An update on ITSx and HMMER 3.1
An ITSx user yesterday made me aware of an information-problem (thanks Suzanne!) regarding the use of ITSx in combination with the HMMER 3.1 beta. I have not been entirely clear on why you might get the “Error: bad format, binary auxfiles, (…) binary auxfiles are in an outdated HMMER format (3/b); please hmmpress your HMM file again” error message when running ITSx with HMMER 3.1 installed. You might think that following the instructions for Metaxa might do the trick. As you will notice, however, it will not. Instead you will be presented with the following error message: “Error: Failed to open binary auxfiles”. This is because while Metaxa 1.1.2 will re-create the HMM-files if needed, ITSx does not. Instead, ITSx has the option "--reset T" which can be added to the command line to recreate the HMM-files for the current HMMER version installed (regardless of which 3.x version).
Thus, the solution for the “bad format, binary auxfiles” error is to simply add "--reset T" (without quotes) to the ITSx command line and run the software again. You only need to do this once, unless you update HMMER and/or get the same error message again for some other reason. The Metaxa-post has been updated to clarify this as well.
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Tried the –reset T. I get …
Preparing HMM database (should be quick)
Checking and handling input sequence data (should not take long)…
and then nothing, even after a very long time.
Hi Jerry,
You should run the software normally with an input file and output file, and then just add the “–reset T” option. Maybe somewhat counter-intuitive. You should only need to add the –reset option once.
Good luck!
Johan
Hi Johan,
I have an identical error with ITSx. The problem is not fixed even adding “-reset T”.
Please let me know when you have a solution.
Yongjie
[yongjie@n0000 ITS_sequences]$ ITSx -i sequences.fasta -o test -reset T
ITSx — Identifies ITS sequences and extracts the ITS region
by Johan Bengtsson-Palme et al., University of Gothenburg
Version: 1.0.9
—————————————————————–
Fri Aug 29 15:31:09 2014 : Preparing HMM database (should be quick)…
Fri Aug 29 15:31:09 2014 : Checking and handling input sequence data (should not take long)…
Fri Aug 29 15:31:10 2014 : Comparing sequences to HMM database (this may take a long while)…
Error: bad format, binary auxfiles, /global/home/groups/software/modules/ITSx/1.0.9/bin/ITSx_db/HMMs/A.hmm:
binary auxfiles are in an outdated HMMER format (3/b); please hmmpress your HMM file again
Fri Aug 29 15:31:10 2014 : Alveolates analysis of main strand finished.
Dear Yongjie,
I think I have spotted the error immediately (but the blog formatting might fool me). The reset option is supposed to have DOUBLE dashes before the word reset (but I think that gets interpreted as a long dash in the formatting of the comments). Please try that (as it is specified in the ITSx help, option -h). If it doesn’t work please get back to me!
Good luck!
Johan
Hi Johan,
I have still an identical error with ITSx. The problem is not fixed even adding double dashes “–reset T”.
prt-bordez:unidentified Lho$ ITSx -i unidentified.fasta -o test -t F –reset T
ITSx — Identifies ITS sequences and extracts the ITS region
by Johan Bengtsson-Palme et al., University of Gothenburg
Version: 1.0.10
—————————————————————–
Tue Nov 4 11:22:02 2014 : Preparing HMM database (should be quick)…
Tue Nov 4 11:22:02 2014 : Checking and handling input sequence data (should not take long)…
Tue Nov 4 11:22:02 2014 : Comparing sequences to HMM database (this may take a long while)…
Error: bad format, binary auxfiles, /usr/bin/ITSx_db/HMMs/F.hmm:
binary auxfiles are in an outdated HMMER format (3/b); please hmmpress your HMM file again
Tue Nov 4 11:22:02 2014 : Fungi analysis of main strand finished.
Error: bad format, binary auxfiles, /usr/bin/ITSx_db/HMMs/F.hmm:
binary auxfiles are in an outdated HMMER format (3/b); please hmmpress your HMM file again
Tue Nov 4 11:22:02 2014 : Fungi analysis of complementary strand finished.
Tue Nov 4 11:22:02 2014 : Analysing results of HMM-scan (this might take quite some time)…
Tue Nov 4 11:22:02 2014 : Extraction finished!
I have installed HMMER 3.1.b.1…
Please let me know when you have a solution
Hi Johan,
I found the solution. My problem is that i have remove the HMM file with extension as describe in the metataxa post.
Thank you
Dear Laurent,
I am a bit surprised to learn that you got ITSx to work using the solution suggested for Metaxa (that have not worked for me). I guess you then had to run ITSx with the “–reset T” option the first time immediately after deleting the hmm.xxx files, is that right?
Happy to hear that it is working now in any case!
Johan