Alejandro Hernandez Wences

Hi, You need to run the remaining steps manually as expemplified in the Step_by_Step_script.sh script found in the Sample directory, at least to complete the last metassembly where metassemble stopped. You'll need to figure out the last step that finished correctly, the main steps are: 1)computing the CE-statistic for the input assemblies (bowtie2 for alginments and mateAn for the actual computation), 2) whole genome alignment (nucmer), 3) merging the assemblies through the WGA (asseMerge), 4) computing...

Could you make just a sanity check of the file ID/CEstat/BWTaln/ID.mtp.err just to make sure the problem is not in the Bowtie2 alignment step. If thats ok I am guessing the sequence names in your assemblies are causing troubles, could you simplify them? avoid using white spaces and characters such as ":". You can parse the sam files directly, but if the alignments are not so costly I would recommend just rerunning them with the new sequence names in the fasta files of your assemblies. On Wed, Oct...

Hi Katherine, You should try compiling mummer in the 64-bit version as explained here: https://sourceforge.net/p/mummer/mailman/message/22416185/ On Tue, Oct 10, 2017 at 1:56 PM, Katherine Dougan kdougan91@users.sf.net wrote: Hello everyone, I am attempting to merge two draft genome assemblies of a dinoflagellate species. Upon running metassembler, I am receiving this following error: /home/kdoug023/programs/MUMmer3.23/mummer: suffix tree construction failed: textlen=920760240 larger than maximal...

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 recommend: -l 100 -c 500; and if it still takes too much time use -l 250 anc -c 500. This two parameters can be used to leverage sensitivity and computational load in the whole genome alignment step, please refer to the nucmer manual for further explanation of what they do exactly. On Tue, Aug 29, 2017 at 11:59 PM,...

Hi, Could you post the entire output for the first time you tried "make install" on the root directory of the package? This will give me a better hint of what could be going on. Thanks. On Wed, Aug 2, 2017 at 9:45 PM, Nate Port nateport@users.sf.net wrote: Hi, I've run into this same issue, where only the GAGE binary is placed in the bin folder. Erics-MacBook-Pro:Metassembler MartensLab$ make mkdir /Applications/Metassembler/bin cd /Applications/Metassembler/GAGE; /Applications/Xcode.app/ Contents/Developer/usr/bin/make...

Hi, You can find an example configuration file on the root directory of the package ("Config1"). Regarding the parameters for external programs, the mandatory bowtie parameters are: bowtie2_read1=<path1>[,...,<pathN>] bowtie2_read2=<path1>[,...,<pathN>] bowtie2_maxins=<int> bowtie2_minins=<int> Please refer to the corresponding manual to find out about these. Also, it is recommended that you set the nucmer parameters: nucmer_l=<int> nucmer_c=<int> Again, please refer to the corresponding manual....

Hi, All the python scripts in the package work on python 2, the package does not requires python3. Try using python2 and let me know if you find any troubles. Wences On Wed, Jun 21, 2017 at 11:03 AM, Charles Bridges cmb12@users.sf.net wrote: Hello, I've taken Wences' advice to use the python wrapper to run the sample dataset instead of using the step-by-step script. I've run into the issue that Metassembler v1.5 requires python3, but the metassemble.py wrapper seems to be written using python2 syntax....

Yes the output is expected since you are running the Step_by_Step.sh script, this is a bash script that performs a metassembly by calling each of the programs required in each step of the process (for example by calling bowtie, nucmer, etc). On the other hand, the manual refers to the wrapper "metassemble" which is a python script that does the same (performing a whole metassembly) but for any set of input parameters, which are specified through a config file. This wrapper does create all the directory...