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BenLangmead / bowtie2

A fast and sensitive gapped read aligner
GNU General Public License v3.0
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2.5.1 mingw binary release do not contain *.exe files. #429

Closed sis6789 closed 8 months ago

sis6789 commented 1 year ago

2.5.1 mingw binary release do not contain *.exe files.

sis6789 commented 1 year ago

D:\Downloads\bowtie2-2.5.1-mingw-x86_64 디렉터리

23-01-18 12:04

. 23-03-28 10:59 .. 23-01-18 11:26 1,307 AUTHORS 23-01-18 11:29 26,907 bowtie2 23-01-18 11:46 22,135,684 bowtie2-align-l 23-01-18 12:01 19,081,019 bowtie2-align-l-debug 23-01-18 11:39 22,175,673 bowtie2-align-s 23-01-18 11:57 19,074,355 bowtie2-align-s-debug 23-01-16 07:57 3,602 bowtie2-build 23-01-18 11:33 9,601,803 bowtie2-build-l 23-01-18 11:52 9,583,233 bowtie2-build-l-debug 23-01-18 11:31 9,608,107 bowtie2-build-s 23-01-18 11:51 9,577,475 bowtie2-build-s-debug 23-01-18 11:29 41 bowtie2-build.bat 23-01-16 07:57 2,762 bowtie2-inspect 23-01-18 11:49 8,344,907 bowtie2-inspect-l 23-01-18 12:03 6,071,189 bowtie2-inspect-l-debug 23-01-18 11:48 8,360,822 bowtie2-inspect-s 23-01-18 12:02 6,076,868 bowtie2-inspect-s-debug 23-01-18 11:29 43 bowtie2-inspect.bat 23-01-18 11:29 32 bowtie2.bat 23-01-18 11:29 5 BOWTIE2_VERSION 23-01-18 12:03 doc 23-01-18 12:03 example 23-01-16 07:57 35,147 LICENSE 23-01-18 11:29 87,462 MANUAL 23-01-16 07:57 116,698 MANUAL.markdown 23-01-18 11:29 32,850 NEWS 23-01-18 11:29 6,285 README.md 23-01-18 12:03 scripts 23-01-16 07:57 248 TUTORIAL 26개 파일 150,004,524 바이트 5개 디렉터리 1,759,212,859,392 바이트 남음

ch4rr0 commented 1 year ago

Hello, my apologies for this mistake. I will re-upload the Windows package later. In the meantime you can manually add the .exe extension to the binaries and that should work.

sis6789 commented 1 year ago

Thank you for your effort.나의 iPhone에서 보냄2023. 4. 4. 02:26, ch4rr0 @.***> 작성: Hello, my apologies for this mistake. I will re-upload the Windows package later. In the meantime you can manually add the .exe extension to the binaries and that should work.

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: @.***>

sis6789 commented 1 year ago

Would you check my problem? I have mailed this to @.***

My problem is as follow:

In blastn subject query, two 15bp long fasta file can used for subject query as follow command: blastn -subject short.fasta -query query.fasta -task blastn -perc_identity 95 -outfmt "10 qseqid ..."

I have tried following steps to use bowtie2 with same data. bowtie2-build-s -f short.fasta read12 bowtie2 -x read12 --local --no-hd --no-sq --no-unal --no-discordant -p 2 -k 1 -U query.fastq -S out.sam

The result is 100% un-aligned!

In another case with 110bp fasta, bowtie2 have done well.

Would you advise me, what is the preoblem? Does minimum length exist for index fasta?

If possible, I want to know the problem and solutions.

I can not find web pages abount minimum length of index fasta. And there is no length description in bowtie2 manual.

2023년 4월 4일 (화) 오전 2:26, ch4rr0 @.***>님이 작성:

Hello, my apologies for this mistake. I will re-upload the Windows package later. In the meantime you can manually add the .exe extension to the binaries and that should work.

— Reply to this email directly, view it on GitHub https://github.com/BenLangmead/bowtie2/issues/429#issuecomment-1494706537, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCWLZ2BYGANRDQLR4FAIIDW7MB37ANCNFSM6AAAAAAWJ4F6UM . You are receiving this because you authored the thread.Message ID: @.***>

ch4rr0 commented 1 year ago

Bowtie may be the answer, but we don't have any windows binaries currently available. I'll try to put one together sometime today if you're willing to wait.

ch4rr0 commented 1 year ago

Hello,

Bowtie works better for short reads. You can find a bowtie package for Windows here: http://0x0.st/HXHr.zip

The link is only valid for 24 hours, below is the file hash.

c8cbd8ab407e1cab954cac769f133fbd bowtie-1.3.1-mingw-aarch64.zip

Let me know if you have any questions.

sis6789 commented 1 year ago

Thanks, I'll check it out.

2023년 4월 6일 (목) 오전 12:51, ch4rr0 @.***>님이 작성:

Hello,

Bowtie works better for short reads. You can find a bowtie package for Windows here: http://0x0.st/HXHr.zip

The link is only valid for 24 hours, below is the file hash.

c8cbd8ab407e1cab954cac769f133fbd bowtie-1.3.1-mingw-aarch64.zip

Let me know if you have any questions.

— Reply to this email directly, view it on GitHub https://github.com/BenLangmead/bowtie2/issues/429#issuecomment-1497723007, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCWLZ32JTQL5LM2XDW2PH3W7WIH5ANCNFSM6AAAAAAWJ4F6UM . You are receiving this because you authored the thread.Message ID: @.***>