error in builddatabase
weirdo-onlooker opened this issue · 2 comments
During the database construction process,
"BuildDatabase -name hhh_YQtrio0 -engine ncbi genome/hhh_YQtrio0.fasta" , I also tried to remove the engine option，
finally I received the following message:
Building database hhh_YQtrio0:
Reading genome/hhh_YQtrio0.fasta...
The makeblastdb program exited with code 1. Please check your input file(s) for potential formating errors.
/ifs1/User/lengliang/yaozc/biosoft/rmblast-2.14.1/bin/makeblastdb returned: /ifs1/User/lengliang/yaozc/biosoft/rmblast-2.14.1/bin/makeblastdb: /lib64/libm.so.6: version GLIBC_2.29' not found (required by /ifs1/User/lengliang/yaozc/biosoft/rmblast-2.14.1/bin/makeblastdb) /ifs1/User/lengliang/yaozc/biosoft/rmblast-2.14.1/bin/makeblastdb: /lib64/libc.so.6: version GLIBC_2.33' not found (required by /ifs1/User/lengliang/yaozc/biosoft/rmblast-2.14.1/bin/makeblastdb)
/ifs1/User/lengliang/yaozc/biosoft/rmblast-2.14.1/bin/makeblastdb: /lib64/libc.so.6: version GLIBC_2.32' not found (required by /ifs1/User/lengliang/yaozc/biosoft/rmblast-2.14.1/bin/makeblastdb) /ifs1/User/lengliang/yaozc/biosoft/rmblast-2.14.1/bin/makeblastdb: /lib64/libc.so.6: version GLIBC_2.34' not found (required by /ifs1/User/lengliang/yaozc/biosoft/rmblast-2.14.1/bin/makeblastdb)
The command used was: /ifs1/User/lengliang/yaozc/biosoft/rmblast-2.14.1/bin/makeblastdb -blastdb_version 4 -out hhh_YQtrio0 -parse_seqids -dbtype nucl -in ./RM_9ImDCpo 2>&1
Died at /ifs1/User/lengliang/yaozc/biosoft/RepeatModeler-2.0.5/BuildDatabase line 331.
I have checked my fasta file and there seems to be no issue with it. I attempted to upgrade the GLIBC version, but failed and do not have root permissions. I also tried to downgrade the rmblast version to 2.11.0, but it requires reconfiguration, which also encountered issues. Now I want to replace rmblast with another software, and I don't want to rerun perl ./configure. Where can I modify this configuration file?
this is my fasta file(part):
h1tg000001l
CTGAGTTTTCATGTATAATGATGAATTAGGCTAAGCATATGTTGCTTTATGTATGTAAATCTGTTTGTATGGTTGATTGTTTGTACTAAATTCACATTGTGATGCAGTTGCATTTCATATTATAATGCAGTAGGTTTTTATTTTAACTGTGATGCAGTAGGTTGTTTGT......
Hi,
I also had this problem when I used rmblast-2.14.1. I fixed the issue "GLIBC_2.29 not found" by replacing the rmblast-2.14.1 with rmblast-2.14.0.
Have a try!
Good luck!
Fan
If you would like to stick with the latest rmblast I would suggest simply compiling it from source (instructions here: http://www.repeatmasker.org/rmblast/ ). This will ensure that the correct GLIBC is used when building the binary.