hh-suite
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Published
20 hours ago •
soedinglab
soedinglab
test result variance on a big endian (s390x) system
Expected Behavior
tests pass
Current Behavior
- 14:56:11.112 INFO: Search results will be written to query.hhr
- 14:56:11.167 INFO: query.a3m is in A2M, A3M or FASTA format
- 14:56:11.588 INFO: Alternative alignment: 0
- 14:56:11.643 INFO: 1 alignments done
- 14:56:11.655 INFO: Realigning 1 HMM-HMM alignments using Maximum Accuracy algorithm
Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3
Match_columns 431
No_of_seqs 49 out of 118
Neff 4.29223
Searched_HMMs 1
Date Wed Sep 2 14:56:11 2020
Command hhalign -i query.a3m -t query.a3m
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 9E-168 9E-168 1246.9 0.0 431 1-431 1-431 (431)
query.a3m 0 32127 464 0
query.a3m 0 32666 2 0
query.a3m 0 32666 86 0
Reading context library for pseudocounts from internal ...
Reading abstract state alphabet from internal ...
Processing entry: query.a3m
Adding cs-pseudocounts (admix=0.30) ...
- 14:56:13.088 INFO: Search results will be written to query.hhr
- 14:56:13.089 INFO: Searching 1 column state sequences.
- 14:56:13.142 INFO: query.a3m is in A2M, A3M or FASTA format
- 14:56:13.166 INFO: Iteration 1
- 14:56:13.522 INFO: Prefiltering database
- 14:56:13.890 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1
- 14:56:13.894 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1
- 14:56:13.894 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1
- 14:56:13.894 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment
- 14:56:13.924 INFO: Alternative alignment: 0
- 14:56:13.979 INFO: 1 alignments done
- 14:56:13.979 INFO: Alternative alignment: 1
- 14:56:14.036 INFO: 1 alignments done
- 14:56:14.036 INFO: Alternative alignment: 2
- 14:56:14.090 INFO: 1 alignments done
- 14:56:14.090 INFO: Alternative alignment: 3
- 14:56:14.146 INFO: 1 alignments done
- 14:56:15.359 INFO: Premerge done
- 14:56:15.359 INFO: Realigning 4 HMM-HMM alignments using Maximum Accuracy algorithm
- 14:56:15.412 INFO: 7 sequences belonging to 7 database HMMs found with an E-value < 0.001
Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3
Match_columns 431
No_of_seqs 59 out of 236
Neff 4.27431
Searched_HMMs 1
Date Wed Sep 2 14:56:15 2020
Command hhblits -i query.a3m -d single -blasttab blits_app_res -n 1
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 1E-167 5E-169 1249.5 0.0 12 330-341 336-347 (431)
2 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 1E-167 5E-169 1249.5 0.0 431 1-431 1-431 (431)
3 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 1E-167 5E-169 1249.5 0.0 6 293-298 311-316 (431)
4 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 1E-167 5E-169 1249.5 0.0 13 336-348 330-342 (431)
- 14:56:15.432 INFO: Searching 1 column state sequences.
- 14:56:15.478 INFO: Thread 0 query.a3m
- 14:56:15.485 INFO: query.a3m is in A2M, A3M or FASTA format
- 14:56:15.510 INFO: Iteration 1
- 14:56:16.235 INFO: Prefiltering database
- 14:56:16.979 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1
- 14:56:16.984 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1
- 14:56:16.984 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1
- 14:56:16.984 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment
- 14:56:16.997 INFO: Alternative alignment: 0
- 14:56:17.050 INFO: 1 alignments done
- 14:56:17.050 INFO: Alternative alignment: 1
- 14:56:17.107 INFO: 1 alignments done
- 14:56:17.107 INFO: Alternative alignment: 2
- 14:56:17.164 INFO: 1 alignments done
- 14:56:17.164 INFO: Alternative alignment: 3
- 14:56:17.221 INFO: 1 alignments done
- 14:56:19.608 INFO: Premerge done
- 14:56:19.608 INFO: Realigning 4 HMM-HMM alignments using Maximum Accuracy algorithm
- 14:56:19.663 INFO: 7 sequences belonging to 7 database HMMs found with an E-value < 0.001
- 14:56:19.684 INFO: Search results will be written to query.hhr
- 14:56:19.742 INFO: query.a3m is in A2M, A3M or FASTA format
- 14:56:19.769 INFO: Searching 1 database HHMs without prefiltering
- 14:56:19.769 INFO: Iteration 1
- 14:56:20.167 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment
- 14:56:20.202 INFO: Alternative alignment: 0
- 14:56:20.265 INFO: 1 alignments done
- 14:56:20.265 INFO: Alternative alignment: 1
- 14:56:20.327 INFO: 1 alignments done
- 14:56:20.327 INFO: Alternative alignment: 2
- 14:56:20.389 INFO: 1 alignments done
- 14:56:20.390 INFO: Alternative alignment: 3
- 14:56:20.451 INFO: 1 alignments done
- 14:56:21.832 INFO: Premerge done
- 14:56:21.832 INFO: Realigning 4 HMM-HMM alignments using Maximum Accuracy algorithm
- 14:56:21.891 INFO: 7 sequences belonging to 7 database HMMs found with an E-value < 0.001
Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3
Match_columns 431
No_of_seqs 49 out of 236
Neff 4.29341
Searched_HMMs 1
Date Wed Sep 2 14:56:21 2020
Command hhsearch -i query.a3m -d single -blasttab search_app_res
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 5E-169 5E-169 1249.5 0.0 11 331-341 337-347 (431)
2 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 5E-169 5E-169 1249.5 0.0 431 1-431 1-431 (431)
3 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 5E-169 5E-169 1249.5 0.0 8 46-53 49-56 (431)
4 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 5E-169 5E-169 1249.5 0.0 13 336-348 330-342 (431)
- 14:56:21.961 INFO: Thread 0 query.a3m
- 14:56:21.969 INFO: query.a3m is in A2M, A3M or FASTA format
- 14:56:21.993 INFO: Searching 1 database HHMs without prefiltering
- 14:56:21.993 INFO: Iteration 1
- 14:56:22.720 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment
- 14:56:22.735 INFO: Alternative alignment: 0
- 14:56:22.783 INFO: 1 alignments done
- 14:56:22.783 INFO: Alternative alignment: 1
- 14:56:22.836 INFO: 1 alignments done
- 14:56:22.836 INFO: Alternative alignment: 2
- 14:56:22.889 INFO: 1 alignments done
- 14:56:22.889 INFO: Alternative alignment: 3
- 14:56:22.943 INFO: 1 alignments done
- 14:56:25.181 INFO: Premerge done
- 14:56:25.181 INFO: Realigning 4 HMM-HMM alignments using Maximum Accuracy algorithm
- 14:56:25.233 INFO: 7 sequences belonging to 7 database HMMs found with an E-value < 0.001
1c1
< sp|Q5VUD6|FA69B_HUMAN query 0.007 431 9 0 330 341 336 347 864.0
---
> sp|Q5VUD6|FA69B_HUMAN query 0.007 431 8 0 331 341 337 347 864.0
3c3
< sp|Q5VUD6|FA69B_HUMAN query 0.005 431 4 0 293 298 311 316 864.0
---
> sp|Q5VUD6|FA69B_HUMAN query 0.007 431 5 0 46 53 49 56 864.0
Steps to Reproduce (for bugs)
Build on a s390x system. If need be I can construct a Dockerfile that cross-builds and uses qemu for execution
HH-suite Output (for bugs)
https://buildd.debian.org/status/fetch.php?pkg=hhsuite&arch=s390x&ver=3.3.0%2Bds-4&stamp=1599058588&raw=0
Context
Providing context helps us come up with a solution and improve our documentation for the future.
Your Environment
Include as many relevant details about the environment you experienced the issue in.
- Version/Git commit used: https://github.com/soedinglab/hh-suite/releases/tag/v3.3.0
- Server specifications (especially CPU support for AVX2/SSE and amount of system memory): https://db.debian.org/machines.cgi?host=zandonai IBM System z15 , 8GiB memory
- Operating system and version: Debian's development distribution a.k.a "unstable"
Sorry, I think this issue will stay open for a while. I don't think we can really afford the time to investigate an endianness issue in a project we don't have any funding for. Thanks for finding and documenting the problem though!
