Metawatt [ERROR] String out of range in Six frame Pfam module

Question

[dark.lord]

Hi all,

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] Redundant : 35524
Metawatt [INFO|2:07:40] Wanted : 27
Metawatt [INFO|2:07:40] Force download : 0
Metawatt [INFO|2:07:40] Archaea : 116
Metawatt [INFO|2:07:40] Bacteria : 1583
Metawatt [INFO|2:07:40] Eukaryota : 32
Metawatt [INFO|2:07:40] Viruses : 474
Metawatt [INFO|2:07:41] Keeping existing uppercase contig file "/scratch2/sscilipo/KARASIK/metagenome/Metawatt_binning/Metawatt_2/tmp/scaffolds.fasta.uc.fasta" - file is up to date. 
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)
at org.metawatt.modules.ModuleRunner.doInBackground(ModuleRunner.java:99)
at org.metawatt.modules.ModuleRunner.doInBackground(ModuleRunner.java:54)
at javax.swing.SwingWorker$1.call(SwingWorker.java:296)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at javax.swing.SwingWorker.run(SwingWorker.java:335)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)

I found a thread with a similar error but no answer: https://sourceforge.net/p/metawatt/discussion/general/thread/c4dba671/?limit=25#fa29

Do you have any idea about what could be the issue? I am using untouched databases/ as I downloaded from Metawatt; also, the module did work in several instances. Might it be due to the input file somehow?

[Pierre Lindenbaum]

do you have any empty sequence in your fasta file ?

[dark.lord]

Already checked with a couple of one liners found on this thread: Removing All Empty Fasta Sequences From A File (Was: Editing The Headers Of The Fasta Format Sequence)

There are no empty sequences.

[Pierre Lindenbaum]

how about your previous questions ?

• Plasmidome recovery from metagenomes: why and how?
  • Trimmomatic output: how to include unpaired reads in the assembly?

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

[dark.lord]

Thanks for the reminder, done both.