ffindex_order issue and observation about hh-suite HOT 10 CLOSED

Could you post the first few lines of each file:

Something like:

head -n 10 test_{a3m,hhm}{,_new}.ff{data,index} test_cs219.ffindex sorting*

Also please update to the latest git version (including git submodules).

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thanks much for the quick reply. here are the file heads:

heads.txt

by the way, i was using downloaded a3m and hhm files from SCOPe2.06 as a test case.

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update: i just learned today that my "work-around" described at the beginning no longer work. in short, i can use ffindex_order to optimize the a3m.{ffdata,ffindex}, but NOT the hhm.{ffdata,ffindex}. here is the typical error message:

~/triad/tools/hhsuite/hhsuite-latest/bin/ffindex_order sorting_hhm test_hhm.ffdata test_hhm.ffindex test_hhm_new.ffdata test_hhm_new.ffindex
ffindex_order: Problem with data file. Is the file empty or is another process reading it?: Invalid argument
ffindex_index_parse failed: Invalid argument

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by the way, i was using a git clone from today (6jul2017). still seeing the same issue.

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For your new issue, it sounds like you have overwritten the test_hhm.ffindex with something else.

Could you check that the databases are still complete and then either upload the *_{a3m,hhm,cs219}.ff{data,index} files somewhere and link them here, or if the data is very sensitive, please send me them to me directly at milot at mirdita dot de

Best regards,
Milot

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hi milot,
i am attaching a small directory called test. it has 3 sets of a3m and hhm files. the file prefixes are the pdb IDs. i was using them to test the making and optimizing of the hhsuite v3 databases. the log file shows the error. the file "sorting_a3m" is the "sorting.dat" in the user guide. thanks very much for your help.
fred
test.tar.gz

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I think you changed the output name of hhmake. Its building files like '1JSF.blits.hhm' now.
You can fix your workaround by doing something like this:

awk '{ gsub(/\.a3m/, ".blits.hhm"); print $0 }' sorting_a3m > sorting_hhm

However you should do this as the very first step after you build the a3m ffindex database, remove the file extensions from the index:

awk '{ gsub(/\.a3m/, ""); print $0 }' test_a3m.ffindex > test_a3m.ffindex_tmp && mv test_a3m.ffindex_tmp test_a3m.ffindex

I still have no idea what the root cause of your issue is, but please try to rebuild the hhm and cs219 ffindex database with this renamed test_a3m.ffindex. This should in general yield less issues (since all files will share the same key).

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hi milot,
yes that was it. it was my bad. i forgot the name prefixes matter. however, i still need to use 2 separate "sorting.dat" files - one for a3m and one for hhm. in the user guide, it seemed like the same "sorting.dat" can be used for both cases. how is that?
fred

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I am not where your .hhm endings come from in your index files. ffindex_apply(_mpi) should continue to use the initial key (XXXX.a3m). So all the files SHOULD have the same keys, then sorting.dat should also work for all files.

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got it. perhaps a line in the user guide warning users about alternative names may be handy at times. thanks a whole bunch again. warm regards, fred

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