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mapleforest / HaploMerger2

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Issue with batch.B jobs #5

Open m-gemmell opened 7 years ago

m-gemmell commented 7 years ago

Dear developers

Hello I have been trying to run Haplomerger2 with an assembly created by canu form PacBio data. I have tried to run batchB1 to bacthB5 However I have not been able to get it to work with it creating many empty files. I have tried looking at the log files but I can't figure out what the issue is. One thing I noticed is that although I have run batchB1 there are not .seq/.fa files or x.seq/fa files but there are the nib files.

I would appreciate any help and if you would like any more info you need to help me please do not hesitate to ask.

Thanks for reading Matthew Gemmell

mapleforest commented 7 years ago

Dear Gemmell，

Based on the infomation you provided, I cannot troubleshoot the problem.

After .nib are created, .fa could be deleted.

For starter, I recommend you at least test HM2 on you computer with the provided Example 1 and 2.

Run the examples step by step to check the output and to get fimilar with the results.

In these two examples, each step only take seconds to finish.

Also you may check if

  1. HM2 can access to lastz and chainNet program through your PATH,

  2. you have assign sufficient file handles (you can get detailed information in the manual).

Hope this would help. Do not hesitate to contact me again.

Best regards,

在 2017/6/14 22:40, Matthew Gemmell 写道:

Dear developers

Hello I have been trying to run Haplomerger2 with an assembly created by canu form PacBio data. I have tried to run batchB1 to bacthB5 However I have not been able to get it to work with it creating many empty files. I have tried looking at the log files but I can't figure out what the issue is. One thing I noticed is that although I have run batchB1 there are not .seq/.fa files or x.seq/fa files but there are the nib files.

I would appreciate any help and if you would like any more info you need to help me please do not hesitate to ask.

Thanks for reading Matthew Gemmell

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best regards,

黄盛丰 Shengfeng Huang 中山大学生命科学学院 School of life sciences, Sun Yat-sen university hshengf2@mail.sysu.edu.cn http://sklbc.sysu.edu.cn/Team/User/info.aspx?typeid=283&pid=46

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m-gemmell commented 7 years ago

Hello

I have tried to run Example 1 in the Haplomerger manual but if unfortunately did not work. I looked at the log files for step B1 and their seems to be an issue. Below is the contents of log file "_hm.faDnaPolishing.log" ========== Start at Thu Jun 22 10:41:04 BST 2017 ../bin/faDnaPolishing.pl --legalizing --noLeadingN --removeShortSeq=500

--legalizing=1 . --maskShortPortion=0 . --noLeadingN=1 . --removeShortSeq=500 . Problems with the fasta file; no symbol > found !

========== Start at Thu Jun 22 10:41:04 BST 2017 ../bin/faDnaPolishing.pl --legalizing --noLeadingN --removeShortSeq=500

--legalizing=1 . --maskShortPortion=0 . --noLeadingN=1 . --removeShortSeq=500 . Problems with the fasta file; no symbol > found !

========== Start at Thu Jun 22 10:41:04 BST 2017 ../bin/faDnaPolishing.pl --legalizing --noLeadingN --removeShortSeq=500

--legalizing=1 . --maskShortPortion=0 . --noLeadingN=1 . --removeShortSeq=500 . Problems with the fasta file; no symbol > found ! " DO you know how this issue may be occurring?

Thanks for reading Matthew Gemmell

mapleforest commented 7 years ago

dear Matthew，

It is hm.batchB3 but not hm.batchB1 that invoke faDnaPolishing.pl.

You should start with hm.batchB1 and follow the instruction.

Pause after each step and compare the result with the standard result

shown in "project_example1/test1_correct_output".

Usually these problems happen because the environment did not set up correctly.

For starter, make sure to include the executables lastz and chainNet programs to your PATH.

Feel free to contact me if you have further question..

P.S. note that you can pack up the whole example directory and send it to me, it is only a few hundred kb.

So that I can help to pinpoint the problem.

best regards,

Shengfeng.

在 2017/6/22 17:48, Matthew Gemmell 写道:

Hello

I have tried to run Example 1 in the Haplomerger manual but if unfortunately did not work. I looked at the log files for step B1 and their seems to be an issue. Below is the contents of log file "_hm.faDnaPolishing.log" ========== Start at Thu Jun 22 10:41:04 BST 2017 ../bin/faDnaPolishing.pl --legalizing --noLeadingN --removeShortSeq=500

--legalizing=1 . --maskShortPortion=0 . --noLeadingN=1 . --removeShortSeq=500 . Problems with the fasta file; no symbol > found !

========== Start at Thu Jun 22 10:41:04 BST 2017 ../bin/faDnaPolishing.pl --legalizing --noLeadingN --removeShortSeq=500

--legalizing=1 . --maskShortPortion=0 . --noLeadingN=1 . --removeShortSeq=500 . Problems with the fasta file; no symbol > found !

========== Start at Thu Jun 22 10:41:04 BST 2017 ../bin/faDnaPolishing.pl --legalizing --noLeadingN --removeShortSeq=500

--legalizing=1 . --maskShortPortion=0 . --noLeadingN=1 . --removeShortSeq=500 . Problems with the fasta file; no symbol > found ! " DO you know how this issue may be occurring?

Thanks for reading Matthew Gemmell

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/mapleforest/HaploMerger2/issues/5#issuecomment-310332149, or mute the thread https://github.com/notifications/unsubscribe-auth/AOtnAEsvkvQYDn20EU5a0iMQyhCpYp82ks5sGjhsgaJpZM4N5--q.

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best regards,

黄盛丰 Shengfeng Huang 中山大学生命科学学院 School of life sciences, Sun Yat-sen university hshengf2@mail.sysu.edu.cn http://sklbc.sysu.edu.cn/Team/User/info.aspx?typeid=283&pid=46

本邮件及其附件含有发送给特定个人和用于特定目的的保密信息。如果您不是预期的收件人，请立即删除本邮件并通知发件人。严禁任何非预期的收件人使用、传播、分发或复制本邮件或其附件。 This email and its attachments may contain confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this email and notify the sender immediately. Any use, dissemination, distribution, or copying of this email or its attachments by persons other than the intended recipient(s), is strictly prohibited.

mapleforest commented 7 years ago

Clearly， faDnaPolishing.pl was expecting result files, which were not created corrected in your case.

Send me the whole example directory. I will look into it.

在 2017/6/22 17:48, Matthew Gemmell 写道:

Hello

I have tried to run Example 1 in the Haplomerger manual but if unfortunately did not work. I looked at the log files for step B1 and their seems to be an issue. Below is the contents of log file "_hm.faDnaPolishing.log" ========== Start at Thu Jun 22 10:41:04 BST 2017 ../bin/faDnaPolishing.pl --legalizing --noLeadingN --removeShortSeq=500

--legalizing=1 . --maskShortPortion=0 . --noLeadingN=1 . --removeShortSeq=500 . Problems with the fasta file; no symbol > found !

========== Start at Thu Jun 22 10:41:04 BST 2017 ../bin/faDnaPolishing.pl --legalizing --noLeadingN --removeShortSeq=500

--legalizing=1 . --maskShortPortion=0 . --noLeadingN=1 . --removeShortSeq=500 . Problems with the fasta file; no symbol > found !

========== Start at Thu Jun 22 10:41:04 BST 2017 ../bin/faDnaPolishing.pl --legalizing --noLeadingN --removeShortSeq=500

--legalizing=1 . --maskShortPortion=0 . --noLeadingN=1 . --removeShortSeq=500 . Problems with the fasta file; no symbol > found ! " DO you know how this issue may be occurring?

Thanks for reading Matthew Gemmell

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/mapleforest/HaploMerger2/issues/5#issuecomment-310332149, or mute the thread https://github.com/notifications/unsubscribe-auth/AOtnAEsvkvQYDn20EU5a0iMQyhCpYp82ks5sGjhsgaJpZM4N5--q.

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best regards,

黄盛丰 Shengfeng Huang 中山大学生命科学学院 School of life sciences, Sun Yat-sen university hshengf2@mail.sysu.edu.cn http://sklbc.sysu.edu.cn/Team/User/info.aspx?typeid=283&pid=46

本邮件及其附件含有发送给特定个人和用于特定目的的保密信息。如果您不是预期的收件人，请立即删除本邮件并通知发件人。严禁任何非预期的收件人使用、传播、分发或复制本邮件或其附件。 This email and its attachments may contain confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this email and notify the sender immediately. Any use, dissemination, distribution, or copying of this email or its attachments by persons other than the intended recipient(s), is strictly prohibited.

m-gemmell commented 7 years ago

Dear Shenfeng

Sorry for the late reply. Thank you for the help. I was wondering if it would still be ok to send you the example directory? If so what would be the best way to send it to you?

Thanks for reading Matthew Gemmell

mapleforest commented 7 years ago

Send it to my email address: hshengf2@mail.sysu.edu.cn.

Run a clean one. then pack the whole directory and send it to this email.

It is ideal to send both example1 and 2 to me.

I will look into it.

best regards,

Shengfeng.

在 2017/7/26 19:07, Matthew Gemmell 写道:

Dear Shenfeng

Sorry for the late reply. Thank you for the help. I was wondering if it would still be ok to send you the example directory? If so what would be the best way to send it to you?

Thanks for reading Matthew Gemmell

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/mapleforest/HaploMerger2/issues/5#issuecomment-318022358, or mute the thread https://github.com/notifications/unsubscribe-auth/AOtnAImjyAy9sSdrFqI8vcXSDy4HKnn_ks5sRx3dgaJpZM4N5--q.

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best regards,

黄盛丰 Shengfeng Huang 中山大学生命科学学院 School of life sciences, Sun Yat-sen university hshengf2@mail.sysu.edu.cn http://sklbc.sysu.edu.cn/Team/User/info.aspx?typeid=283&pid=46

本邮件及其附件含有发送给特定个人和用于特定目的的保密信息。如果您不是预期的收件人，请立即删除本邮件并通知发件人。严禁任何非预期的收件人使用、传播、分发或复制本邮件或其附件。 This email and its attachments may contain confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this email and notify the sender immediately. Any use, dissemination, distribution, or copying of this email or its attachments by persons other than the intended recipient(s), is strictly prohibited.

m-gemmell commented 7 years ago

Hello

I Appeared to have got it working by changing the order of paths in my PATH. The examples run fine and now I am running Hamplomerger2 on my own data.

I will comment and close this thread if it works or let you know if it does not work.

Thanks for reading Matthew Gemmell

mapleforest commented 7 years ago

OK. If you still worry. Try example 3, it only takes 2hours to finish.

在 2017/7/28 17:19, Matthew Gemmell 写道:

Hello

I Appeared to have got it working by changing the order of paths in my PATH. The examples run fine and now I am running Hamplomerger2 on my own data.

I will comment and close this thread if it works or let you know if it does not work.

Thanks for reading Matthew Gemmell

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/mapleforest/HaploMerger2/issues/5#issuecomment-318604250, or mute the thread https://github.com/notifications/unsubscribe-auth/AOtnAE8ZIqpsTu1b_Co4KUfgZpntL_ZAks5sSaesgaJpZM4N5--q.

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best regards,

黄盛丰 Shengfeng Huang 中山大学生命科学学院 School of life sciences, Sun Yat-sen university hshengf2@mail.sysu.edu.cn http://sklbc.sysu.edu.cn/Team/User/info.aspx?typeid=283&pid=46

本邮件及其附件含有发送给特定个人和用于特定目的的保密信息。如果您不是预期的收件人，请立即删除本邮件并通知发件人。严禁任何非预期的收件人使用、传播、分发或复制本邮件或其附件。 This email and its attachments may contain confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this email and notify the sender immediately. Any use, dissemination, distribution, or copying of this email or its attachments by persons other than the intended recipient(s), is strictly prohibited.

Haoran-Xue commented 5 years ago

Hello

I Appeared to have got it working by changing the order of paths in my PATH. The examples run fine and now I am running Hamplomerger2 on my own data.

I will comment and close this thread if it works or let you know if it does not work.

Thanks for reading Matthew Gemmell

Hello Matthew,

Do you mind to tell me how did you change the order of paths in your PATH? I'm running example 1 and have the same error as you mentioned.

Best regards, Haoran