mackevinbraza commented 7 months ago

After successfully installing RF2NA in my linux workstation, I tried to run these commands

# run Protein/RNA prediction
../run_RF2NA.sh rna_pred rna_binding_protein.fa R:RNA.fa
# run Protein/DNA prediction
../run_RF2NA.sh dna_pred dna_binding_protein.fa D:DNA.fa

However, when I checked the stderror files in both the rna_pred and dna_pred, these stderror files showed that I am missing

11:22:32.786 ERROR:     could not open file 'RoseTTAFold2NA/example/dna_pred/hhblits/t000_.1e-3.bfd.a3m'
cp: cannot stat 'RoseTTAFold2NA/example/dna_pred/hhblits/t000_.1e-3.bfd.id90cov50.a3m': No such file or directory

I also have updated Conda packages, which are all up to date.

Is there anything that I can do to fix these test runs?

Thank you!

Sincerely, Kevin

AngelaAmari commented 7 months ago

I guess it is the second line in the error log right? Is it segmentation fault like this: /RoseTTAFold2NA/input_prep/make_protein_msa.sh: line 28: 27325 Segmentation fault $HHBLITS_UR30 -i $prev_a3m -oa3m $tmpdir/t000.$e.a3m -e $e -v 0 I am having the exact same issue...

ChrisLou-bioinfo commented 7 months ago

check the path of database

AngelaAmari commented 7 months ago

check the path of database

Hi Chris,

Could you elaborate more on this? I don't quite understand...Thanks!

mackevinbraza commented 7 months ago

I am not sure what else can be done for the test scripts to work. Does anyone have figured out what else can I try to make this work?

11:22:32.786 ERROR:     could not open file 'RoseTTAFold2NA/example/dna_pred/hhblits/t000_.1e-3.bfd.a3m'
cp: cannot stat 'RoseTTAFold2NA/example/dna_pred/hhblits/t000_.1e-3.bfd.id90cov50.a3m': No such file or directory

AngelaAmari commented 7 months ago

I am not sure what else can be done for the test scripts to work. Does anyone have figured out what else can I try to make this work?
11:22:32.786 ERROR:   could not open file 'RoseTTAFold2NA/example/dna_pred/hhblits/t000_.1e-3.bfd.a3m'
cp: cannot stat 'RoseTTAFold2NA/example/dna_pred/hhblits/t000_.1e-3.bfd.id90cov50.a3m': No such file or directory

If it is segmentation fault, maybe try compile the hhsuite from source? See: https://github.com/RosettaCommons/RoseTTAFold It is weird that I have no such issue on my local machine but yes when trying to install in on a cluster...

ShuZishan commented 4 months ago

Have you resolved this issue? I've encountered the same problem: Running HHblits against UniRef30 with E-value cutoff 1e-6

17:52:28.566 WARNING: Ignoring unknown option 4
17:52:28.566 ERROR: In /opt/conda/conda-bld/hhsuite_1690046720367/work/src/ffindexdatabase.cpp:11: FFindexDatabase:
17:52:28.566 ERROR: could not open file '/UniRef30_2020_06_cs219.ffdata'
17:52:28.568 INFO: Input file = /hhblits/t000_.1e-6.a3m
17:52:28.568 INFO: Output file = /hhblits/t000_.1e-6.id90cov75.a3m
17:52:28.568 ERROR: In /opt/conda/conda-bld/hhsuite_1690046720367/work/src/hhfilter.cpp:177: main:
17:52:28.568 ERROR: could not open file '/hhblits/t000_.1e-6.a3m'
17:52:28.570 INFO: Input file = /hhblits/t000_.1e-6.a3m
17:52:28.570 INFO: Output file = /hhblits/t000_.1e-6.id90cov50.a3m
17:52:28.570 ERROR: In /opt/conda/conda-bld/hhsuite_1690046720367/work/src/hhfilter.cpp:177: main:
17:52:28.570 ERROR: could not open file '/hhblits/t000_.1e-6.a3m'

grep: /hhblits/t000.1e-6.id90cov75.a3m: No such file or directory grep: /hhblits/t000.1e-6.id90cov50.a3m: No such file or directory Could you provide me with some advice? Thank you.

muuu23333 commented 3 months ago

Have you resolved this issue? I've encountered the same problem: Running HHblits against UniRef30 with E-value cutoff 1e-6

17:52:28.566 WARNING: Ignoring unknown option 4

17:52:28.566 ERROR: In /opt/conda/conda-bld/hhsuite_1690046720367/work/src/ffindexdatabase.cpp:11: FFindexDatabase:

17:52:28.566 ERROR: could not open file '/UniRef30_2020_06_cs219.ffdata'

17:52:28.568 INFO: Input file = /hhblits/t000_.1e-6.a3m

17:52:28.568 INFO: Output file = /hhblits/t000_.1e-6.id90cov75.a3m

17:52:28.568 ERROR: In /opt/conda/conda-bld/hhsuite_1690046720367/work/src/hhfilter.cpp:177: main:

17:52:28.568 ERROR: could not open file '/hhblits/t000_.1e-6.a3m'

17:52:28.570 INFO: Input file = /hhblits/t000_.1e-6.a3m

17:52:28.570 INFO: Output file = /hhblits/t000_.1e-6.id90cov50.a3m

17:52:28.570 ERROR: In /opt/conda/conda-bld/hhsuite_1690046720367/work/src/hhfilter.cpp:177: main:

17:52:28.570 ERROR: could not open file '/hhblits/t000_.1e-6.a3m'

grep: /hhblits/t000.1e-6.id90cov75.a3m: No such file or directory grep: /hhblits/t000.1e-6.id90cov50.a3m: No such file or directory Could you provide me with some advice? Thank you.

Have you resolved this issue?

WangGuanxi0530 commented 3 months ago

I have solved the problem. After downloading the hhsuite package on my computer, this error was no longer reported.

download

git clone https://github.com/soedinglab/hh-suite.git cd hh-suite


I'm not sure if this can help you, as everyone's server environment is different. I hope it can be of assistance to you.

AngelaAmari commented 3 months ago

I have solved the problem. After downloading the hhsuite package on my computer, this error was no longer reported.

download

git clone https://github.com/soedinglab/hh-suite.git cd hh-suite
I'm not sure if this can help you, as everyone's server environment is different. I hope it can be of assistance to you.

Yes like I have said, try to compile hhsuite from source.

uw-ipd / RoseTTAFold2NA

Test run_RF2na.sh for DNA and RNA Error - missing a3m files #72

download

download