Activity for Michael Schatz
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Michael Schatz posted a comment on discussion General Discussion
Hi Bob, Thanks for the note. Columns 1-8 are the only ones that are needed to assemble the final contigs using meta2fasta.pl. The additional columns are debugging codes and coordinates of the original assemblies encoding the status of the CE statistic over the breakpoints of the alignments. Since they are not used in the downstream analysis, you can safely ignore them. Good luck Mike
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There is also a script here that can be used to run the alignments in parallel on an sge-based grid: https://github.com/fritzsedlazeck/sge_mummer It will require a bit of code editing, but can get the job done Good luck Mike On Wed, Aug 30, 2017 at 11:20 AM, Alejandro Hernandez Wences ahwences@users.sf.net wrote: You should try usign different -l and -c paramteres for nucmer (this can be done with the parameters nucmer_l and nucmer_c in the conf file). For large or very repetitive genomes I would...
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ERROR! The markdown supplied could not be parsed correctly. Did you forget to surround a code snippet with "~~~~"?Thanks for your interest, but unfortunately interleaved fastq files are not supported. Id recommend you deinterleave the fastq files using a script like this: https://gist.github.com/nathanhaigh/3521724 Good luck! Mike On Mon, May 29, 2017 at 9:22 PM, Charles Bridges <cmb12@users.sf.net> wrote: > Hi, I'm trying to figure out how to use a single, interleaved paired-end > library in metassembler....
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Yeah, there must be tons of repeats if it is still stuck in nucmer. As painful as it is, Id kill the job and start again with different nucmer settings. I would recommend: -l 100 -c 500 This will (modestly) reduce sensitivity, but could finish in less than a day. If it takes more than a day, boost up -l 100 to -l 250 and try again Good luck! Mike On Wed, May 17, 2017 at 11:02 AM, Astrid astridboehne@users.sf.net wrote: Hi Michael Yes that is what I saw in your paper and it is a species closely related...
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Can you tell what phase of the program is currently running? We successfully merged the fish genome from the Assemblathon 2 data set in ~1 day. Here are the notes on it from the supplemental material: For all Fish assemblies and metassemblies we used the available 2Kb mate-pair libraries: 801KYABXX.2 and 801KYABXX.3 Mapping: bowtie2 --maxins 3000 --minins 1000 --threads 16 CE-statistic: mateAn -A 1500 -B 2600 WGA: nucmer –maxmatch -l 50 -c 300 Merges: asseMerge with default options Runtime Requirements:...
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Hi Tim, Glad we are making progress. Im guessing what happened is one of your assemblies...
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Hi Tim, I'm not at my desk but I think one is supposed to have contigs and one will...
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It is not well tested, and I would try a very small example first to confirm that...
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That explains it! Mike On Tue, Jan 24, 2017 at 11:39 AM, Daniel Barrell dgb@users.sf.net...
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Hmm, in that case I can only guess there is something unusual about your data compared...
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It is hard to tell from these error messages, but it looks like your input data are...
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You can run it with paired end data, just in our testing we dont see a lot of improvement....
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Yes, I bet it is related to the Statistics/Descriptive module errors. Can you try...
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I dont think it is supported to provide comma separated reads like this. Can you...
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Are you able to run on the included test data? That will help isolate if it is a...
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No, the point of it is to merge together multiple assemblies into a single consensus...
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You would just use the output of the metassembler from the first library size as...
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Both of these are in the source tree: https://sourceforge.net/p/metassembler/code/ci/master/tree/...
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Hi Gregory, The metassembler relies on the mate pair library to decide which assembly...
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It is very hard to tell from just that. Im guessing either the assembly somehow failed...
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Thanks for sending this. I bet the code is confused because the read names have ".1"...
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It must be the reads have a different format than is expected. Could you share a...
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Are you able to run the example dataset end to end? That will help determine if it...
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ERROR! The markdown supplied could not be parsed correctly. Did you forget to surround...
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ERROR! The markdown supplied could not be parsed correctly. Did you forget to surround...
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ERROR! The markdown supplied could not be parsed correctly. Did you forget to surround...
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Sorry, that's a required data type so that it can evaluate which sequence is more...
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clean up old code
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Update docs and license file
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Nice catch! At least now we have a workaround. Let me know if you would like to chat...
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Thank you. Wences, can you try looking at these? Thank you, Mike On Wed, Mar 25,...
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Thanks Bastian. Lets us know if you have any progress narrowing down which assemblies...
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Let us know how it goes without that one assembly. Otherwise, we will probably have...
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Does the sample data run correctly to completion? If you exclude the one assembly...
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Thanks Bastien. It seems different compilers have different requirements. Thank you...
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No indication if test.sh was successful or not
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Updated expected output now that we have the new format
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Tools in support/ aren't compiled by the Makefile
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Fixed, added second makefile for support tools
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Running with no parameters gives segmentation fault
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Fixed
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Compile fails with g++ 4.6.4
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Fixed Makefile
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Increase default stacksize to support longer reads
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CloudBurst
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MUMmerGPU
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update README with test script
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Add pan genome test
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Update readme
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Add source and simple test file
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update readme
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update readme
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Initial commit
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Hi Val, Thanks for working on this. Here is another example where a sequence on chr21...
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Uniqueness miscomputed by Ns in Bowtie 1.0.0
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