RemiAllio / MitoFinder

MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data
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./install error #30

Closed hemao-hm closed 2 years ago

hemao-hm commented 2 years ago

I met errors when I run ./install ,here is the roport: mkdir -p /home/hm/bioapp/MitoFinder/mitfi/infernal-1.0.2/exec/bin for file in cmalign cmbuild cmcalibrate cmemit cmscore cmsearch cmstat; do\ cp src/$file /home/hm/bioapp/MitoFinder/mitfi/infernal-1.0.2/exec/bin/;\ done cp: cannot stat ‘src/cmalign’: No such file or directory cp: cannot stat ‘src/cmbuild’: No such file or directory cp: cannot stat ‘src/cmcalibrate’: No such file or directory cp: cannot stat ‘src/cmemit’: No such file or directory cp: cannot stat ‘src/cmscore’: No such file or directory cp: cannot stat ‘src/cmsearch’: No such file or directory cp: cannot stat ‘src/cmstat’: No such file or directory Makefile:205: recipe for target 'install' failed make: *** [install] Error 1 I checked those directory or file ,they are all exited, but with suffix '.c'. Is this mean I need to install C++ or something? Thank you very much for your response. :)

hemao-hm commented 2 years ago

Hi, I just found that the problem maybe exited earlier ,here is the report: In file included from /usr/local/include/assert.h:5:0, from esl-alimanip.c:10: /usr/local/include/except.h:5:44: fatal error: config.h: No such file or directory

include / For HAVE_PTHREAD /

                                        ^

compilation terminated. Makefile:53: recipe for target 'esl-alimanip.o' failed make[2]: *** [esl-alimanip.o] Error 1 It seems lost a file called “config.h" .

RemiAllio commented 2 years ago

Hi,

Thank you for contacting me.

Indeed, there is an error during the installation of infernal.

Before digging into this error, is it possible for you to use the MitoFinder singularity container? If so, it will be much easier to use it (see Run MitoFinder with Singularity).

Best regards, Rémi

hemao-hm commented 2 years ago

Hi, Sorry  for the late reply. I have tried to use MitoFinder singularity,but when reported errors when I run commend "singularity pull --arch amd64 library://remiallio/default/mitofinder:v1.4.1" Here is the report:  INFO:    Downloading library image FATAL:   While pulling library image: error fetching image: unable to download image: error downloading image: Get "https://s3.amazonaws.com/sylabs-production-library-new/bson.10026b/61557e355adf5f68aab62001?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAJ4Q7QTCPFOAQ6WPQ%2F20211126%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20211126T060755Z&X-Amz-Expires=86400&X-Amz-SignedHeaders=host&response-content-disposition=attachment%3B%20filename%3D%22mitofinder_v1.4.1.sif%22&X-Amz-Signature=c5b328c0c37274889babe7bc3d1a3da7f1c65535d6e10d2c21d568c53bfa0c16": dial tcp 127.0.0.2:443: connect: connection refused

It seems that there are barriers.So I tried to copy this address to install it using VPN ,and I get a file(about 913M) called "mitofinder_v1.4.1.sif"indeed. But when I run commend " mitofinder_v1.4.1.sif -v" Reported :"-sh: /home/hm/bioapp/mitofinder/mitofinder_v1.4.1.sif: Permission denied'  I have no idea about what to do. Thank you again for everything you've done。 -------------- 原始邮件 ------------------ 发件人: "RemiAllio/MitoFinder" @.>; 发送时间: 2021年11月25日(星期四) 晚上6:24 @.>; @.**@.>; 主题: Re: [RemiAllio/MitoFinder] ./install error (Issue #30)

Hi,

Thank you for contacting me.

Indeed, there is an error during the installation of infernal.

Before digging into this error, is it possible for you to use the MitoFinder singularity container? If so, it will be much easier to use it (see Run MitoFinder with Singularity).

Best regards, Rémi

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

RemiAllio commented 2 years ago

Hi,

Ok, it seems you got the right container but you don't have the right to run it. Please, could you try to change the rights of the file as follows:

chmod 777 ./mitofinder_v1.4.1.sif

Let me know if you can run it then, Best, Rémi

hemao-hm commented 2 years ago

Hello,

It works . Thank you very much for all your assistance.

------------------ 原始邮件 ------------------ 发件人: "RemiAllio/MitoFinder" @.>; 发送时间: 2021年11月26日(星期五) 晚上7:13 @.>; @.**@.>; 主题: Re: [RemiAllio/MitoFinder] ./install error (Issue #30)

Hi,

Ok, it seems you got the right container but you don't have the right to run it. Please, could you try to change the rights of the file as follows:

chmod 777 ./mitofinder_v1.4.1.sif

Let me know if you can run it then, Best, Rémi

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

RemiAllio commented 2 years ago

Hi,

Glad to hear that! :grinning:

Best, Rémi