Activity for metassembler
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Bob Harris posted a comment on discussion General Discussion
The sample in v1.5 appears to limit insert lengths to [1000,3000] for bowtie but to [1300,2300] for mateAn. Is this is mistake, or is there a reason why I should use different limits for the same sequencing run? For example, in my data I estimate most of the inserts are in [100,1100] with a mode around 500. Is there some reason I should tighten up that interval for mateAn?
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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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Page 10 of the MANUAL describes columns 1-8 of the .metassem file. However, after running the provided example (for version 1.5), the .metassem file has another 10 columns. Posting this so that other users will know. I have no illusion that a package that was last updated 4 years ago is actively being supported.
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Chris Keeling posted a comment on discussion General Discussion
Hello all, Is it possible to use the sequence data from a 10X Chromium library run for the mate-pair information for bowtie2 for use in Metassembler? In that case, how would you suggest setting bowtie2_maxins, bowtie2_minins, mateAn_A, and mateAn_B in the config file? Chris
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Carlos Farkas posted a comment on discussion General Discussion
Hi All I'm trying to merge contigs from a mini-metagenome built with SPAdes and Metaspades asemblers using the step_by_step script. CE statisticts looks fine and metassemble MergePipeline worked outputting a fasta file. When the pipeline tried to retrieve sequences in the last step of Metassembler, the following error appear: ---------- Loading Fastas ---------- ---Loading A.fa ---Loading B.fa ---------- Retrieving sequences ---------- Error: B.A_0 300901 447 0 NODE_3_length_300922_cov_62.4173 300901...
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Katherine Dougan posted a comment on discussion General Discussion
Thanks for the feedback! That's kind of what I gathered (but I was hoping there was an easier way) so I have already started running the individual steps.
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Alejandro Hernandez Wences posted a comment on discussion General Discussion
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...
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Hello, I tried looking through the manual to figure out if it was possible to resume a run rather than starting all the way at the beginning. It seems to have ~1 week run time on the species I am working on and I would rather not re-start after fixing an error that resulted from an incorrect path to a file. Is it possible to resume after correcting the error in the config file? Thanks! Katherine
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HoYong LEE posted a comment on discussion General Discussion
Thanks for your help. I have another problems. I tried to use long read fasta with metassembler results. It works well till nucmer. when running nucmer, error happen like prenuc: tigrinc.cc:337: int ReadString(FILE, char&, long int&, char, int): Assertion 'Len > 0 && Line [Len - 1] == '\n'' failed. Aborted (core dumped) ERROR: prenuc returned non-zero ERROR: Could not parse delta file, MergePipeline/B.A.delta error no: 400 ERROR: Could not parse delta file, MergePipeline/B.A.1delta error no: 402...
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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...
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Ah, thank you! I fixed that. I made it farther but the process once again failed and I got this error: 4: FINISHING DATA ERROR: cannot open /scratch/kdoug023/genome_reads/metassembler_output//frac65/CEstat/frac65.ce/frac65.mateAn. I went back to see if I could find this file but couldn't find it. I also have an error within that folder, the ID.ce folder in CEstat: Error: Your sam file contains no headers and you didn't provide any file with contig sizes. I think I'm doing something wrong in my configuration...
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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...
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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 textlen=536870908 ERROR: mummer and/or mgaps returned non-zero ERROR: Could not parse delta file, /scratch/kdoug023/genome_reads/metassembler_output//Metassembly/Qfrac65.600m/Qfrac65.600m.delta error no: 400 ERROR: Could not...
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Kenny Tsang posted a comment on discussion General Discussion
Dear all, I have one illumina TruSeq long read assembly and three MiSeq 2x75 short reads assemblies. I want to merge the long read assembly to each of the short reads assemblies so that at the end I will have three total assmblies: 1) Long read scaffold + Velvet scaffolds 2) Long read scaffold + AbySS scaffolds 3) Long read scaffold + SOAP scaffolds However, I do not know how to denife the parameters in the config file, it looks like this: [global] mateAn_A=200 mateAn_B=300 bowtie2_read1=/lustre/projects/holfordlab/ktsang/TSSLR-BDA11_LongRead.fastq...
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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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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,...
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Hi. I'm Lee. I'm now running Metassembler using Pig-tailed rhesus data(154G). it works well(bowtie2, mateAn, etc) but have problem in MUMmer : [TIME]. I searched and changed MUMmer because my reference sequence is larger than is supported by default. After changing, It makes another file (B.A.ntref - 3G , B.A.mgaps - 140G). I think it is used when making B.A.delta. but it take too much time ( 17 days now and still working - 43G). Is there any method to reduce time like parallel processing? And I...
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Nate Port posted a comment on discussion General Discussion
Hi Alejandro, This is all the output I get from running 'make install' in the root 'Metassembler' directory the first time (I did a clean install to verify): mkdir /Applications/Metassembler/bin cd /Applications/Metassembler/GAGE; /Applications/Xcode.app/Contents/Developer/usr/bin/make all /usr/bin/sed -e 's?/bin/bash?/bin/sh?g' \ -e 's?__GAGE_DIR?/Applications/Metassembler/GAGE?g' \ gage.sh > /Applications/Metassembler/bin/gage chmod 755 /Applications/Metassembler/bin/gage Like the OP I am also...
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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...
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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....
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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 all /usr/bin/sed -e 's?/bin/bash?/bin/sh?g' \ -e 's?__GAGE_DIR?/Applications/Metassembler/GAGE?g' \ gage.sh > /Applications/Metassembler/bin/gage chmod 755 /Applications/Metassembler/bin/gage [bin directory appears with only gage in...
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Dava posted a comment on discussion General Discussion
Dear all I am new in this field. in need more clarified information about configuration file contents. in the manual: "Parameters for the bowtie2, mateAn, nucmer, asseMerge, and meta2fasta programs can be specified" is that mean some parameters of all of these programs should specified mandatory or few of them depending on the purpuse or data that i have ? for example i have A assemly (bowtie2 aligned PE illumina sequencing reads to pacbio long read sequence assembly and improved by pilon) and B...
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Hi. I'm Lee. Sorry for bothering you. I have a question about mateAn I'm trying to change bowtie2 to nvBowtie in Metassembler to compare each performance. and i got errors. "Error reading SAM file". this error happen when it execute 'mateAn'. i compare each samfile and there are no difference except for header file position. is it related with sam file size? i found that each *.sam file size is different(nvBowtie's result is smaller than bowtie2) - some value is missing in nvBowtie. So can't work...
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Hi. I'm Lee. Sorry for bothering you. I have a question about mateAn I'm trying to change bowtie2 to nvBowtie in Metassembler to compare each performance. and i got errors. "Error reading SAM file". this error happen when it execute 'mateAn'. i compare each samfile and there are no difference except for header file position. is it related with sam file size? i found that each *.sam file size is different(nvBowtie's result is smaller than bowtie2) - some value is missing in nvBowtie. So can't work...
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Hi. I'm Lee. Sorry for bothering you. I have a question about mateAn I'm trying to change bowtie2 to nvBowtie in Metassembler to compare each performance. and i got errors. "Error reading SAM file". this error happen when it execute 'mateAn'. i compare each samfile there are no difference except for header file position. is it related with sam file size? i found that each *.sam file size is different(nvBowtie's result is smaller than bowtie2) - some value is missing in nvBowtie. So can't work well....
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Charles Bridges posted a comment on discussion General Discussion
After consultation with my HPC support staff I have gotten metassemble wrapper to run using python2. Still working out the kinks, will let you know how it goes. Thanks!
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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....
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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. I cannot load both python2 and python3 on my HPC cluster. Am I missing something? How do users reconcile this? Thank you! Charles
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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...
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Thank you Wences. I've replaced the directory paths appropriately, and most of the program is running as expected. Now, I'm not sure if the program has run to completion. Based on the description of directories that should be created found in the Manual, I believe the program is hung up after the asseMerge or meta2fasta. I have directory /M1/, which contains 19 or so files including B.A.fasta, but around 8 of those files are 0 bytes. I'm also lacking the M1/Metassembly/ directory, and my stdout file...
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Yes, the problem is the binary files can't be found. This should be fixed if you run the script from within the sample/meta1 directory, or if you modify the Step_by_Step_script.sh and/or the Metassemble_script.sh scripts by simply changing any line of the form: ../../bin/BinFile to: BinFile. The latter can be done with the following bash commands: sed 's#^../../bin/##' Step_by_Step_script.sh > Step_by_Step_script.sh and: sed 's#^../../bin/##' Metassemble_script.sh > Metassemble_script.sh Wences On...
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Hello, When running the sample data on an HPC cluster, the assembly fails. The /MergePipline folder is created with directories /A.CEstat and /B.CEstat, each of those contain /BWTaln directories containing files (which look to be appropriate size), but the /A.ce or /B.ce directories are empty. /BWTaln/A.mtp.2k.err (and B..err) show 92-93% alignment rate. /MergePipeline/M1 directory is empty. I've written the stdout and sterr to files, which I'll paste below. The main error seems to be that metassembler...
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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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Hi, I'm trying to figure out how to use a single, interleaved paired-end library in metassembler. I'm running the latest release of Bowtie2, v2.3.2 which allows the user to use a single library using the parameter --interleaved. Will metassembler pass this parameter to Bowtie2? How is this written in the metassembler config file under the [global] section? I imagine something like: bowtie2_interleaved Thanks for your help.
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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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Astrid posted a comment on discussion General Discussion
Hi Michael Yes that is what I saw in your paper and it is a species closely related to the one from the Assemblathon. I was guessing that the issue is nucmer? I realized that I am using a rather old version of Mummer, maybe that is the problem that it goes so slow? telling from the logs, it is stuck at this step (though doing something since the file QSpadesFemales.CeleraFemales.mgaps keeps changing) ---- Merging SpadesFemales and CeleraFemales ==> QSpadesFemales.CeleraFemales ---------- Run bash...
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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 Michael, I have a metassembly runt that takes already 4 weeks merging a Spades and a Celera fish genome assembly (1GB genome size maximum). Telling from you rpaper this should have been finishes long time ago, Here is a copy of my spec file [global] Mate-pair mapping parameters: bowtie2_threads=8 bowtie2_read1=all_1P.fastq bowtie2_read2=all_2P.fastq bowtie2_maxins=1000 bowtie2_minins=10 genomeLength=950000000 meta2fasta_keepUnaligned=3 meta2fasta_sizeUnaligned=350 350 nucmer_l=50 nucmer_c=300...
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Andre Soares posted a comment on discussion General Discussion
Hi, I finished installing metassembler, I checked for all the requirements beforehand. I just finished running ./Metassemble_script.sh as instructed in the manual/readme, and after running for a while it spit to the screen: (...) ---------- Run bash command ---------- contig stats: /home/myuser/Metassembler/bin/RepStats ./MergeMetassemble/B.A_InitialCtgStats ./MergeMetassemble/A/A.ctgs.fasta.lengths.stats ./MergeMetassemble/B/B.ctgs.fasta.lengths.stats ... 1: n=1 [245000, 245000] 245000.0 +/- 0.0...
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I solved the proble, metassemble needs a value bigger than 0 for bowtie2_minins (apparetntly)...
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Hi I have installed metassembler and the testdatset runs through smoothly Now I tried...
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Tim Hewitt posted a comment on discussion General Discussion
Hi Mike, This is good to know. I do believe I had quite a few very short contigs...
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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 Mike, the full metassembly appeared to be successful - it seems removing whitespace...
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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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Thanks Mike. I tried what you suggested and got an output without error. I'll go...
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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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Thanks Mike. My reads are actually "innies", so I changed the bowtie2 option on line...
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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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Daniel Barrell posted a comment on discussion General Discussion
Hi Mike, Yes, the reads had been filtered with kontaminant and there were mismatches...
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Hmm, in that case I can only guess there is something unusual about your data compared...
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Hi Mike, I fixed Statistics::Descriptive but am still having the same problem of...
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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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Hi Mike, I also have the ERROR reading read pairs from SAM file error. I'm not sure...
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Hi Mike, I also have the ERROR reading read pairs from SAM file error, here's where...
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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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Mark posted a comment on discussion General Discussion
Hello Is it true that only mate-pair reads, not paired end reads, can be used by...
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Thanks, trying to fix it now and will retry, but I'm wondering why it still worked...
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Yes, I bet it is related to the Statistics/Descriptive module errors. Can you try...
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Hi Michael, I'm having the exact same problem as Marcus, even after concatenating...
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I dont think it is supported to provide comma separated reads like this. Can you...
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marcus naymik posted a comment on discussion General Discussion
Yes, the test data completes fine. I have 8 paired end fastqs we sequenced for the...
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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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I am trying to metassemble 3 de novo assemblies (k64, chicago, and k80) which all...
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I am trying to metassemble 3 de novo assemblies which all seem to pass the initial...
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I am trying to metassemble 3 de novo assemblies which all seem to pass the initial...
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No, the point of it is to merge together multiple assemblies into a single consensus...
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Habib R posted a comment on discussion General Discussion
So, you just give metassembler one input fasta, right?
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You would just use the output of the metassembler from the first library size as...
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When you said: Our program works with libraries of one insert size at a time, so...
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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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Carlos Morais posted a comment on discussion General Discussion
Hi, I could not find any file explicitly stating the software license. Please provide...
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Hi, Try installing it by typing: make Scr make scripts This will avoid installing...
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Salvador Espada-Hinojosa posted a comment on discussion General Discussion
hi, I'm in a MacOSX 10.10 and when I follow the README instructions I don't manage...
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Hi Gregory, The metassembler relies on the mate pair library to decide which assembly...
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Gregory Rice modified a comment on discussion General Discussion
Does metassembler only work with mate-pair libraries, or will it work with illumina...
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Does metassembler only work with mate-pair libraries, or will it work with illumina...
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Erliang Zeng posted a comment on discussion General Discussion
Hi Mike, Thank you for your help. Just want to update you, which may also help others....
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It is very hard to tell from just that. Im guessing either the assembly somehow failed...
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Hello Mike, Thank you for your message about changing the jump libray format. We...
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Thanks for sending this. I bet the code is confused because the read names have ".1"...
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Hi Mike, Here is top reads from our jump libraries: jump.1.fq: @SRR924201.34653342.1...
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It must be the reads have a different format than is expected. Could you share a...
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zhixiu lu posted a comment on discussion General Discussion
Hi,Mike I am a researcher in Dr Zeng's lab, and I have been working with the program....
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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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Hello, I am using metassembler. It looks good till when I tried to run mateAn: mateAn...
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Hello, I am using metassembler. It looks good till when I tried to run mateAn: mateAn...
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Hello, I am using metassembler. It looks good till when I tried to using mateAn:...
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Hello, I amusing metassembler. It looks good till when I tried to using mateAn: mateAn...
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Hi, yes that would be helpful, can you host it someplace where we could download...
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Hi, These are scaffolds present in the primary assembly (or secondary assembly respectively)...
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Carlos Llorens posted a comment on discussion General Discussion
Hi again Wences, i am finishing a metassembly based on several assemblies and have...
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Ok thank you i´ll d so. crlx
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Hi, Our program works with libraries of one insert size at a time, so you'll need...
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Hola Alejandro, About this question i also have two mate pair libraries of 5kb and...
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Jonathan Featherston posted a comment on discussion General Discussion
Maybe the best would be if I can forward you a sam file to see if you can get mateAN...
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Hi Alejandro Samtools view of q20 mappings doesn't seems too bad: 76549018 1516943537...
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Hi there. Sorry about my slow response. I think mails from soureforge are getting...
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Hi, Though it is still an option I really doubt that the problem is a lack of memory....
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