[Problem] Six frame Pfam
Binner for assembled metagenomes
Status: Beta
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Hi Marc,
I have a problem with the execution of the Six frame Pfam module.
As describe in your documentation I had compiled the conserved-genes.hmm and rrna.hmm with hmmpress (hmm-3.1b2) which resulted in the wanted files: conserved-genes.hmm.h3i , h3f, h3m, h3p and rrna.hmm.xxx (as above).
For some reason I got the error message (see below).
I tried to A) use a databases by somebody else B) tried another hmm version for compilation, c) re did the compilation from newly downloaded databases c) reset the link in the project folder to the database and d)ran the pipeline to let metawatt execute the hmmpress command. None of these approaches could solve the issue.
Is there a way to see what actual database name/ file name is called by the six frame Pfam module? Maybe it calls another file name?
In case you have an idea how to solve the problem, I would appreciate if you can share your thoughts:)
Thanks and best regards from Bremen,
David
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metawatt & dependencies
metawatt 3.5.2
hmmer-3.1b2
all core dependecies work
Six frame Pfam Error message:
java.lang.Exception: No hmm profile databases in database folder!
at org.metawatt.modules.ContigHMMProfileScan.run(ContigHMMProfileScan.java:58)
at org.metawatt.modules.ModuleRunner.processModule(ModuleRunner.java:177)
at org.metawatt.modules.ModuleRunner.processModuleWrapperInterceptOptimize(ModuleRunner.java:162)
at org.metawatt.modules.ModuleRunner.doInBackground(ModuleRunner.java:91)
at org.metawatt.modules.ModuleRunner.doInBackground(ModuleRunner.java:54)
at javax.swing.SwingWorker$1.call(SwingWorker.java:295)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at javax.swing.SwingWorker.run(SwingWorker.java:334)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
check dependencies
Metawatt [INFO|9:40:48] Total time used: 0.006 minutes
Metawatt [INFO|9:43:31] prodigal -h
[prodigal, -h]
Usage: prodigal [-a trans_file] [-c] [-d nuc_file] [-f output_type]
Metawatt [INFO|9:43:31] diamond -h
[diamond, -h]
Syntax:
Metawatt [INFO|9:43:31] hmmscan -h
[hmmscan, -h]
Usage: hmmscan [-options] <hmmdb> <seqfile>
Metawatt [INFO|9:43:31] hmmbuild -h
[hmmbuild, -h]
Usage: hmmbuild [-options] <hmmfile_out> <msafile>
Metawatt [INFO|9:43:31] hmmpress -h
[hmmpress, -h]
Usage: hmmpress [-options] <hmmfile>
Metawatt [INFO|9:43:31] hmmalign -h
[hmmalign, -h]
Usage: hmmalign [-options] <hmmfile> <seqfile>
Metawatt [INFO|9:43:31] nhmmer -h
[nhmmer, -h]
Usage: nhmmer [options] <query hmmfile|alignfile=""> <target seqfile="">
Metawatt [INFO|9:43:31] bbmap.sh -h
[bbmap.sh, -h]
BBMap v35.x
Metawatt [INFO|9:43:31] aragorn -h
[aragorn, -h]
ARAGORN v1.2.36 Dean Laslett
Metawatt [INFO|9:43:31] mafft -h
[mafft, -h]
http://mafft.cbrc.jp/alignment/software/
Metawatt [INFO|9:43:31] FastTreeMP -h
[FastTreeMP, -h]
Common options (must be before the alignment file):
Metawatt [INFO|9:43:31] usearch
[usearch]
http://drive5.com/usearch
Metawatt [INFO|9:43:31]
Core dependencies
Prodigal: OK
Diamond: OK
HMMER: OK
BBMap: OK
Batik: OK
Aragorn: OK
Hi Marc,
Unfortunately I have to admit that the issue was easily solved in the end. At some point I must have stopped to reload the project after making changes to the metawatt database folder. I lost track what changes made the database work, in the end. The key was, as you suggested, to close the project, and reload the project after each change I made to the database.
Best
david