Closed zhangrengang closed 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.
Hello!
Thank you for reporting the issue. I'll take a look on it immediately!
Adam
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
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
.
Hi @agudys, I have compiled successfully in another computer. Now the results are robust. Thanks a lot.
@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
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
@zhangrengang
I'll prepare a new release and update bioconda to the latest version.
Adam
@zhangrengang The latest kmer-db revision has been uploaded to bioconda. Adam
@agudys Thanks again.
Here is an example of input (the two sequences have the same 7 kmers):
My commands and logs:
As shown above, the two sequences share 0 kmers by
kmer-db
. It seems to be a bug.