Funannotate iprscan Creates empty file
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Entering edit mode
11 weeks ago
Umer ▴ 50

Hey, I have been following the annotation steps mentioned at https://funannotate.readthedocs.io/en/latest/tutorials.html#genome-assembly-and-rna-seq.

I have completed the following with no error so far

  1. Repeatmasking using RepeatMasker/Modeler seprately
  2. funannotate Clean (worked without any error)
  3. funannotate Sort (worked without any error)
  4. funannotate Train (worked without any error)
  5. funannotate Predict (worked without any error)
  6. funannotate Update (worked without any error)

Now I am trying the Fnnannotate iprscan locally on linux using the commands

Try 1

Command: funannotate iprscan --input ./assembly_annotation/ --method local --cpus 14 2>&1 | tee -a iprscan.log

Results: it runs without any error. Resulting file in path ./assembly_annotation/annotation_misc/iprscan.xml is empty with only one line </protein-matches>

The Log File looks like this (there were around 607 line of "Progress:" so i trimmed that)

Running InterProScan5 on 16440 proteins
Important: you need to manually configure your interproscan.properties file for embedded workers.
Will try to launch 14 interproscan processes, adjust -c,--cpus for your system
     Progress: 0 complete, 0 failed, 16 remaining            
     Progress: 1 complete, 0 failed, 15 remaining        
     Progress: 2 complete, 0 failed, 14 remaining        
     Progress: 3 complete, 0 failed, 13 remaining        
     Progress: 4 complete, 0 failed, 12 remaining        
     Progress: 5 complete, 0 failed, 11 remaining        
     Progress: 8 complete, 0 failed, 8 remaining        
     Progress: 9 complete, 0 failed, 7 remaining        
     Progress: 10 complete, 0 failed, 6 remaining        
     Progress: 12 complete, 0 failed, 4 remaining        
     Progress: 13 complete, 0 failed, 3 remaining        
     Progress: 14 complete, 0 failed, 2 remaining        
     Progress: 15 complete, 0 failed, 1 remaining        
     Progress: 16 complete, 0 failed, 0 remaining        
InterProScan5 search has completed successfully!
Results are here: ./assembly_annotation/annotate_misc/iprscan.xml

Try 2

I have tried it in different way as Command: funannotate iprscan --input ./assembly_annotation/update_results/genome.proteins.fa --out ./assembly_annotation/interproscan/iprscan.xml --method local --cpus 14 2>&1 | tee -a iprscan2.log

Results: it ran again without any error. Resulting file in path ./assembly_annotation/interproscan/iprscan.xml is empty with only one line </protein-matches>

The Log File looks like this (again there were around 607 line of "Progress:" so i trimmed that)

Running InterProScan5 on 16440 proteins
Important: you need to manually configure your interproscan.properties file for embedded workers.
Will try to launch 14 interproscan processes, adjust -c,--cpus for your system
     Progress: 0 complete, 0 failed, 16 remaining            
     Progress: 1 complete, 0 failed, 15 remaining        
     Progress: 2 complete, 0 failed, 14 remaining        
     Progress: 3 complete, 0 failed, 13 remaining        
     Progress: 4 complete, 0 failed, 12 remaining        
     Progress: 5 complete, 0 failed, 11 remaining        
     Progress: 8 complete, 0 failed, 8 remaining        
     Progress: 9 complete, 0 failed, 7 remaining        
     Progress: 10 complete, 0 failed, 6 remaining        
     Progress: 12 complete, 0 failed, 4 remaining        
     Progress: 13 complete, 0 failed, 3 remaining        
     Progress: 14 complete, 0 failed, 2 remaining        
     Progress: 15 complete, 0 failed, 1 remaining        
     Progress: 16 complete, 0 failed, 0 remaining 
InterProScan5 search has completed successfully!
Results are here: ./assembly_annotation/interproscan/iprscan.xml
funannotate interproscan fungus annotation • 190 views
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Entering edit mode

Try 3

I tried running interproscan.sh , (not the funannotate wrapper) as described here https://github.com/nextgenusfs/funannotate/issues/841#issuecomment-1328140589

which interproscan.sh >>>> /home/user/miniconda3/envs/funannotate/bin/interproscan.sh

Command: interproscan.sh -i ./assembly_annotation/update_results/*.proteins.fa --output-dir ./assembly_annotation/interproscan/ -goterms -pa -f XML 2>&1 | tee -a iprscan3.log

Results: "InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details "

The Log File looks like this I could not find the log file interprpscan created so here is the output printed on the terminal.

Kindly Help with this error/Bug.

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