rpmchugh
commented
5 months ago 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
Open mvorlander opened 5 months ago
rpmchugh
commented
5 months ago 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
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