Dureshahwarwaseem
commented
5 years ago Having trouble in accessing database uniclust30_2018_08on linux ..when i access the database uniclust30_2018_08 with following commands hhblits -cpu 4 -i data/query.seq -d databases/uniclust30_2018_08/uniclust30_2018_08 -oa3m query.a3m -n 2 So an error message prompt that could'nt open uniclust30_2018_08 ffdata file .. Kindly help how to solve this issue?
kaihami
:exclamation: Make to check out our User Guide. I am attempting to create a hh-suite database from a directory containing many .a3m files. So far I am currently using hh-suite version 3. When I pass the following command: python /storage/hpc/data/fqg7h/hh-suite/scripts/hhsuitedb.py --cpu 1 -o /storage/hpc/data/fqg7h/T0951_db/T0951_db --ia3m /storage/hpc/data/fqg7h/T0951_a3m/ --force
I get an error. The file /storage/hpc/data/fqg7h/hmmer-3.1b2-linux-intel-x86_64/src/T0951_db/T0951_db_hhm.ffindex is not found in the directory while the other files are empty.
Expected Behavior
Current Behavior
Steps to Reproduce (for bugs)
Please make sure to execute the reproduction steps.
HH-suite Output (for bugs)
ffindex_build: fread: Is a directory /storage/hpc/data/fqg7h/hh-suite/lib/ffindex/src/ffindex.c:231 ffindex_insert_filestream: : Is a directory ffindex_apply_mpi: Problem with data file. Is the file empty or is another process reading it?: Invalid argument /storage/hpc/data/fqg7h/hh-suite/lib/ffindex/src/ffindex_apply_mpi.c:367 ffindex_index_parse: /tmp/tmptqi8on/large.ffindex: Invalid argument The MPI_Finalize() function was called before MPI_INIT was invoked. This is disallowed by the MPI standard. *** Your MPI job will now abort. [lewis4-r710-login-node223:23941] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!
Primary job terminated normally, but 1 process returned a non-zero exit code. Per user-direction, the job has been aborted.
mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was:
Process name: [[62006,1],0] Exit code: 1
Traceback (most recent call last): File "/storage/hpc/data/fqg7h/hh-suite/scripts/hhsuitedb.py", line 482, in
main()
File "/storage/hpc/data/fqg7h/hh-suite/scripts/hhsuitedb.py", line 478, in main
check_database(options.output_basename, options.nr_cores, options.force_mode)
File "/storage/hpc/data/fqg7h/hh-suite/scripts/hhsuitedb.py", line 376, in check_database
calculate_hhm(threads, output_basename+"_a3m", output_basename+"_hhm")
File "/storage/hpc/data/fqg7h/hh-suite/scripts/hhsuitedb.py", line 106, in calculate_hhm
check_call(" ".join(["mpirun", "-np", threads, "ffindex_apply_mpi", a3m_base_path+".ffdata", large_a3m_index, "-d", hhm_base_path+".ffdata", "-i", hhm_base_path+".ffindex", "--", "hhmake", "-v", str(0), "-i", "stdin", "-o" ,"stdout"]), shell=True)
File "/usr/lib64/python2.7/subprocess.py", line 542, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'mpirun -np 1 ffindex_apply_mpi /storage/hpc/data/fqg7h/T0951_db/T0951_db_a3m.ffdata /tmp/tmptqi8on/large.ffindex -d /storage/hpc/data/fqg7h/T0951_db/T0951_db_hhm.ffdata -i /storage/hpc/data/fqg7h/T0951_db/T0951_db_hhm.ffindex -- hhmake -v 0 -i stdin -o stdout' returned non-zero exit status 1
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Context
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Your Environment
Linux -Centos cluster Include as many relevant details about the environment you experienced the issue in.