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Error when run NCBIminer #1

Open lychen83 opened 5 years ago

lychen83 commented 5 years ago

Hello, I am using the NCBIminer. I used a configure file as following: _feature type: gene CDS feature name: rbcL ribulose‐1,5‐bisphosphate carboxylase/oxygenase large subunit initial query:

gi|194400737|gb|EU713435.1| ATGTCACACAAACAGGACTAAGCAAATGTGGATTAAGGCTGGT GTTAAGATATAAATTAACTTATTATACTCCGATATGAAACAAGG TAGGTATTTGCAGCCTTTCGATAACTCCTCAACCCGATTCCCC CGGAAGAA taxon list: Campanulaceae\Codonopsis Campanulaceae\Campanumoea Output prefix: Demo1_

I run the NCBIminner on my wirndows 10. I got errors as: _Index exceeds matrix dimensions. Error in C:\Users\CHENLI~1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blaststat.m (line 132) Error in C:\Users\CHENLI~1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blaststat.m (line 62) Error in C:\Users\CHENLI~1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blast_new.m (line 36) Error in C:\Users\CHENLI~1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminerv2.0\blastref.m (line 23) Error in C:\Users\CHENLI~1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer\NCBIminer.m (line 54) Error in NCBIminner.txt (line 1)

Could you kindly help me resolve this problem?

Thank you so much

Best

Lingyun

greengirl commented 5 years ago

Dear Linyun,

NCBImier was already updated to ver3.0 and will be upload to github tomorrow. I hope new version could help your problem.

Kind regards

Xiaoting

xiaotingxu@pku.edu.cn

From: lychen83 Date: 2019-03-02 04:04 To: greengirl/NCBIminer CC: Subscribed Subject: [greengirl/NCBIminer] Error when run NCBIminer (#1) Hello, I am using the NCBIminer. I used a configure file as following: feature type: gene CDS feature name: rbcL ribulose‐1,5‐bisphosphate carboxylase/oxygenase large subunit initial query: gi|194400737|gb|EU713435.1| ATGTCACACAAACAGGACTAAGCAAATGTGGATTAAGGCTGGT GTTAAGATATAAATTAACTTATTATACTCCGATATGAAACAAGG TAGGTATTTGCAGCCTTTCGATAACTCCTCAACCCGATTCCCC CGGAAGAA taxon list: Campanulaceae\Codonopsis Campanulaceae\Campanumoea Output prefix: Demo1 I run the NCBIminner on my wirndows 10. I got errors as: Index exceeds matrix dimensions. Error in C:\Users\CHENLI1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blaststat.m (line 132) Error in C:\Users\CHENLI1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blaststat.m (line 62) Error in C:\Users\CHENLI1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blast_new.m (line 36) Error in C:\Users\CHENLI1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blastref.m (line 23) Error in C:\Users\CHENLI~1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer\NCBIminer.m (line 54) Error in NCBIminner.txt (line 1) Could you kindly help me resolve this problem? Thank you so much Best Lingyun — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

greengirl commented 5 years ago

Dear Linyun,

Here attached the NCBIminer V3.0. It will upload to GitHub soon.

Xioating

发送自 Windows 10 版邮件应用

发件人: lychen83 发送时间: 2019年3月2日 4:05 收件人: greengirl/NCBIminer 抄送: Subscribed 主题: [greengirl/NCBIminer] Error when run NCBIminer (#1)

Hello, I am using the NCBIminer. I used a configure file as following: feature type: gene CDS feature name: rbcL ribulose‐1,5‐bisphosphate carboxylase/oxygenase large subunit initial query: gi|194400737|gb|EU713435.1| ATGTCACACAAACAGGACTAAGCAAATGTGGATTAAGGCTGGT GTTAAGATATAAATTAACTTATTATACTCCGATATGAAACAAGG TAGGTATTTGCAGCCTTTCGATAACTCCTCAACCCGATTCCCC CGGAAGAA taxon list: Campanulaceae\Codonopsis Campanulaceae\Campanumoea Output prefix: Demo1 I run the NCBIminner on my wirndows 10. I got errors as: Index exceeds matrix dimensions. Error in C:\Users\CHENLI1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blaststat.m (line 132) Error in C:\Users\CHENLI1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blaststat.m (line 62) Error in C:\Users\CHENLI1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blast_new.m (line 36) Error in C:\Users\CHENLI1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blastref.m (line 23) Error in C:\Users\CHENLI~1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer\NCBIminer.m (line 54) Error in NCBIminner.txt (line 1) Could you kindly help me resolve this problem? Thank you so much Best Lingyun — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

lychen83 commented 5 years ago

Hi Xiaoting,

Sorry, I did not see the attached NCBIminner in the last email. Could you kindly check it?

Thank you so much.

Best, Lingyun

lychen83@qq.com

From: greengirl Date: 2019-03-02 18:59 To: greengirl/NCBIminer CC: lychen83; Author Subject: Re: [greengirl/NCBIminer] Error when run NCBIminer (#1) Dear Linyun,

Here attached the NCBIminer V3.0. It will upload to GitHub soon.

Xioating

发送自 Windows 10 版邮件应用

发件人: lychen83 发送时间: 2019年3月2日 4:05 收件人: greengirl/NCBIminer 抄送: Subscribed 主题: [greengirl/NCBIminer] Error when run NCBIminer (#1)

Hello, I am using the NCBIminer. I used a configure file as following: feature type: gene CDS feature name: rbcL ribulose‐1,5‐bisphosphate carboxylase/oxygenase large subunit initial query: gi|194400737|gb|EU713435.1| ATGTCACACAAACAGGACTAAGCAAATGTGGATTAAGGCTGGT GTTAAGATATAAATTAACTTATTATACTCCGATATGAAACAAGG TAGGTATTTGCAGCCTTTCGATAACTCCTCAACCCGATTCCCC CGGAAGAA taxon list: Campanulaceae\Codonopsis Campanulaceae\Campanumoea Output prefix: Demo1 I run the NCBIminner on my wirndows 10. I got errors as: Index exceeds matrix dimensions. Error in C:\Users\CHENLI1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blaststat.m (line 132) Error in C:\Users\CHENLI1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blaststat.m (line 62) Error in C:\Users\CHENLI1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blast_new.m (line 36) Error in C:\Users\CHENLI1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blastref.m (line 23) Error in C:\Users\CHENLI~1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer\NCBIminer.m (line 54) Error in NCBIminner.txt (line 1) Could you kindly help me resolve this problem? Thank you so much Best Lingyun — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

greengirl commented 5 years ago

How about now?

发送自 Windows 10 版邮件应用

发件人: lychen83 发送时间: 2019年3月2日 4:05 收件人: greengirl/NCBIminer 抄送: Subscribed 主题: [greengirl/NCBIminer] Error when run NCBIminer (#1)

Hello, I am using the NCBIminer. I used a configure file as following: feature type: gene CDS feature name: rbcL ribulose‐1,5‐bisphosphate carboxylase/oxygenase large subunit initial query: gi|194400737|gb|EU713435.1| ATGTCACACAAACAGGACTAAGCAAATGTGGATTAAGGCTGGT GTTAAGATATAAATTAACTTATTATACTCCGATATGAAACAAGG TAGGTATTTGCAGCCTTTCGATAACTCCTCAACCCGATTCCCC CGGAAGAA taxon list: Campanulaceae\Codonopsis Campanulaceae\Campanumoea Output prefix: Demo1 I run the NCBIminner on my wirndows 10. I got errors as: Index exceeds matrix dimensions. Error in C:\Users\CHENLI1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blaststat.m (line 132) Error in C:\Users\CHENLI1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blaststat.m (line 62) Error in C:\Users\CHENLI1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blast_new.m (line 36) Error in C:\Users\CHENLI1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blastref.m (line 23) Error in C:\Users\CHENLI~1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer\NCBIminer.m (line 54) Error in NCBIminner.txt (line 1) Could you kindly help me resolve this problem? Thank you so much Best Lingyun — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

lychen83 commented 5 years ago

Sorry, I did not see the v3.0 in the github, not in my email either. The v2.0 still not working on my PC. I have problems in installing the matlab on my linux workstation Thank you

Lingyun

lychen83@qq.com

From: greengirl Date: 2019-03-03 07:07 To: greengirl/NCBIminer CC: lychen83; Author Subject: Re: [greengirl/NCBIminer] Error when run NCBIminer (#1) How about now?

发送自 Windows 10 版邮件应用

发件人: lychen83 发送时间: 2019年3月2日 4:05 收件人: greengirl/NCBIminer 抄送: Subscribed 主题: [greengirl/NCBIminer] Error when run NCBIminer (#1)

Hello, I am using the NCBIminer. I used a configure file as following: feature type: gene CDS feature name: rbcL ribulose‐1,5‐bisphosphate carboxylase/oxygenase large subunit initial query: gi|194400737|gb|EU713435.1| ATGTCACACAAACAGGACTAAGCAAATGTGGATTAAGGCTGGT GTTAAGATATAAATTAACTTATTATACTCCGATATGAAACAAGG TAGGTATTTGCAGCCTTTCGATAACTCCTCAACCCGATTCCCC CGGAAGAA taxon list: Campanulaceae\Codonopsis Campanulaceae\Campanumoea Output prefix: Demo1 I run the NCBIminner on my wirndows 10. I got errors as: Index exceeds matrix dimensions. Error in C:\Users\CHENLI1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blaststat.m (line 132) Error in C:\Users\CHENLI1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blaststat.m (line 62) Error in C:\Users\CHENLI1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blast_new.m (line 36) Error in C:\Users\CHENLI1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blastref.m (line 23) Error in C:\Users\CHENLI~1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer\NCBIminer.m (line 54) Error in NCBIminner.txt (line 1) Could you kindly help me resolve this problem? Thank you so much Best Lingyun — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

greengirl commented 5 years ago

Did you see a zip file named as NCBIminerV3.0_for_redistribution.zip?

You can unzip it and open the folder "for_redistribution" then you will find an excutable appliation "MyAppInstaller_web.exe". If you run MyAppInstaller_web.exe the MATLAB runtime environment will be downloaded and installed as well as the NCBIminer.

Xiaoting

xiaotingxu@pku.edu.cn

From: xiaotingxu@pku.edu.cn Date: 2019-03-02 06:45 To: greengirl/NCBIminer Subject: Re: [greengirl/NCBIminer] Error when run NCBIminer (#1) Dear Linyun,

NCBImier was already updated to ver3.0 and will be upload to github tomorrow. I hope new version could help your problem.

Kind regards

Xiaoting

xiaotingxu@pku.edu.cn

From: lychen83 Date: 2019-03-02 04:04 To: greengirl/NCBIminer CC: Subscribed Subject: [greengirl/NCBIminer] Error when run NCBIminer (#1) Hello, I am using the NCBIminer. I used a configure file as following: feature type: gene CDS feature name: rbcL ribulose‐1,5‐bisphosphate carboxylase/oxygenase large subunit initial query: gi|194400737|gb|EU713435.1| ATGTCACACAAACAGGACTAAGCAAATGTGGATTAAGGCTGGT GTTAAGATATAAATTAACTTATTATACTCCGATATGAAACAAGG TAGGTATTTGCAGCCTTTCGATAACTCCTCAACCCGATTCCCC CGGAAGAA taxon list: Campanulaceae\Codonopsis Campanulaceae\Campanumoea Output prefix: Demo1 I run the NCBIminner on my wirndows 10. I got errors as: Index exceeds matrix dimensions. Error in C:\Users\CHENLI1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blaststat.m (line 132) Error in C:\Users\CHENLI1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blaststat.m (line 62) Error in C:\Users\CHENLI1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blast_new.m (line 36) Error in C:\Users\CHENLI1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blastref.m (line 23) Error in C:\Users\CHENLI~1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer\NCBIminer.m (line 54) Error in NCBIminner.txt (line 1) Could you kindly help me resolve this problem? Thank you so much Best Lingyun — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

greengirl commented 5 years ago

I send you a windows version. It should be OK. BTW do you have QQ or wechat? If you can add me qq:93059554. I can send you the software by qq.

Xiaoting

xiaotingxu@pku.edu.cn

From: lychen83 Date: 2019-03-03 21:21 To: greengirl/NCBIminer CC: greengirl; Comment Subject: Re: [greengirl/NCBIminer] Error when run NCBIminer (#1)

Sorry, I did not see the v3.0 in the github, not in my email either. The v2.0 still not working on my PC. I have problems in installing the matlab on my linux workstation Thank you

Lingyun

lychen83@qq.com

From: greengirl Date: 2019-03-03 07:07 To: greengirl/NCBIminer CC: lychen83; Author Subject: Re: [greengirl/NCBIminer] Error when run NCBIminer (#1) How about now?

发送自 Windows 10 版邮件应用

发件人: lychen83 发送时间: 2019年3月2日 4:05 收件人: greengirl/NCBIminer 抄送: Subscribed 主题: [greengirl/NCBIminer] Error when run NCBIminer (#1)

Hello, I am using the NCBIminer. I used a configure file as following: feature type: gene CDS feature name: rbcL ribulose‐1,5‐bisphosphate carboxylase/oxygenase large subunit initial query: gi|194400737|gb|EU713435.1| ATGTCACACAAACAGGACTAAGCAAATGTGGATTAAGGCTGGT GTTAAGATATAAATTAACTTATTATACTCCGATATGAAACAAGG TAGGTATTTGCAGCCTTTCGATAACTCCTCAACCCGATTCCCC CGGAAGAA taxon list: Campanulaceae\Codonopsis Campanulaceae\Campanumoea Output prefix: Demo1 I run the NCBIminner on my wirndows 10. I got errors as: Index exceeds matrix dimensions. Error in C:\Users\CHENLI1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blaststat.m (line 132) Error in C:\Users\CHENLI1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blaststat.m (line 62) Error in C:\Users\CHENLI1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blast_new.m (line 36) Error in C:\Users\CHENLI1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer_v2.0\blastref.m (line 23) Error in C:\Users\CHENLI~1\AppData\Local\Temp\Chen Lingyun\mcrCache8.4\NCBImi0\NCBIminer\NCBIminer.m (line 54) Error in NCBIminner.txt (line 1) Could you kindly help me resolve this problem? Thank you so much Best Lingyun — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread. — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.