Marc Strous posted a comment on discussion General Discussion

Hi everybody, I have also experienced the problem - it has become more difficult to have scripted access to the ncbi databases. Unfortunately, I think it the time has come to archive Metawatt and switch to a more modern binner. When you compare the performance with new tools, such as MetaBat2, I would recommend everybody to make the switch... Thanks for using metawatt over the years! Best wishes, Marc On 5/5/19 12:55 AM, zhongpeiwen wrote: Hello! I've got the following error when updating databases:...

zhongpeiwen posted a comment on discussion General Discussion

Hello! I've got the following error when updating databases: java -jar MetaWatt-3.5.3/dist/MetaWatt-3.5.3.jar --run example/ Processing NCBI queries for database update... Metawatt [INFO|1:16:09] (1/4) Processing "Eukaryota"... Metawatt [INFO|1:16:09] Polling NCBI for new assemblies for superkingdom "Eukaryota" unique at rank "phylum"... Metawatt [SEVERE|1:17:13] Module returned error: java.net.ConnectException: Connection timed out (Connection timed out) Could you please tell me how can I fix this...

ashone posted a comment on discussion General Discussion

Hello, I have the same problem.Does anyone know how to solve it ? Thanks.

Javier posted a comment on discussion General Discussion

Hello I've got the following error when updating databases, and the pipeline stops: java.io.IOException: Server returned HTTP response code: 502 for URL: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/epost.fcgi?db=taxonomy&id=395600,1444160,1444161,1444174,1444175,1444172,1444173,1444170,1444171,1444168,2099583,1444169,2558279,1444214,2558278,330084,1444215,2558277,1444212,2558276,1444213,1444210,1444211,1444208,1444209,1444222,2558286,395631,1444223,1444220,2558284,1051003,1444221,2558283,1051004,1444218,2558282,1051005,1444219,2558281,1247613,1051006,1444216,2558280,1444217,1444198,1444199,1444196,1444197,1444194,1444192,2423,1444193,1444206,1444207,2426,1444204,1444205,1444202,1444203,1444200,1444201,1313172,1444246,526729,1444247,2434,1444244,2492837,1968541,1444245,1444242,1444243,1444240,1313171,1444241,1444254,1444255,1444252,1444253,1444250,1247647,1444251,1247646,1444248,1247645,1444249,1247644,1444230,1444231,1444228,1444226,1444227,1444224,1444225,1444238,1444239,1444236,1444237,1444234,1444235,1444232,1444233,2099584,1051056,1444278,1051057,1444279,1051058,1444276,1051059,1444277,1051060,1444274,1051061,1444275,1051062,1444272,1444273,1771959,1444282,1444280,1444281,592313,1444262,1444263,1444260,1247649,1444261,1247648,1444258,1444259,1444256,1444257,264636,1444270,1444271,1444268,1444269,1444266,2558362,592308,1444267,1444264,1051055,1444265,1444310,1444311,1444308,1444309,1182166,1444306,1182167,1444307,1182164,1182165,1968598,1182170,1182171,1182168,68042,1182169,1182174,1444314,1903056,2099693,1444315,788929,1182175,1182172,2099695,1182173,1444294,1051072,1444295,1444292,1051074,1444293,1051075,1444290,1444291,1444288,1444289,592361,1247731,1247730,1247729,1182192,1247728,199136,330214,1182193,1313264,1247735,1247734,1313265,1247733,1247732,1247738,1247737&WebEnv=NCID_1_262402316_130.14.22.33_9001_1556012434_2103301775_0MetA0_S_MegaStore...

Marc Strous posted a comment on discussion General Discussion

Hi Javier, The authors have used the description of Metawatt as it was originally published. However, later on differential coverage was added. Coverage was also used during the cami binning challenge. I'm not sure how the spectacularly good results were obtained using Metawatt with the high complexity community. I was unable to reproduce these very good results. It is good but not that good. A new, improved version of metawatt wil be made available later this year. Best wishes, Marc On 06/06/2018...

Binnerman posted a comment on discussion General Discussion

Dear all, In the CAMI challenge paper: https://www.nature.com/articles/nmeth.4458 your tool is described as a "genome binner using tetranucleotide frequencies" (suppl. table 1) while all the other binning tools are also described as multiple sample coverage binners. The autors claim that they we running Metawatt with standard parameters, but since they do not consider Metawatt as a multiple coverage binners I do not know if they made use of this feature or they were just binning contigs by composition...

learst posted a comment on discussion General Discussion

I guess i must be pretty dumb, as I've spent half a day going through the wiki but I can't seem to figure out how to set up metawat and execute it on the command line. First i installed metawatt through the conda. Apparently this is a modular software, but I can't seem to find any of the modules or how to execute them. Things I've managed to do so far ## call up the GUI java -jar $metawatt ## check dependencies java -jar $metawatt --check-dependencies Beyond that I've no idea how to run any commands...

Stefano Scilipoti modified a comment on discussion General Discussion

Hi Marc, I get this error when running the Six frame Pfam module: Metawatt [INFO|2:07:40] Running "Six frame Pfam"... Metawatt [INFO|2:07:40] Set HMM evalue [1.0E-10] Metawatt [INFO|2:07:40] Set processors used [30] Metawatt [INFO|2:07:40] Set mimimum length for HMM profile hits [50] Metawatt [INFO|2:07:40] Loaded taxa from file "/scratch2/sscilipo/KARASIK/metagenome/Metawatt_binning/Metawatt_2/databases/reference-taxonomy.txt": Metawatt [INFO|2:07:40] With seq data : 2205 Metawatt [INFO|2:07:40]...

Stefano Scilipoti posted a comment on discussion General Discussion

Hi Marc, I get this error when running the Six frame Pfam module: Metawatt [INFO|2:07:41] Translating contigs in six frames... Metawatt [SEVERE|2:08:39] Module returned error: java.lang.StringIndexOutOfBoundsException: String index out of range: -1 at java.lang.String.substring(String.java:1875) at org.metawatt.modules.ContigHMMProfileScan.run(ContigHMMProfileScan.java:94) at org.metawatt.modules.ModuleRunner.processModule(ModuleRunner.java:177) at org.metawatt.modules.ModuleRunner.processModuleWrapperInterceptOptimize(ModuleRunner.java:162)...

Vimac Nolla posted a comment on discussion General Discussion

Hi, The easiest way to update the databases is to directly run the first module of the pipeline, "Update databases". This will update the provided databases (see "Update databases" pipeline module wiki). I hope this helps. Vimac

palomo11 posted a comment on discussion General Discussion

Dear Shawn (or Marc), Were you able to to biuld the database? Is there any where we can find an accessible database? Thanks in advance!

Vimac Nolla posted a comment on discussion General Discussion

Hi, I managed to fix the problem. It seems like java was unable to find the /jni and /current directories in usr/local/bin. So I just copied the two directories from my BBMap folder to usr/local/bin and it worked. Vimac

Oscar posted a comment on discussion General Discussion

Hi, I'm also having the same issue. I'm running the latest version of metawatt and the generated bins contain all "inifinity" abundance. As Vimac, I checked the logfile and I find this error realted to Bbmap: Metawatt [INFO|12:38:17] Running "Map reads to contigs"... Metawatt [INFO|12:38:17] Map faster [true] Metawatt [INFO|12:38:17] Minimum Percent ID [98.0] Metawatt [INFO|12:38:17] Contig connection threshold [400 bp] Metawatt [INFO|12:38:17] Set processors used [4] Metawatt [INFO|12:38:17] Use...

Shawn MOK posted a comment on discussion General Discussion

Dear Kinestetika, Hello, I am trying to set up metawatt. But sadly, it seems that the database http://coe30.coe.ucalgary.ca/~mstrous/metawatt-databases.tar.gz is no longer accessible. Could you give me some advices to fix this problem? And long for you reply! Many thanks! Shawn MOK

Vimac Nolla posted a comment on discussion General Discussion

Hi Marc, I'm running Metawatt 3.5.3 and even though the pipeline seems to work fine, it ends with two issues: The generated bins have an "Infinity" abundance. The BBMap seems not to work even though the dependencies check is ok for BBMap. I've checked the logbook and the only errors I could find are related to align2.BBMap: Metawatt [INFO|4:43:52] Running "Map reads to contigs"... Metawatt [INFO|4:43:52] Map faster [true] Metawatt [INFO|4:43:52] Minimum Percent ID [98.0] Metawatt [INFO|4:43:52] Contig...

Vimac Nolla posted a comment on discussion General Discussion

Hi Marc, So installing an older version on Diamond, v0.8.0 did the trick :) Vimac

Vimac Nolla posted a comment on discussion General Discussion

Hi Marc, Currently I'm using diamond 0.9.9 which should be ok according to the wiki. I will try with an older version to see if there is some issue with v0.9.9. Vimac

Marc Strous posted a comment on discussion General Discussion

Dear Vimac, most probably a new version of diamond has been released that uses a different format. Another possibility is that you did not create a database successfully. What happens when you use an the version of diamond mentioned on the MetaWatt wiki? Best wishes, Marc On 09/28/2017 06:16 AM, Vimac Nolla wrote: Dear Marc, I'm tryning to run the latest version of metawatt 3.5.3 and I have some errors while running Diamond. I'm running it on a Ubuntu 14 with Biolinux8 and 32GB of RAM The depenencies...

Vimac Nolla posted a comment on discussion General Discussion

Dear Marc, I'm tryning to run the latest version of metawatt 3.5.3 and I have some errors while running Diamond. I'm running it on a Ubuntu 14 with Biolinux8 and 32GB of RAM The depenencies test gives Ok for all of them including Diamond and if I perform the runn everything seems ok, I obtain multiple bins, however the bins do not contain any taxonomic information. Looking at the logbook I see the following isues: The first module "Update databases" does not produce the "reference-genomes.faa.dmnd"....

Yevhen Vainshtein modified a comment on discussion General Discussion

Hello, have exactly the same problem. I am runnig the MetaWatt on a multi-core system with sufficient memory. I cheched - the single mafft module disttbfast is running on a single core, while 128 is available. The module is using currently about 360GB of RAM and for a moment running for 20 hours. Does anybody solved the problem? Thanks.

Yevhen Vainshtein modified a comment on discussion General Discussion

I've just start using the MetaWatt. I had a similar issue recently - in fully automated mode the pipeline does not work as suppose. What helped - is a runnig of every individual module manually, step by step

Yevhen Vainshtein posted a comment on discussion General Discussion

I've just starting using the MetaWatt. I had a similar issue recently - in fully automated mode the pipeline does not work as suppose. What helped - is a runnig of every individual module manually, step by step

Yevhen Vainshtein posted a comment on discussion General Discussion

Hello, have exactly the same problem. I am runnig the MetaWatt on a multi-core system with sufficient memory. I cheched - the single mafft module disttbfast is running on a single core, while 128 is available. The module is using currently about 360GB of RAM. Does anybody solved the problem? Thanks.

Michael Stephens posted a comment on discussion General Discussion

Hello, I've been trying to run metawatt for some time now and I havent had any luck getting it to bin my assemblies. I've had the program properly installed on a computing cluster and all of the depencies are installed and recognized by metawatt. I've made the proper input (assembly.fasta and reads.fastq.gz) and output directories under the project name/ directory but when I choose that under the file/open project I dont get any results. It seems as though it isnt running any of the modules and is...

Luca Zoccarato modified a comment on discussion General Discussion

Hi, I get an error in the execution of the Six frame Pfam and I hope you can help me. The error is: Metawatt [INFO|11:50:02] Translating contigs in six frames... Metawatt [INFO|12:00:24] Profile DB "conserved-genes.hmm" has 138 profiles (total length 17744 characters). Metawatt [INFO|12:00:24] Running HMMer search... Metawatt [INFO|12:00:24] hmmsearch -E 1.00e-10 /home/zoccarato/Desktop/working_dir/genom_comp/2_Metawatt/databases/conserved-genes.hmm /project/ag-grossart/SOFTWARE/MetaWatt-3.5.3/tmp/all_gnm.fasta.6frame.translated.fasta...

Luca Zoccarato modified a comment on discussion General Discussion

Hi, I get an error in the execution of the Six frame Pfam and I hope you can help me. The error is: Metawatt [INFO|11:50:02] Translating contigs in six frames... Metawatt [INFO|12:00:24] Profile DB "conserved-genes.hmm" has 138 profiles (total length 17744 characters). Metawatt [INFO|12:00:24] Running HMMer search... Metawatt [INFO|12:00:24] hmmsearch -E 1.00e-10 /home/zoccarato/Desktop/working_dir/genom_comp/2_Metawatt/databases/conserved-genes.hmm /project/ag-grossart/SOFTWARE/MetaWatt-3.5.3/tmp/all_gnm.fasta.6frame.translated.fasta...

Luca Zoccarato posted a comment on discussion General Discussion

Hi, I get an error in the execution of the Six frame Pfam and I hope you can help me. The error is: Metawatt [INFO|11:50:02] Translating contigs in six frames... Metawatt [INFO|12:00:24] Profile DB "conserved-genes.hmm" has 138 profiles (total length 17744 characters). Metawatt [INFO|12:00:24] Running HMMer search... Metawatt [INFO|12:00:24] hmmsearch -E 1.00e-10 /home/zoccarato/Desktop/working_dir/genom_comp/2_Metawatt/databases/conserved-genes.hmm /project/ag-grossart/SOFTWARE/MetaWatt-3.5.3/tmp/all_gnm.fasta.6frame.translated.fasta...

Ilnam Kang posted a comment on discussion General Discussion

Hello, I installed and runned MetaWatt for the first time today. Every step (module?)...

Alexis Fonseca modified a comment on discussion General Discussion

Hi, The easiest way to fix up this is using a earlier version of Diamond. As you...

Alexis Fonseca modified a comment on discussion General Discussion

Hi, The easier way to fix up this is using a earlier viersion of Diamond. As you...

Alexis Fonseca posted a comment on discussion General Discussion

Hi, The easier way to fix up this is using a earlier viersion of Diamond. As you...

Neslihan Tas posted a comment on discussion General Discussion

Hi Marc, I am getting the same error as decribed above. Issue is not having the Diaomond...

Cecilia Valdna Juhlin posted a comment on discussion General Discussion

Hello! We are having some problems running metawatt-3.5.3. The errors generated are:...

Kshitij Tandon posted a comment on discussion General Discussion

Hi, I am also facing the same issue of Diamond:ERROR ( NO annotation possible) Can...

Marc Strous posted a comment on discussion General Discussion

Hi Maria, guess I don't need to point out that diamond is not working... you may...

Maria posted a comment on discussion General Discussion

Hello. I am using Metawatt version 3.5.3. I have installed all dependencies and they...

Shakya(Damayanthi Herath) posted a comment on discussion General Discussion

Hi, I try to run Metawatt with 2 datasets, but in both the cases, the program takes...

Yu Bin Wang posted a comment on discussion General Discussion

Hi Marc, Thanks, I can't wait to try. Regards, Yu Bin

Marc Strous posted a comment on discussion General Discussion

Hi Michal, I uploaded a new version - check it out... Best wishes, Marc On 11/18/2016...

Marc Strous posted a comment on discussion General Discussion

Hi Yu Bin, thanks for exploring this issue.... I uploaded a new version of metawatt...

metawatt released /MetaWatt-3.5.3.zip

Yu Bin Wang posted a comment on discussion General Discussion

Hello Marc, I also got this problem like Michal said, so I take a look into the src...

Michal Kaminski posted a comment on discussion General Discussion

Hello Marc, Any suggestions what should I do if the Update Database module doesn't...

Marc Strous committed [af9667]

version 4.0

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version 4.0

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version 4.0

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version 4.0

Marc Strous posted a comment on discussion General Discussion

Hi Maria, Indeed, this doesn't work anymore, but metawatt will create a database...

Maria Pachiadaki posted a comment on discussion General Discussion

Hello Marc, I get the following error when I am trying to download the metawatt databases....

Marc Strous committed [7d31d5]

toward version 4.0

Marc Strous committed [a8b1cc]

final state of version 3.5.2. Next commits will...

David Colatriano posted a comment on discussion General Discussion

Hello Dr. Strous I have successfully run MetaWatt 3.5.2, but am unsure as to how...

Arthi Ramachandran posted a comment on discussion General Discussion

Hi! I was wondering whether this issue has been solved? I am having the same issues...

Sotirios Vasileiadis posted a comment on discussion General Discussion

Hi Marc, I will follow your advice and get back to you in case of any issues... looking...

Marc Strous posted a comment on discussion General Discussion

Hi Sotirios, Thank you for trying metawatt and reporting this problem. I am aware...

Sotirios Vasileiadis modified a comment on discussion General Discussion

Hi Marc, To begin with, many thanks for the amazing pipeline (second time I am using...

Sotirios Vasileiadis posted a comment on discussion General Discussion

Hi Marc, To begin with, many thanks for the amazing pipeline (second time I am using...

Marc Strous posted a comment on discussion General Discussion

Hi Bibaswan, Yes it should run fine. Probably you would do the analysis in command...

Bibaswan Ghoshal posted a comment on discussion General Discussion

Hi, Can metawatt be run from a Linux cluster? I have all the dependancies installed...

Marc Strous posted a comment on discussion General Discussion

Hi Maria, in the latest versions you no longer import contigs and read files via...

Maria Pachiadaki posted a comment on discussion General Discussion

A short update Marc. I also tested it in an Ubuntu virtual machine and I get the...

Maria Pachiadaki posted a comment on discussion General Discussion

Hello Marc, I have a rather stupid question. I cannot find the way to import the...

Marc Strous posted a comment on discussion General Discussion

Hi Danny, this is not entirely trivial, as the ncbi address is not only used for...

Danny Ionescu posted a comment on discussion General Discussion

Hi Marc Unfortunately I still have an issue with updating the databases. Our new...

David Probandt posted a comment on discussion General Discussion

Hi Marc, Unfortunately I have to admit that the issue was easily solved in the end....

David Probandt posted a comment on discussion General Discussion

Hi Marc, I have a problem with the execution of the Six frame Pfam module. As describe...

Marc Strous posted a comment on discussion General Discussion

Hi Jeroen, Although I have not yet expe rienced the "hanging" of the optimize bins...

<REDACTED> modified a comment on discussion General Discussion

edit: found it myself. Please delete post

<REDACTED> modified a comment on discussion General Discussion

Hello everyone, I'm encountering a problem using MetaWatt 3.5.2. The module [Bin...

<REDACTED> posted a comment on discussion General Discussion

Hello everyone, I'm encountering a problem using MetaWatt 3.5.2. The module [Bin...

<REDACTED> posted a comment on discussion General Discussion

This seems to work to grab a float out of the header... ([0-9]+)([.,]+[0-9]+)

<REDACTED> modified a comment on discussion General Discussion

Dear Marc and Metawatt users, I've got a FASTA file with headers that contain coverage...

<REDACTED> modified a comment on discussion General Discussion

Dear Marc and Metawatt users, I've got a FASTA file with headers that contain coverage...

<REDACTED> modified a comment on discussion General Discussion

Dear Marc and Metawatt users, I've got a FASTA file with headers that contain coverage...

<REDACTED> modified a comment on discussion General Discussion

Dear Marc and Metawatt users, I've got a FASTA file with headers that contain coverage...

<REDACTED> modified a comment on discussion General Discussion

Dear Marc and Metawatt users, I've got a FASTA file with headers that contain coverage...

<REDACTED> posted a comment on discussion General Discussion

Dear Marc and Metawatt users, I've got a FASTA file with headers that contain coverage...

Marc Strous committed [1282f3]

final changes, version 3.5.2

Marc Strous modified a wiki page

Home

metawatt released /MetaWatt-3.5.2.zip

Marco Guenthel posted a comment on discussion General Discussion

Thank you very much for your quick response and the update! Best wishes, Marco

Dimitri Meier posted a comment on discussion General Discussion

Hi Marc, the database I use is just the one generated by Metawatt during the database...

Marc Strous posted a comment on discussion General Discussion

Marco, I new version has been released (3.5.1) that allows you to copy paste data...

metawatt released /MetaWatt-3.5.1.zip

Marc Strous modified a wiki page

Home

Marc Strous committed [302a73]

final changes, version 3.4.1

Marc Strous posted a comment on discussion General Discussion

Hi Dimitry, Thanks for investigating this problem! It should not occur if you use...

Dimitri Meier posted a comment on discussion General Discussion

Hi Marc, came across this issue a while ago, but had no time to post it here. With...

Marc Strous posted a comment on discussion General Discussion

Hi Marco, you're right, the export options could be improved. I'll work on that and...

Marc Strous modified a wiki page

User interface

Marco Guenthel posted a comment on discussion General Discussion

Hi all, I am using the newest version of Metawatt and the software is working fine...

Marc Strous posted a comment on discussion General Discussion

Hi Lars, in the current version you can only export an entire binset. This is done...

Lars Schreiber posted a comment on discussion General Discussion

Dear Marc, After succesfully running through the MetaWatt pipeline (latest version...

Stepan Toshchakov posted a comment on discussion General Discussion

Dear Marc, I have the same issue that John described. Can I kindly ask you to send...

JohnForadKelley modified a comment on discussion General Discussion

Diamond - Linux 64bit binary file v0.7.2 Metawatt-3.1.1 For the past week or more...

Marc Strous posted a comment on discussion General Discussion

Hi Rafael, The procedure is documented here: https://sourceforge.net/p/metawatt/wiki/Update%20databases/...

Marc Strous modified a wiki page

Update databases

Marc Strous modified a wiki page

Update databases