User: wjar6718

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wjar67180
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Posts by wjar6718

<prev • 16 results • page 1 of 2 • next >
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Is the Abyss contig and scaffold phased?
... Hi, Just wondering whether or not Abyss a contig or scaffold is phased into a particular strand of the DNA (although synthetic). My guess would be 'Yes' because 1. The tool uses pair-end information 2. When I align scaffolds to human reference, hg19 and check via IGV (http://software.broadinstitut ...
genome assembly abyss written 13 months ago by wjar67180 • updated 13 months ago by benv710
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Answer: A: CNVkit runtime for WGS?
... THX very great program indeed. PS - WGS ran 3-4 days using -p 12   James ...
written 3.0 years ago by wjar67180
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Answer: A: CNVkit runtime for WGS?
... I fixed the name, ran 'cnvkit.py fix' and got the following call: "Correcting for GC bias... Correcting for density bias... Weighting bins by relative coverage depths in reference Weighting bins by coverage spread in reference Processing antitarget: Clean3_mergedL7L8_150911_FR07887821 Traceback (mo ...
written 3.0 years ago by wjar67180
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Answer: A: CNVkit runtime for WGS?
... Hi Etal, With the WGS data, I have seen the following error when using cnvkit.py fix: "  File "/cnvkit/cnvlib/commands.py", line 574, in _cmd_fix     % (tgt_raw.sample_id, anti_raw.sample_id)) ValueError: Sample IDs do not match:'Clean3_mergedL7L8_150911_FR07887821_targetcoverage' (target) vs. 'Cl ...
written 3.1 years ago by wjar67180
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Answer: A: CNVkit runtime for WGS?
... Thx Etal, I try it out for your easy-to-use package and will tell you. Cheers, James ...
written 3.1 years ago by wjar67180
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CNVkit runtime for WGS?
... Hello, I am a new cnvkit user. It is necessary that I have to use cnvkit with my WGS of a T-N pair (45x and 29x coverages). I am running them with 4 processes (each for 16GB). Now the program is still running for 2 days and I think it is is the fix step (for a whole day now) because I can see my re ...
cnvkit written 3.1 years ago by wjar67180
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Answer: A: svtyper tool: ValueError: mate not found
... Now just add -M flag in svtyper! James ...
written 3.4 years ago by wjar67180
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Comment: C: ABySS - Out of memory using 64 cores (520GB)
... Login nodes for testing are okay and the abyss tests were run only for few hours before stopped. Weerachai ...
written 3.5 years ago by wjar67180
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Comment: C: ABySS - Out of memory using 64 cores (520GB)
... $ulimit -a Last login: Thu Aug 13 18:36:05 2015 from 129.94.14.94 Rocks 6.0 (Mamba) Profile built 12:24 30-Jun-2015 Kickstarted 12:37 30-Jun-2015 -bash-4.1$ ulimit -a core file size          (blocks, -c) 0 data seg size           (kbytes, -d) unlimited scheduling priority             (-e) 0 file s ...
written 3.5 years ago by wjar67180
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Comment: C: ABySS - Out of memory using 64 cores (520GB)
... Now I have no clues of IP address or ssh'able hostname for compute nodes. The admin would not allow me to get them I think. Thx anyway Philipp ...
written 3.5 years ago by wjar67180

Latest awards to wjar6718

Popular Question 2.8 years ago, created a question with more than 1,000 views. For ABySS - Out of memory using 64 cores (520GB)
Popular Question 2.8 years ago, created a question with more than 1,000 views. For CNVkit runtime for WGS?

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