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snayfach / MIDAS

An integrated pipeline for estimating strain-level genomic variation from metagenomic data
http://dx.doi.org/10.1101/gr.201863.115
GNU General Public License v3.0
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Error: could not execute bowtie2 binary #110

Open BoyanZhou opened 4 years ago

BoyanZhou commented 4 years ago

Hi,

I had a problem when I used "run_midas.py". It reported "Error: could not execute bowtie2 binary: /gpfs/data/lilab/home/zhoub03/software/MIDAS/bin/Linux/bowtie2 (exited with error code 127)". However that "bowtie2" was under the path and executable. I also downloaded bowtie2-2.3.2-linux-x86_64.zip and copied the new bowtie2 binaries to the target path. It still reported the same error. I would appreciate it if you could help me solve this problem. Thank you so much!

BoyanZhou commented 4 years ago

Hi, I have not solved this problem. It seems that this software was built on python2. But my version python/cpu/2.7.15 did not work on it.

Best, Boyan

qiileee notifications@github.com 于2020年9月24日周四 上午12:13写道：

I used python2.7, but when I installed dependencies biopython, there is an error that I must used python3.7.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/snayfach/MIDAS/issues/110#issuecomment-698100564, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF4MBKUZAUH5S4KDQ6GXKHTSHLBPZANCNFSM4RPOARLA .

qiileee commented 4 years ago

Hi, I tried to use "pip" to install these required dependencies instead of "conda", and there is no errors reported in test module. Maybe you can retry it. Thanks for your repy. Best, Qiilee ------------------ 原始邮件 ------------------ 发件人: "snayfach/MIDAS" <notifications@github.com>; 发送时间: 2020年9月27日(星期天) 中午12:23 收件人: "snayfach/MIDAS"<MIDAS@noreply.github.com>; 抄送: "eeeer"<1246858671@qq.com>;"Comment"<comment@noreply.github.com>; 主题: Re: [snayfach/MIDAS] Error: could not execute bowtie2 binary (#110)

Hi, I have not solved this problem. It seems that this software was built on python2. But my version python/cpu/2.7.15 did not work on it.

Best, Boyan

qiileee <notifications@github.com> 于2020年9月24日周四 上午12:13写道：

> I used python2.7, but when I installed dependencies biopython, there is an > error that I must used python3.7. > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <https://github.com/snayfach/MIDAS/issues/110#issuecomment-698100564&gt;, or > unsubscribe > <https://github.com/notifications/unsubscribe-auth/AF4MBKUZAUH5S4KDQ6GXKHTSHLBPZANCNFSM4RPOARLA&gt; > . >

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

BoyanZhou commented 4 years ago

Hi,

Which version of Python do you use? Thank you!

Best, Boyan

qiileee notifications@github.com 于2020年9月27日周日 上午12:34写道：

Hi, I tried to use "pip" to install these required dependencies instead of "conda", and there is no errors reported in test module. Maybe you can retry it. Thanks for your repy. Best, Qiilee ------------------ 原始邮件 ------------------ 发件人: "snayfach/MIDAS" <notifications@github.com>; 发送时间: 2020年9月27日(星期天) 中午12:23 收件人: "snayfach/MIDAS"<MIDAS@noreply.github.com>; 抄送: "eeeer"<1246858671@qq.com>;"Comment"< comment@noreply.github.com>; 主题: Re: [snayfach/MIDAS] Error: could not execute bowtie2 binary (#110)

Hi, I have not solved this problem. It seems that this software was built on python2. But my version python/cpu/2.7.15 did not work on it.

Best, Boyan

qiileee <notifications@github.com> 于2020年9月24日周四 上午12:13写道：

> I used python2.7, but when I installed dependencies biopython, there is an > error that I must used python3.7. > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > < https://github.com/snayfach/MIDAS/issues/110#issuecomment-698100564&gt;, or > unsubscribe > < https://github.com/notifications/unsubscribe-auth/AF4MBKUZAUH5S4KDQ6GXKHTSHLBPZANCNFSM4RPOARLA&gt;

> . >

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/snayfach/MIDAS/issues/110#issuecomment-699584089, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF4MBKUYVC774JZUUX2CNB3SH26ERANCNFSM4RPOARLA .

qiileee commented 4 years ago

Hi, python2.7 Best, Qiilee

---Original--- From: "Boyan Zhou"<notifications@github.com> Date: Sun, Sep 27, 2020 22:43 PM To: "snayfach/MIDAS"<MIDAS@noreply.github.com>; Cc: "Comment"<comment@noreply.github.com>;"qiileee"<1246858671@qq.com>; Subject: Re: [snayfach/MIDAS] Error: could not execute bowtie2 binary (#110)

Hi,

Which version of Python do you use? Thank you!

Best, Boyan

qiileee <notifications@github.com> 于2020年9月27日周日 上午12:34写道：

> Hi, > I tried to use "pip" to install these required dependencies instead of > "conda", and there is no errors reported in test module. Maybe you can > retry it. Thanks for your repy. > Best, > Qiilee > ------------------&nbsp;原始邮件&nbsp;------------------ > 发件人: "snayfach/MIDAS" <notifications@github.com&gt;; > 发送时间:&nbsp;2020年9月27日(星期天) 中午12:23 > 收件人:&nbsp;"snayfach/MIDAS"<MIDAS@noreply.github.com&gt;; > 抄送:&nbsp;"eeeer"<1246858671@qq.com&gt;;"Comment"< > comment@noreply.github.com&gt;; > 主题:&nbsp;Re: [snayfach/MIDAS] Error: could not execute bowtie2 binary > (#110) > > > > > > Hi, > I have not solved this problem. It seems that this software was built on > python2. But my version python/cpu/2.7.15 did not work on it. > > Best, > Boyan > > qiileee <notifications@github.com&gt; 于2020年9月24日周四 上午12:13写道： > > &gt; I used python2.7, but when I installed dependencies biopython, there > is an > &gt; error that I must used python3.7. > &gt; > &gt; — > &gt; You are receiving this because you authored the thread. > &gt; Reply to this email directly, view it on GitHub > &gt; < > https://github.com/snayfach/MIDAS/issues/110#issuecomment-698100564&amp;gt;, > or > &gt; unsubscribe > &gt; < > https://github.com/notifications/unsubscribe-auth/AF4MBKUZAUH5S4KDQ6GXKHTSHLBPZANCNFSM4RPOARLA&amp;gt; > > &gt; . > &gt; > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub, or unsubscribe. > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <https://github.com/snayfach/MIDAS/issues/110#issuecomment-699584089&gt;, or > unsubscribe > <https://github.com/notifications/unsubscribe-auth/AF4MBKUYVC774JZUUX2CNB3SH26ERANCNFSM4RPOARLA&gt; > . >

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BoyanZhou commented 4 years ago

Thank you for your kindly help!

qiileee notifications@github.com 于2020年9月27日周日 上午10:55写道：

Hi, python2.7 Best, Qiilee

---Original--- From: "Boyan Zhou"<notifications@github.com> Date: Sun, Sep 27, 2020 22:43 PM To: "snayfach/MIDAS"<MIDAS@noreply.github.com>; Cc: "Comment"<comment@noreply.github.com>;"qiileee"<1246858671@qq.com>;

Subject: Re: [snayfach/MIDAS] Error: could not execute bowtie2 binary (#110)

Hi,

Which version of Python do you use? Thank you!

Best, Boyan

qiileee <notifications@github.com> 于2020年9月27日周日 上午12:34写道：

> Hi, > I tried to use "pip" to install these required dependencies instead of > "conda", and there is no errors reported in test module. Maybe you can > retry it. Thanks for your repy. > Best, > Qiilee > ------------------&nbsp;原始邮件&nbsp;------------------ > 发件人: "snayfach/MIDAS" <notifications@github.com&gt;; > 发送时间:&nbsp;2020年9月27日(星期天) 中午12:23 > 收件人:&nbsp;"snayfach/MIDAS"<MIDAS@noreply.github.com&gt;; > 抄送:&nbsp;"eeeer"<1246858671@qq.com&gt;;"Comment"< > comment@noreply.github.com&gt;; > 主题:&nbsp;Re: [snayfach/MIDAS] Error: could not execute bowtie2 binary > (#110) > > > > > > Hi, > I have not solved this problem. It seems that this software was built on > python2. But my version python/cpu/2.7.15 did not work on it. > > Best, > Boyan > > qiileee <notifications@github.com&gt; 于2020年9月24日周四 上午12:13写道： > > &gt; I used python2.7, but when I installed dependencies biopython, there > is an > &gt; error that I must used python3.7. > &gt; > &gt; — > &gt; You are receiving this because you authored the thread. > &gt; Reply to this email directly, view it on GitHub > &gt; < > https://github.com/snayfach/MIDAS/issues/110#issuecomment-698100564&amp;gt;,

> or > &gt; unsubscribe > &gt; < > https://github.com/notifications/unsubscribe-auth/AF4MBKUZAUH5S4KDQ6GXKHTSHLBPZANCNFSM4RPOARLA&amp;gt;

> > &gt; . > &gt; > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub, or unsubscribe. > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > < https://github.com/snayfach/MIDAS/issues/110#issuecomment-699584089&gt;, or > unsubscribe > < https://github.com/notifications/unsubscribe-auth/AF4MBKUYVC774JZUUX2CNB3SH26ERANCNFSM4RPOARLA&gt;

> . >

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/snayfach/MIDAS/issues/110#issuecomment-699645542, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF4MBKSVBEESJUM2WQ2KIDTSH5G45ANCNFSM4RPOARLA .