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If you haven’t been set up or have used the HPC previously, click on this link for information on how to get access to and use the HPC:
Need a link here for HPC access and usage
Creating a shared workspace on the HPC
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To request a node using PBS, submit a shell script containing your RAM/CPU/analysis time requirements and the code needed to run your analysis. For an overview of submitting a PBS job, see here:
Need a link here for creating PBS jobs
Alternatively, you can start up an ‘interactive’ node, using the following:
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m54105_201123_035001 | m54105_201125_211823 | m54105_201125_005856 | m54105_201126_173825 | ||
ZMWs input (A) | 330737 | 263116 | 217071 | 170793 | |
ZMWs generating CCS (B) | 209855 (63.45%) | 177981 (67.64%) | 138732 (63.91%) | 116886 (68.44%) | |
ZMWs filtered (C) | 120882 (36.55%) | 85135 (32.36%) | 78339 (36.09%) | 53907 (31.56%) | |
Exclusive ZMW counts for (C) | |||||
Median length filter | 0 (0.00%) | 0 (0.00%) | Below SNR threshold | 0 (0.00%) | 0 (0.00%) |
Below SNR threshold | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | |
Lacking full passes | 54483 (45.07%) | 39690 (46.62%) | 32964 (42.08%) | 22249 (41.27%) | |
Heteroduplex insertions | 470 (0.39%) | 306 (0.36%) | 280 (0.36%) | 191 (0.35%) | |
Coverage drops | 82 (0.07%) | 34 (0.04%) | 53 (0.07%) | 32 (0.06%) | |
Insufficient draft cov | 1045 (0.86%) | 889 (1.04%) | 635 (0.81%) | 610 (1.13%) | |
Draft too different | 809 (0.67%) | 337 (0.40%) | 430 (0.55%) | 160 (0.30%) | |
Draft generation error | 3212 (2.66%) | 1570 (1.84%) | 1767 (2.26%) | 1354 (2.51%) | |
Draft above --max-length | 2 (0.00%) | 1 (0.00%) | 0 (0.00%) | 0 (0.00%) | |
Draft below --min-length | 0 (0.00%) | 0 (0.00%) | Reads failed polishing 0 (0.00%) | 0 (0.00%) | |
Reads failed polishing | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | |
Empty coverage windows | 14 (0.01%) | 13 (0.02%) | 11 (0.01%) | 10 (0.02%) | |
CCS did not converge | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 1 (0.00%) | |
CCS below minimum RQ | 60767 (50.27%) | 42296 (49.68%) | 42199 (53.87%) | 29300 (54.35%) | |
Unknown error | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) |
Demultiplexing
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