MSA error when running prediction with short poly-U RNA

[mvorlander]

Dear Rosetta team,

I amt rying to predict Protein structures with short poly-U RNAs to identify putative RNA binding sites in proteins. However, the program fails because no database hits are found. Attached are the log messages.

Would be great to get this to work!

Best wishes and many thanks,
Matthias

make_msa.PolyU.stdout:

RF2NA running ...
Run cmscan on Rfam
Rfam families:
Run blastn on RNACentral
Run blastn on nt
Cluster sequences
Realign all with nhmmer
no hits found

make_msa.PolyU.stderr
rm: cannot remove 'rfam1.list.split.': No such file or directory
rm: cannot remove 'rfam2.list.split.': No such file or directory
rm: cannot remove 'blastn1.list.split.': No such file or directory
BLAST Database error: No alias or index file found for nucleotide database [/opt/RoseTTAFold2NA/RNA/nt] in search path [/groups/plaschka/matthias.vorlaender/temp/testpolyUwDHC15::]
rm: cannot remove 'blastn2.list.split.': No such file or directory
grep: db: No such file or directory
rm: cannot remove 'cdhitest2d.db': No such file or directory
rm: cannot remove 'cdhitest2d.db.clstr': No such file or directory
rm: cannot remove 'db.clstr': No such file or directory

Error: Unable to guess alphabet for the query file PolyU.fa

Alignment input open failed.
couldn't open nhmmer.a2m for reading

• 11:17:35.241 INFO: Input file = PolyU.wquery.unfilt.afa

• 11:17:35.241 INFO: Output file = PolyU.afa

• 11:17:35.243 WARNING: No sequence name preceding following line in PolyU.wquery.unfilt.afa:
  'RF2NA running ...'

• 11:17:35.243 ERROR: In /opt/conda/conda-bld/hhsuite_1690046720367/work/src/hhalignment.cpp:502: Read:

• 11:17:35.243 ERROR: No sequences found in file PolyU.wquery.unfilt.afa

grep: PolyU.afa: No such file or directory

Error: Unable to guess alphabet for the query file PolyU.fa

Alignment input open failed.
couldn't open nhmmer.a2m for reading

• 11:17:35.543 INFO: Input file = PolyU.wquery.unfilt.afa

• 11:17:35.543 INFO: Output file = PolyU.afa

• 11:17:35.544 WARNING: No sequence name preceding following line in PolyU.wquery.unfilt.afa:
  'RF2NA running ...'

• 11:17:35.544 ERROR: In /opt/conda/conda-bld/hhsuite_1690046720367/work/src/hhalignment.cpp:502: Read:

• 11:17:35.544 ERROR: No sequences found in file PolyU.wquery.unfilt.afa

Error: Unable to guess alphabet for the query file PolyU.fa

Alignment input open failed.
couldn't open nhmmer.a2m for reading

• 11:17:35.833 INFO: Input file = PolyU.wquery.unfilt.afa

• 11:17:35.833 INFO: Output file = PolyU.afa

• 11:17:35.833 WARNING: No sequence name preceding following line in PolyU.wquery.unfilt.afa:
  'RF2NA running ...'

• 11:17:35.833 ERROR: In /opt/conda/conda-bld/hhsuite_1690046720367/work/src/hhalignment.cpp:502: Read:

• 11:17:35.833 ERROR: No sequences found in file PolyU.wquery.unfilt.afa

Error: Unable to guess alphabet for the query file PolyU.fa

Alignment input open failed.
couldn't open nhmmer.a2m for reading

• 11:17:36.116 INFO: Input file = PolyU.wquery.unfilt.afa

• 11:17:36.116 INFO: Output file = PolyU.afa

• 11:17:36.117 WARNING: No sequence name preceding following line in PolyU.wquery.unfilt.afa:
  'RF2NA running ...'

• 11:17:36.117 ERROR: In /opt/conda/conda-bld/hhsuite_1690046720367/work/src/hhalignment.cpp:502: Read:

• 11:17:36.117 ERROR: No sequences found in file PolyU.wquery.unfilt.afa

Error: Unable to guess alphabet for the query file PolyU.fa

Alignment input open failed.
couldn't open nhmmer.a2m for reading

• 11:17:36.412 INFO: Input file = PolyU.wquery.unfilt.afa

• 11:17:36.412 INFO: Output file = PolyU.afa

• 11:17:36.412 WARNING: No sequence name preceding following line in PolyU.wquery.unfilt.afa:
  'RF2NA running ...'

• 11:17:36.412 ERROR: In /opt/conda/conda-bld/hhsuite_1690046720367/work/src/hhalignment.cpp:502: Read:

• 11:17:36.412 ERROR: No sequences found in file PolyU.wquery.unfilt.afa

Error: Unable to guess alphabet for the query file PolyU.fa

Alignment input open failed.
couldn't open nhmmer.a2m for reading

• 11:17:36.699 INFO: Input file = PolyU.wquery.unfilt.afa

• 11:17:36.699 INFO: Output file = PolyU.afa

• 11:17:36.700 WARNING: No sequence name preceding following line in PolyU.wquery.unfilt.afa:
  'RF2NA running ...'

• 11:17:36.700 ERROR: In /opt/conda/conda-bld/hhsuite_1690046720367/work/src/hhalignment.cpp:502: Read:

• 11:17:36.700 ERROR: No sequences found in file PolyU.wquery.unfilt.afa

rm: cannot remove 'nhmmer.a2m': No such file or directory

[rpmchugh]

If you're able to generate the msas for your proteins of interest, you should be able to predict the complexes with poly-U RNA by using network/predict.py directly

[anar-rzayev]

@mvorlander Were you able to fix this issue? I am also facing a similar problem for my cas9 protein - RNA complex