hi !
i am trying to build a customized databases, using the workflow that recorded in "user guide"
first step using "ffindex_from_fasta" to convert the input FASTA file. command like below:
"ffindex_from_fasta -s all-neighbours-refer-and-metagenome.fa.ffdata all-neighbours-refer-and-metagenome.fa.ffindex all-neighbours-refer-and-metagenome.fa"
it is works. but in the next step, using "hhblits_omp" to get MSA file.
"hhblits_omp -i all-neighbours-refer-and-metagenome.fa -d /home/projects/ku_00041/data/hh-suite-database/UniRef30_2020_06 -oa3m all-neighbours-refer-and-metagenome_a3m_ww_ss -n 2 -cpu 35"
but it not working, the error like:
------------------------------------------------------------------error--------------------------------------------------------------
09:13:31.134 INFO: EIC29417.1--(EIC29420.1) is in A2M, A3M or FASTA format
09:13:31.162 INFO: Iteration 1
09:13:31.697 ERROR: Error in /opt/conda/conda-bld/hhsuite_1616660820288/work/src/hhfunc.cpp:83: ReadQueryFile:
' 09:13:31.697 ERROR: unrecognized input file format in '3300029656.a:Ga0245165_100003_39¸
09:13:31.697 ERROR: line = 4--(DD08414.1)
09:13:31.698 ERROR: Error in /opt/conda/conda-bld/hhsuite_1616660820288/work/src/hhfunc.cpp:83: ReadQueryFile:
09:13:31.698 ERROR: unrecognized input file format in '3300011605.a:Ga0120982_100063_27*'
09:13:31.698 ERROR: line = --(CF53703.1)
09:13:31.698 INFO: CRP04010.1--(CRP04742.1) is in A2M, A3M or FASTA format
09:13:31.698 ERROR: Error in /opt/conda/conda-bld/hhsuite_1616660820288/work/src/hhfunc.cpp:83: ReadQueryFile:
09:13:31.698 ERROR: unrecognized input file format in 'AEY01231.1--(AEY01220.1)'
09:13:31.698 ERROR: line = -AEY01231.1--(AEY01220.1)
:exclamation: Make to check out our User Guide.
hi ! i am trying to build a customized databases, using the workflow that recorded in "user guide"
first step using "ffindex_from_fasta" to convert the input FASTA file. command like below: "ffindex_from_fasta -s all-neighbours-refer-and-metagenome.fa.ffdata all-neighbours-refer-and-metagenome.fa.ffindex all-neighbours-refer-and-metagenome.fa"
it is works. but in the next step, using "hhblits_omp" to get MSA file. "hhblits_omp -i all-neighbours-refer-and-metagenome.fa -d /home/projects/ku_00041/data/hh-suite-database/UniRef30_2020_06 -oa3m all-neighbours-refer-and-metagenome_a3m_ww_ss -n 2 -cpu 35"
but it not working, the error like: ------------------------------------------------------------------error--------------------------------------------------------------
09:13:31.134 INFO: EIC29417.1--(EIC29420.1) is in A2M, A3M or FASTA format
09:13:31.162 INFO: Iteration 1
09:13:31.697 ERROR: Error in /opt/conda/conda-bld/hhsuite_1616660820288/work/src/hhfunc.cpp:83: ReadQueryFile:
' 09:13:31.697 ERROR: unrecognized input file format in '3300029656.a:Ga0245165_100003_39¸
09:13:31.697 ERROR: line = 4--(DD08414.1)
09:13:31.698 ERROR: Error in /opt/conda/conda-bld/hhsuite_1616660820288/work/src/hhfunc.cpp:83: ReadQueryFile:
09:13:31.698 ERROR: unrecognized input file format in '3300011605.a:Ga0120982_100063_27*'
09:13:31.698 ERROR: line = --(CF53703.1)
09:13:31.698 INFO: CRP04010.1--(CRP04742.1) is in A2M, A3M or FASTA format
09:13:31.698 ERROR: Error in /opt/conda/conda-bld/hhsuite_1616660820288/work/src/hhfunc.cpp:83: ReadQueryFile:
09:13:31.698 ERROR: unrecognized input file format in 'AEY01231.1--(AEY01220.1)'
09:13:31.698 ERROR: line = -AEY01231.1--(AEY01220.1)
here is my fasta file:![image](https://user-images.githubusercontent.com/58076352/132816722-b66ed636-3c1e-4d86-a490-f619d1596d4e.png)
and the version is 3.30
so do you have any idea about this error.
best, wanli