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Published 20 hours ago • verified publisher icon RosettaCommons

Error: Unrecognized HMM file format in '1507521083'

Open A-Talavera opened this issue 3 years ago • 3 comments

Hi, I am trying to run RoseTTAFold using the command line ../run_e2e_ver.sh input.fa e2e-test , but after some time I get the error shown bellow. Is it there a way to fix this issue? Thanks in advance. Ariel

From the file make_msa.stderr

  • 15:37:50.594 ERROR: In /opt/conda/conda-bld/hhsuite_1616660820288/work/src/hhdatabase.cpp:443: getTemplateHMM:

  • 15:37:50.594 ERROR: Unrecognized HMM file format in '1507521083'.

  • 15:37:50.594 ERROR: Context: '---------------

  • 15:37:50.594 ERROR: >SRR3954470_15597843

  • 15:37:50.594 ERROR: -------------------------------------------------------------------------------------------------------------------------------------------RGAEL--SRA--laavrHRLRADIAGAKATVRAQALPRVDLDPEAAERLL----aHAVRAALAAGAQRIEVVARAEGGRAHVEVRDDAPPP----GPEALVPFGTPRGRGALvgAGMSLAI---CAriv---------------------------------------------------------------------------------------------------------------------------------------------------------------------'

  • 15:37:52.294 INFO: Input file = /data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-30.a3m

  • 15:37:52.294 INFO: Output file = /data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-30.id90cov75.a3m

  • 15:37:52.294 ERROR: In /opt/conda/conda-bld/hhsuite_1616660820288/work/src/hhfilter.cpp:177: main:

  • 15:37:52.294 ERROR: could not open file '/data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-30.a3m'

  • 15:37:52.296 INFO: Input file = /data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-30.a3m

  • 15:37:52.297 INFO: Output file = /data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-30.id90cov50.a3m

  • 15:37:52.297 ERROR: In /opt/conda/conda-bld/hhsuite_1616660820288/work/src/hhfilter.cpp:177: main:

  • 15:37:52.297 ERROR: could not open file '/data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-30.a3m'

grep: /data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-30.id90cov75.a3m: No such file or directory grep: /data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-30.id90cov50.a3m: No such file or directory

  • 15:38:08.756 ERROR: Input file (/data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-30.id90cov50.a3m) could not be opened!

  • 15:38:08.975 INFO: Input file = /data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-10.a3m

  • 15:38:08.975 INFO: Output file = /data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-10.id90cov75.a3m

  • 15:38:08.975 ERROR: In /opt/conda/conda-bld/hhsuite_1616660820288/work/src/hhfilter.cpp:177: main:

  • 15:38:08.975 ERROR: could not open file '/data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-10.a3m'

  • 15:38:08.977 INFO: Input file = /data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-10.a3m

  • 15:38:08.977 INFO: Output file = /data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-10.id90cov50.a3m

  • 15:38:08.977 ERROR: In /opt/conda/conda-bld/hhsuite_1616660820288/work/src/hhfilter.cpp:177: main:

  • 15:38:08.977 ERROR: could not open file '/data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-10.a3m'

grep: /data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-10.id90cov75.a3m: No such file or directory grep: /data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-10.id90cov50.a3m: No such file or directory

  • 15:38:25.391 ERROR: Input file (/data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-10.id90cov50.a3m) could not be opened!

  • 15:38:25.604 INFO: Input file = /data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-6.a3m

  • 15:38:25.604 INFO: Output file = /data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-6.id90cov75.a3m

  • 15:38:25.604 ERROR: In /opt/conda/conda-bld/hhsuite_1616660820288/work/src/hhfilter.cpp:177: main:

  • 15:38:25.604 ERROR: could not open file '/data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-6.a3m'

  • 15:38:25.606 INFO: Input file = /data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-6.a3m

  • 15:38:25.606 INFO: Output file = /data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-6.id90cov50.a3m

  • 15:38:25.606 ERROR: In /opt/conda/conda-bld/hhsuite_1616660820288/work/src/hhfilter.cpp:177: main:

  • 15:38:25.606 ERROR: could not open file '/data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-6.a3m'

grep: /data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-6.id90cov75.a3m: No such file or directory grep: /data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-6.id90cov50.a3m: No such file or directory

  • 15:38:41.967 ERROR: Input file (/data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-6.id90cov50.a3m) could not be opened!

  • 15:38:42.186 INFO: Input file = /data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-3.a3m

  • 15:38:42.186 INFO: Output file = /data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-3.id90cov75.a3m

  • 15:38:42.186 ERROR: In /opt/conda/conda-bld/hhsuite_1616660820288/work/src/hhfilter.cpp:177: main:

  • 15:38:42.186 ERROR: could not open file '/data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-3.a3m'

  • 15:38:42.188 INFO: Input file = /data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-3.a3m

  • 15:38:42.188 INFO: Output file = /data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-3.id90cov50.a3m

  • 15:38:42.188 ERROR: In /opt/conda/conda-bld/hhsuite_1616660820288/work/src/hhfilter.cpp:177: main:

  • 15:38:42.188 ERROR: could not open file '/data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-3.a3m'

grep: /data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-3.id90cov75.a3m: No such file or directory grep: /data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-3.id90cov50.a3m: No such file or directory cp: cannot stat ‘/data/RosettaFold/RoseTTAFold/example/e2e-test/hhblits/t000_.1e-3.id90cov50.a3m’: No such file or directory

A-Talavera avatar Sep 01 '21 14:09 A-Talavera

The error came because the database was broken. I extracted it again and now the RoseTTAFold is running smoothly. Thanks.

A-Talavera avatar Sep 03 '21 12:09 A-Talavera

Hi! I'm having the same problem but it was not solved by extracting the database again. Any hint on what could be wrong and how I can solve it? I'm trying to install and run RoseTTAFold in a HPC environment.

Thanks in advance. With kind regards, Rui João Loureiro

RuiJoaoLoureiro2019 avatar Feb 06 '22 23:02 RuiJoaoLoureiro2019