refresh-bio / kmer-db

Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).
GNU General Public License v3.0
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Unexpected results #15

Closed zhangrengang closed 2 years ago

zhangrengang commented 2 years ago

Here is an example of input (the two sequences have the same 7 kmers):

>TR311
AACCCTAAACCCTAAACCCTAAACCCTAAACCCTA
>TR390
GTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGG

My commands and logs:

$ kmer-db build -multisample-fasta repclust.list repclust.kmer.db
Kmer-db version 1.9.2 (16.08.2021)
S. Deorowicz, A. Gudys, M. Dlugosz, M. Kokot, and A. Danek (c) 2018

Analysis started at Sat Apr  9 21:22:09 2022

Database building mode (from fasta genomes)
Processing samples...
2/2

EXECUTION TIMES
Total: 0.00152775
Kmer sorting/unique time: 1.3175e-05
Database update time:0.000334626
        Hashatable processing (parallel): 0.000160459
                Resize: 3.47906e-07
                Find'n'add: 2.34031e-07
        Sort time (parallel): 3.164e-06
        Pattern extension time (parallel): 6.1979e-05

STATISTICS
Number of samples: 2
Number of patterns: 2 (48 B)
Number of k-mers: 7
K-mer length: 18
Minhash fraction: 1
Workers count: 32

Serializing database...
Storing k-mer hashtables (raw)...
256/256 hashtables stored in 0.000214673 s
Storing patterns...
2/2 patterns stored in 1.648e-06 s

Releasing memory...OK (0.00145166 seconds)

Analysis finished at Sat Apr  9 21:22:09 2022

$ kmer-db all2all repclust.kmer.db repclust.a2a.csv
Kmer-db version 1.9.2 (16.08.2021)
S. Deorowicz, A. Gudys, M. Dlugosz, M. Kokot, and A. Danek (c) 2018

Analysis started at Sat Apr  9 21:22:30 2022

All versus all comparison
Loading k-mer database repclust.kmer.db...
Loading k-mer hashtables (raw)...
256/256 hashtables loaded in 0.000364983 s
Loading patterns...
2/2 patterns loaded in 3.83e-06 s
Calculating matrix of common k-mers...
Decomp   time: 2.9009e-05
Hist     time: 0.000847657
Sample2p time: 0.000129349
OK (0.0252323 seconds)
Storing matrix of common k-mers in repclust.a2a.csv...OK (5.1557e-05 seconds)
Releasing memory...OK (0.000969158 seconds)

Analysis finished at Sat Apr  9 21:22:30 2022

$ cat repclust.a2a.csv
kmer-length: 18 fraction: 1 ,db-samples ,TR311,TR390,
query-samples,total-kmers,7,7,
TR311, 7,
TR390, 7, 0,

As shown above, the two sequences share 0 kmers by kmer-db. It seems to be a bug.

zhangrengang commented 2 years ago

test1.multi.fa.gz test1.a2a.csv-test2.a2a.csv.diff.txt By the way, I also find another bug that kmer-db output different results with the same input. Here is my test:

$ kmer-db build -k 18 -multisample-fasta test1.list test1.kmer.db && kmer-db all2all test1.kmer.db test1.a2a.csv
$ kmer-db build -k 18 -multisample-fasta test2.list test2.kmer.db && kmer-db all2all test2.kmer.db test2.a2a.csv

$ cat test1.list
test1.multi.fa
$ cat test2.list
test2.multi.fa
$ diff test1.multi.fa test2.multi.fa    # no differences
$ diff test1.a2a.csv test2.a2a.csv | wc -l   # many differences
130

$ diff test1.a2a.csv test2.a2a.csv | head 
3735c3735
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The input and differences are attached.

agudys commented 2 years ago

Hello!

Thank you for reporting the issue. I'll take a look on it immediately!

Adam

agudys commented 2 years ago

Dear @zhangrengang,

I have just updated the sources. Both issues you had reported were multithreading-related. The first one exhibited itself for very small samples when the number of k-mers was smaller than the number of threads. As for the second issue - in some cases the rows of output CSV matrix were in the different order than in the input FASTA. If your analyzes relied on the sample names stored in the first column, your results should be correct. However, if you assumed the same ordering of FASTA and CSV, then you need te recompute the stuff.

Could you please confirm that both bugs have been removed in the latest code revision? If so, I would update the release. Thank you!

Regards, Adam

zhangrengang commented 2 years ago

Dear @agudys,

Great job. I‘d like to test it, but I have a compile error:

$ make
g++ -Wall -O3 -m64 -std=c++11 -fopenmp -pthread  -mavx  -I src/kmc_api -I "" -mavx2 -I src/kmc_api -I "" -c src/row_add_avx2.cpp -o src/row_add_avx2.o
src/row_add_avx2.cpp: In function ‘void row_add_avx2(uint32_t*, uint32_t*, uint32_t, uint32_t)’:
src/row_add_avx2.cpp:41:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j + 32 <= num_elems; j += 32)
                     ^
/tmp/cc2VSUBz.s: Assembler messages:
/tmp/cc2VSUBz.s:25: Error: no such instruction: `vpbroadcastd -20(%rbp),%ymm0'
/tmp/cc2VSUBz.s:153: Error: suffix or operands invalid for `vpaddd'
/tmp/cc2VSUBz.s:155: Error: suffix or operands invalid for `vpaddd'
/tmp/cc2VSUBz.s:237: Error: suffix or operands invalid for `vpaddd'
/tmp/cc2VSUBz.s:239: Error: suffix or operands invalid for `vpaddd'
make: *** [src/row_add_avx2.o] Error 1

Would you have any suggestion? Previously I installed kmer-db with conda.

zhangrengang commented 2 years ago

Hi @agudys, I have compiled successfully in another computer. Now the results are robust. Thanks a lot.

agudys commented 2 years ago

@zhangrengang Glad to hear that the results are ok. The errors you mentioned are probably due to lack of AVX2 extensions at the machine (it is strange though, as the makefile should verify this during compilation and use AVX1 variant instead - I'll take a look on that).

Thank you! Adam

zhangrengang commented 2 years ago

Dear @agudys,

Do you have a plan to update kmer-db in conda repo? Based on your excellent kmer-db, we are developing a tool (https://github.com/zhangrengang/REPcluster) to cluser repeat sequences that share kmers, such as (TTTAGGG)m vs (TTTAGGG)n. We are using conda to install kmer-db to make it user-friendly. So it is highly appreciated if you can update kmer-db in conda.

Thanks. Zhang

agudys commented 2 years ago

@zhangrengang

I'll prepare a new release and update bioconda to the latest version.

Adam

agudys commented 2 years ago

@zhangrengang The latest kmer-db revision has been uploaded to bioconda. Adam

zhangrengang commented 2 years ago

@agudys Thanks again.