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simroux / ClusterGenomes

Archive for ClusterGenomes scripts
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Why the cover files cannot generated through the script? #1

Open liaohu1231 opened 4 years ago

simroux commented 4 years ago

The cover file is generated when the script runs successfully. Do you have any error message ?

liaohu1231 commented 4 years ago

The script runs successfully when deleted the line 103-106, I don't know why you write the three line codes.

------------------ 原始邮件 ------------------ 发件人: "simroux/ClusterGenomes" <notifications@github.com>; 发送时间: 2020年9月9日(星期三) 晚上11:53 收件人: "simroux/ClusterGenomes"<ClusterGenomes@noreply.github.com>; 抄送: "1043386801"<1043386801@qq.com>;"Author"<author@noreply.github.com>; 主题: Re: [simroux/ClusterGenomes] Why the cover files cannot generated through the script? (#1)

The cover file is generated when the script runs successfully. Do you have any error message ?

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simroux commented 4 years ago

If this is v5.1, lines 103-106 are here to make sure that the mummer result file used as input is correctly sorted. So while the script may finish, you probably will want to double-check the results, because they may very well be incorrect if it only completes after removing l. 103-106.

liaohu1231 commented 4 years ago

Yes, it's v5.1. However，the script was geneally locked in this step if haven't deleted the three line codes, why is this happening. but we found the results look right after check and have a good effect for cluster of phage genome.

------------------ 原始邮件 ------------------ 发件人: "simroux/ClusterGenomes" <notifications@github.com>; 发送时间: 2020年9月10日(星期四) 凌晨0:16 收件人: "simroux/ClusterGenomes"<ClusterGenomes@noreply.github.com>; 抄送: "1043386801"<1043386801@qq.com>;"Author"<author@noreply.github.com>; 主题: Re: [simroux/ClusterGenomes] Why the cover files cannot generated through the script? (#1)

If this is v5.1, lines 103-106 are here to make sure that the mummer result file used as input is correctly sorted. So while the script may finish, you probably will want to double-check the results, because they may very well be incorrect if it only completes after removing l. 103-106.

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simroux commented 4 years ago

Without seeing the files, I can't say much more than: l. 103-106 are here for a reason, so you should use a version with these lines deleted with caution and knowing that there is a risk of incorrect results.

simroux commented 4 years ago

Most likely what happened was the "sort" function (l. 236-243) did not work as intended. You may want to look at the files XX-nucmer.out.coords and XX-nucmer.out.coords.sorted to check the difference, and see why the latter one (XXX-sorted) is not sorted according to the first column (query sequence).

liaohu1231 commented 4 years ago

Thank you very much，I found it can run successful if only deleted the line 106 <STDIN> just now, so it will generate right results if only deleted line 106. I'm very appreciated for your answer.

---Original--- From: "simroux"<notifications@github.com> Date: Thu, Sep 10, 2020 01:04 AM To: "simroux/ClusterGenomes"<ClusterGenomes@noreply.github.com>; Cc: "Author"<author@noreply.github.com>;"liaohu1231"<1043386801@qq.com>; Subject: Re: [simroux/ClusterGenomes] Why the cover files cannot generated through the script? (#1)

Most likely because the "sort" function (l. 236-243) did not work as intended. You may want to look at the files XX-nucmer.out.coords and XX-nucmer.out.coords.sorted to check the difference, and see why the latter one (XXX-sorted) is not sorted according to the first column (query sequence).

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