Hello. I am using Metawatt version 3.5.3. I have installed all dependencies and they are in the PATH, even Diamond, but I get this error, missing as well gene annotation in the results:
Prodigal: OK
Diamond: ERROR (No annotation possible)
HMMER: OK
BBMap: OK
Batik: OK
Aragorn: OK
MAFFT: OK
Fasttree: OK
USearch:
I see during the test of dependencies that Metawatt call Diamond with -h:
.....
This is Metawatt version 3.5.3
Metawatt [INFO|9:18:27] prodigal -h [prodigal, -h]
Usage: prodigal [-a trans_file][-c][-d nuc_file][-f output_type]
Metawatt [INFO|9:18:27] diamond -h [diamond, -h]
Metawatt [INFO|9:18:27] hmmscan -h [hmmscan, -h]
Usage: hmmscan [-options] <hmmdb> <seqfile>
.....
.... but diamond -h doesn't work in the last version of diamond.
I really appreciate any help you can provide.
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guess I don't need to point out that diamond is not working... you may
look up the diamond commands from the metawatt logbook and copy them
onto the command line to see what error messages you get.
Best wishes,
Marc
On 02/16/2017 01:46 AM, Maria wrote:
Hello. I am using Metawatt version 3.5.3. I have installed all
dependencies and they are in the PATH, even Diamond, but I get this
error, missing as well gene annotation in the results:
Prodigal: OK
Diamond: ERROR (No annotation possible)
HMMER: OK
BBMap: OK
Batik: OK
Aragorn: OK
MAFFT: OK
Fasttree: OK
USearch:
I see during the test of dependencies that Metawatt call Diamond with -h:
.....
This is Metawatt version 3.5.3
Metawatt [INFO|9:18:27] prodigal -h [prodigal, -h]
Usage: prodigal [-a trans_file][-c][-d nuc_file][-f output_type]
Metawatt [INFO|9:18:27] diamond -h [diamond, -h]
Metawatt [INFO|9:18:27] hmmscan -h [hmmscan, -h]
Usage: hmmscan [-options] <hmmdb> <seqfile>
.....
.... but diamond -h doesn't work in the last version of diamond.
Department of Geoscience
University of Calgary
tel: (403) 220 6604
2500 University Drive NW
Calgary, AB, Canada T2N 1N4
Energy Environment and Experiental Learning (EEEL) Building
Room 509
I am getting the same error as decribed above. Issue is not having the Diaomond on PATH or available but how MetaWatt checks for its availability. Diamond (below mentioned version) does not accept -h option
$ diamond -h
Error: Invalid command: -h. To print help message: diamond help
$ diamond help
diamond v0.8.36.98
Could you perhaps provide a fix for this? Or comment further.
Thank you very much in advance
Neslihan
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The easiest way to fix up this is using a earlier version of Diamond. As you said, the last versión of Diamond does not recognize the flag -h, so if you install an older vesion of Diamond (older version uses flag -h), MetaWatt should recognizes to diamond as valid and run.
Last edit: Alexis Fonseca 2017-03-16
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hello. I am using Metawatt version 3.5.3. I have installed all dependencies and they are in the PATH, even Diamond, but I get this error, missing as well gene annotation in the results:
Prodigal: OK
Diamond: ERROR (No annotation possible)
HMMER: OK
BBMap: OK
Batik: OK
Aragorn: OK
MAFFT: OK
Fasttree: OK
USearch:
I see during the test of dependencies that Metawatt call Diamond with -h:
.....
This is Metawatt version 3.5.3
Metawatt [INFO|9:18:27] prodigal -h
[prodigal, -h]
Usage: prodigal [-a trans_file] [-c] [-d nuc_file] [-f output_type]
Metawatt [INFO|9:18:27] diamond -h
[diamond, -h]
Metawatt [INFO|9:18:27] hmmscan -h
[hmmscan, -h]
Usage: hmmscan [-options] <hmmdb> <seqfile>
.....
.... but diamond -h doesn't work in the last version of diamond.
I really appreciate any help you can provide.
Hi Maria,
guess I don't need to point out that diamond is not working... you may
look up the diamond commands from the metawatt logbook and copy them
onto the command line to see what error messages you get.
Best wishes,
Marc
On 02/16/2017 01:46 AM, Maria wrote:
--
Marc Strous
Engineer, Ecologist, Entrepreneur
Energy Bioengineering Group
www.ucalgary.ca/ebg
www.solarbiocells.com
www.fixingtheatmosphere.com
www.linkedin.com/in/strous
www.twitter.com/marc_strous
Department of Geoscience
University of Calgary
tel: (403) 220 6604
2500 University Drive NW
Calgary, AB, Canada T2N 1N4
Energy Environment and Experiental Learning (EEEL) Building
Room 509
Hi,
I am also facing the same issue of Diamond:ERROR ( NO annotation possible)
Can you please help in order to fix it
Hi Marc,
I am getting the same error as decribed above. Issue is not having the Diaomond on PATH or available but how MetaWatt checks for its availability. Diamond (below mentioned version) does not accept -h option
$ diamond -h
Error: Invalid command: -h. To print help message: diamond help
$ diamond help
diamond v0.8.36.98
Could you perhaps provide a fix for this? Or comment further.
Thank you very much in advance
Neslihan
Hi,
The easiest way to fix up this is using a earlier version of Diamond. As you said, the last versión of Diamond does not recognize the flag -h, so if you install an older vesion of Diamond (older version uses flag -h), MetaWatt should recognizes to diamond as valid and run.
Last edit: Alexis Fonseca 2017-03-16