ERROR: Could not read index file...

[nkuhuangyan]

Hi, 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)

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.

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.

[martin-steinegger]

It seems that the .ffindex files are empty or corrupted. Could you check the file sizes of file/home/yanhuang/Desktop/hhsuite/database/uniclust30_2018_08_hhsuite/uniclust30_2018_08_*.ffindex?

[mayuefine]

Same problem occurred to me, the file size of these files as followed :

-rwxr-xr-x 1 mayue root 125G Jan 22 01:05 UniRef30_2020_01_a3m.ffdata -rwxr-xr-x 1 mayue root 613M Jan 22 01:05 UniRef30_2020_01_a3m.ffindex -rwxr-xr-x 1 mayue root 5.5G Jan 22 00:39 UniRef30_2020_01_cs219.ffdata -rwxr-xr-x 1 mayue root 554M Jan 22 00:39 UniRef30_2020_01_cs219.ffindex -rwxr-xr-x 1 mayue root 32G Jan 22 01:41 UniRef30_2020_01_hhm.ffdata -rwxr-xr-x 1 mayue root 18M Jan 22 01:41 UniRef30_2020_01_hhm.ffindex -rwxr-xr-x 1 mayue root 379 Jan 22 01:46 UniRef30_2020_01.md5sums

and I was check the md5sum of these files, seems all good 

UniRef30_2020_01_hhm.ffindex: OK UniRef30_2020_01_cs219.ffindex: OK UniRef30_2020_01_a3m.ffindex: OK UniRef30_2020_01_cs219.ffdata: OK UniRef30_2020_01_hhm.ffdata: OK UniRef30_2020_01_a3m.ffdata: OK

and my  command  is: "hhblits -i t.fa -oa3m t.a3m -d /data/mayue/str/uni/UniRef30_2020_01 -cpu 24", and it give to me this:

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

• 22:43:55.836 WARNING: In /build/hhsuite-rhvmkl/hhsuite-3.0~beta2+dfsg/src/hhdatabase.cpp:50: FFindexDatabase:

• 22:43:55.836 WARNING: Could not read index file/data/mayue/str/uni/UniRef30_2020_01_cs219.ffindex. Is the file empty or corrupted?

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

• 22:43:58.125 WARNING: In /build/hhsuite-rhvmkl/hhsuite-3.0~beta2+dfsg/src/hhdatabase.cpp:50: FFindexDatabase:

• 22:43:58.125 WARNING: Could not read index file/data/mayue/str/uni/UniRef30_2020_01_a3m.ffindex. Is the file empty or corrupted?

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

• 22:43:58.192 WARNING: In /build/hhsuite-rhvmkl/hhsuite-3.0~beta2+dfsg/src/hhdatabase.cpp:50: FFindexDatabase:

• 22:43:58.192 WARNING: Could not read index file/data/mayue/str/uni/UniRef30_2020_01_hhm.ffindex. Is the file empty or corrupted?

Segmentation fault (core dumped)

I think this problem happens because I was used older version of hh-suite(3.0). I have been solved my problem by re-install this software with version 3.1