Why the cover files cannot generated through the script?

[liaohu1231]

No description provided.

[simroux]

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

[liaohu1231]

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

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------------------&nbsp;原始邮件&nbsp;------------------ 发件人: "simroux/ClusterGenomes" <[email protected]&gt;; 发送时间:&nbsp;2020年9月9日(星期三) 晚上11:53 收件人:&nbsp;"simroux/ClusterGenomes"<[email protected]&gt;; 抄送:&nbsp;"1043386801"<[email protected]&gt;;"Author"<[email protected]&gt;; 主题:&nbsp;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 ? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[simroux]

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]

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.

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------------------&nbsp;原始邮件&nbsp;------------------ 发件人: "simroux/ClusterGenomes" <[email protected]&gt;; 发送时间:&nbsp;2020年9月10日(星期四) 凌晨0:16 收件人:&nbsp;"simroux/ClusterGenomes"<[email protected]&gt;; 抄送:&nbsp;"1043386801"<[email protected]&gt;;"Author"<[email protected]&gt;; 主题:&nbsp;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. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[simroux]

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]

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]

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

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---Original--- From: "simroux"<[email protected]&gt; Date: Thu, Sep 10, 2020 01:04 AM To: "simroux/ClusterGenomes"<[email protected]&gt;; Cc: "Author"<[email protected]&gt;;"liaohu1231"<[email protected]&gt;; 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). — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.