few complications trying to run juicer on the SLURM.
In my juicer folder, I have the directories fastq (which contains my two fastq files _R1 and _R2) as well as
aligned debug fastq HIC003 HIC_tmp LICENSE misc README.md references restriction_sites scripts SLURM splits testdata_chr19
I have the SLURM folder from the initial download (I deleted the other pipelines but kept misc, so when I ran the line
ln -s ~/juicer/SLURM scripts
The scripts folder in my juicer directory contains:
juicer_tools.1.7.6_jcuda.0.8.jar juicer_tools.jar README.md scripts
the juicer.sh file is in the scripts directory which is in the scripts directory (but I guess it's also in the SLURM folder).
Here was the output of running the command:
~/juicer/scripts/scripts/juicer.sh -D ~/juicer/
(-: Looking for fastq files...fastq files exist
sbatch: error: invalid partition specified: commons
sbatch: error: Batch job submission failed: Invalid partition name specified
(-: Aligning files matching /home/jau15/juicer/fastq/*_R*.fastq*
in queue commons to genome hg19 with site file /home/jau15/juicer//restriction_sites/hg19_MboI.txt
(-: Created /home/jau15/juicer/splits and /home/jau15/juicer/aligned.
sbatch: error: invalid partition specified: commons
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: commons
sbatch: error: Batch job submission failed: Invalid partition name specified
(-: Starting job to launch other jobs once splitting is complete
sbatch: error: invalid partition specified: commons
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: commons
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: commons
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: Job not submitted: please submit jobs that are less than 5 days long to the medium (or priority) partition.
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: commons
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: Batch job submission failed: Job dependency problem
sbatch: error: invalid partition specified: commons
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: commons
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: commons
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: commons
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: Batch job submission failed: Job dependency problem
sbatch: error: Batch job submission failed: Job dependency problem
sbatch: error: Batch job submission failed: Job dependency problem
sbatch: error: invalid partition specified: commons
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: commons
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: commons
sbatch: error: Batch job submission failed: Invalid partition name specified
(-: Finished adding all jobs... Now is a good time to get that cup of coffee..
I was wondering if you guys could help me figure out what I am doing wrong.
I tried running it with the hour and week, and now got the same issue
sbatch: error: invalid partition specified: hour
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: hour
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: hour
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: week
I am running it with a SLURM, and was wondering what question I should ask the IT people. Would it be what kind of partition format should be specified fo the SLURM?
Best,
Jake
Muhammad Saad Shamim
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