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ERROR: Could not read index file...
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.
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?
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