chm13_asm_ctgs_2021_0104 / Jason Chin

<p>Genome assembly of the CHM13 cell line. Done with a new assembler based on the SHIMMER indexing method. The run time is 1.6 hours with 64 core aarch CPUs. The wall clock time is about 1.6 hours.&nbsp;</p> <p>2021-01-04 08:47:07,980 INFO &nbsp;[pg_asm::utils::layout] Total size: 3055717214<br> 2021-01-04 08:47:07,980 INFO &nbsp;[pg_asm::utils::layout] Longest size: 140284871<br> 2021-01-04 08:47:07,980 INFO &nbsp;[pg_asm::utils::layout] N50: 82577644<br> 2021-01-04 08:47:07,980 INFO &nbsp;[pg_asm::utils::layout] N90: 17313701<br> 2021-01-04 08:47:07,980 INFO &nbsp;[pg_asm::utils::layout] Number of contigs: 357<br> 2021-01-04 08:47:07,980 INFO &nbsp;[pg_asm::utils::layout] Number of Contigs &gt; 100kb: 207</p> <p>2021-01-04 08:48:22,512 INFO &nbsp;[pg_asm] pg_asm run end<br> 2021-01-04 08:48:22,512 INFO &nbsp;[pg_asm] total user cpu time: 272568 seconds = 75.71333 hours<br> 2021-01-04 08:48:22,512 INFO &nbsp;[pg_asm] total system cpu time: 920 seconds = 0.25555554 hours<br> 2021-01-04 08:48:22,512 INFO &nbsp;[pg_asm] total elapse time: 5773.4155 seconds = 1.6037266 hours</p> <p>Here is the result of the CHM13 BAC coverage with the assembly</p> <p><br> Checking attempted with maximum distance from contig end of 1000 bp..Done<br> ******************* BAC SUMMARY ******************<br> &nbsp;TOTAL &nbsp; &nbsp;: 341<br> &nbsp;BP &nbsp; &nbsp; &nbsp; : 51532183<br> ************** Statistics for: _test9.fa ****************<br> BACs closed: 330 (96.7742); BACs attempted: 341 %good = 96.7742; BASES 49874385 (96.783)<br> Median: &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;99.99135<br> MedianQV: &nbsp; &nbsp; &nbsp; &nbsp;40.62984<br> Mean: &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;99.94396<br> MeanQV: &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;32.51511<br> ***** STATS IGNORING INDELS ********************<br> Median: &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;100<br> MedianQV: &nbsp; &nbsp; &nbsp; &nbsp;Inf<br> Mean: &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;99.99418<br> MeanQV: &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;42.34828<br> **********************************************</p>