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cd mkdir smrnaseq_cl cd smrnaseq_cl export NXF_OPTS='-Xms1g -Xmx4g' nextflow run nf-core/smrnaseq -profile test,singularity --outdir results -r 2.3.1 |
Line 1: Move to your home directory.
Line 2: Make a temporary folder called smrnaseq_cl for Nextflow to test the smrnaseq pipeline.
Line 3: Change directory to the newly created folder smrnaseq_cl.
Line 4: In some cases, the Nextflow Java virtual machines can start to request a large amount of memory. We recommend adding the following line to your environment to limit this.
Line 5: Download and run the test code.
This will download the smrnaseq pipeline and then run the test code. It should take ~20-30 minutes to run to completion.
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You can check the full list of jobs that have been submitted by opening a separate terminal and using the command:
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qstat -u $user |
It will display the jobs that have been submitted to the PBS queue.
In For example, in the first screenshootscreenshot, 3 jobs are queued.
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In And in the second screenshot, 6 jobs are running and 2 are queued.
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Not familiar with checking PBS job status? Please refer to Checking on the Job Status section in the Intro to HPC. |
In Going back to the terminal from which you launched the Nextflow analysis, in the screenshot below, taken half way through the Nextflow analysis, several processes have run to completion for all 8 samples tested.
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You can browse a couple of results folders to check what sort of outputs was were
generated by the pipeline.
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You will see a results folder, along with 2 pbs log files: nfrnaseq_test.e[pbs_job_id] and nfrnaseq_test.o[pbs_job_id].
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Not familiar with checking the output of PBS job, review the Checking the Output section of Submitting PBS Jobs part 2 from Intro to HPC. |
The nfrnaseq_test.o* file will provide a log of the nextflow processes. If you scroll at the bottom, you can check whether the pipeline ran successfully. You should see something similar to this:
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