Hi all,

I tried to run hhblits but it gives errors as: Could not read index file...

The command I run is:

hhblits -i input.fa -d /home/yanhuang/Desktop/hhsuite/database/uniclust30_2018_08_hhsuite/uniclust30_2018_08 -o output.hhr -norealign -n 3 -cov 80 -e 0.001

And the output is:

ffindex.c:452 ffindex_index_parse: mlock: Cannot allocate memory

    11:23:20.049 WARNING: In /build/hhsuite-rhvmkl/hhsuite-3.0~beta2+dfsg/src/hhdatabase.cpp:50: FFindexDatabase:

    11:23:20.049 WARNING: Could not read index file/home/yanhuang/Desktop/hhsuite/database/uniclust30_2018_08_hhsuite/uniclust30_2018_08_cs219.ffindex. Is the file empty or corrupted?

ffindex.c:452 ffindex_index_parse: mlock: Cannot allocate memory

    11:23:21.125 WARNING: In /build/hhsuite-rhvmkl/hhsuite-3.0~beta2+dfsg/src/hhdatabase.cpp:50: FFindexDatabase:

    11:23:21.125 WARNING: Could not read index file/home/yanhuang/Desktop/hhsuite/database/uniclust30_2018_08_hhsuite/uniclust30_2018_08_a3m.ffindex. Is the file empty or corrupted?

ffindex.c:452 ffindex_index_parse: mlock: Cannot allocate memory

    11:23:21.148 WARNING: In /build/hhsuite-rhvmkl/hhsuite-3.0~beta2+dfsg/src/hhdatabase.cpp:50: FFindexDatabase:

    11:23:21.148 WARNING: Could not read index file/home/yanhuang/Desktop/hhsuite/database/uniclust30_2018_08_hhsuite/uniclust30_2018_08_hhm.ffindex. Is the file empty or corrupted?

Segmentation fault (core dumped)

And when I tried uniclust30_2018_08 instead of uniclust30_2018_08_hhsuite, similar problem occurs:

ffindex.c:452 ffindex_index_parse: mlock: Cannot allocate memory
- 12:24:37.459 WARNING: In /build/hhsuite-rhvmkl/hhsuite-3.0~beta2+dfsg/src/hhdatabase.cpp:50: FFindexDatabase:

- 12:24:37.459 WARNING:     Could not read index file/home/yanhuang/Desktop/hhsuite/database/uniclust30_2018_08/uniclust30_2018_08_cs219.ffindex. Is the file empty or corrupted?

- 12:24:37.459 ERROR: In /build/hhsuite-rhvmkl/hhsuite-3.0~beta2+dfsg/src/hhdatabase.cpp:40: FFindexDatabase:

- 12:24:37.459 ERROR:   could not open file '/home/yanhuang/Desktop/hhsuite/database/uniclust30_2018_08/uniclust30_2018_08_a3m.ffindex'

The problem could be reproduced on multiple computers, from my desktop computer to my laptop. But one thing I noticed is that when running the same command on other database, everything will be OK.

For example:

hhblits -i input.fa -d /home/yanhuang/Desktop/hhsuite/database/pfamA_32.0/pfam -o output.hhr -norealign -n 3 -cov 80 -e 0.001

gives me everything I need. uniclust30_2018_08 and uniclust30_2018_08_hhsuite are the only ones that would give this problem.

For your information, I am using hhsuite version 3.0.0 (15-03-2015) on Ubuntu 18.04 and my RAM is 32GB. And I have installed it by git clone. Memory overcommit is enabled.

Really appreciate it for your help, thank you.



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