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zhangwei2015 / IMonitor

This script use to analyze the immune repertoire sequenced by high throughtput sequencing
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hello, the cope in the /src is not able to run on ubuntu 20.04.1 LTS, with an err of cannot execute binary file #9

Open shenxiaotianCNS opened 4 years ago

zhangwei2015 commented 4 years ago

I am sorry i missed the link in src. I have corrected it and uploaded the IMonitor-1.4.1 again to GitHub. or you can create the link by yourself: cd src link -s src/cope/cope .

Wei

shenxiaotianCNS commented 4 years ago

I am sorry i missed the link in src. I have corrected it and uploaded the IMonitor-1.4.1 again to GitHub. or you can create the link by yourself: cd src link -s src/cope/cope . Wei

very thankyou for your quick replying but I am sure it is not the link problem. I failed to ran the test data and the problem was input error, where the 2nd step of merge_fq_fq2fa.sh script failed to export the _XHS.merged_fq, XHS_1.fq.gz.left and XHS2.fq.gz.left for the following analysis(the cope procedure). then i ran the cope procedure seperateraly, and i got an error of cannot execute binary file: Exec format error the code i used was /home/shenxiaotian/imonitor/IMonitor-1.4.1/src/cope -a /mnt/i/xujing_ad/BACK/XHS_filter_1.fq.gz -b /mnt/i/xujing_ad/BACK/XHS_filter_2.fq.gz -o /mnt/i/xujing_ad/BACK/XHS.merged_fq -2 /mnt/i/xujing_ad/BACK/XHS_1.fq.gz.left -3 /mnt/i/xujing_ad/BACK/XHS_2.fq.gz.left -l 10 -u 99 -c 0.9 -m 0 -s 64 >/mnt/i/xujing_ad/BACK/XHS.fqMerging.log 2>/mnt/i/xujing_ad/BACK/XHS.fqMerging.err

zhangwei2015 commented 4 years ago

I just ran the test data and there was no problem. "cope" was coded by C programs and so your operating system should have the environment for C programming language. You can just run the cope (: /home/shenxiaotian/imonitor/IMonitor-1.4.1/src/cope), without any input, and find whether the help information of parameters could output.

You'd better show me the error information when you run your data, and then i can find the problems more specifically.

shenxiaotianCNS commented 4 years ago

good morning, hereis my error image image

i think my c environment is ok, i tried with programming a helloworld with c image

i really dont know what can i do. i am running it on image image

or can you email me with .c file? i may try compiling it by my own

zhangwei2015 commented 4 years ago
  1. I suggest you try to use: "Monitor-1.4.1/src/src/cope/cope", not the "Monitor-1.4.1/src/cope". As i mentioned before, "Monitor-1.4.1/src/cope" should be a link. However, when i submitted the file to Github, I copied the files and the link disappeared. If the "Monitor-1.4.1/src/src/cope/cope" does work, it is the problem of link.
  2. you can download the IMonitor-1.4.1.tar.gz again from Github, i updated the file yesterday.
  3. If both the above 2 steps fail, you can install cope you yourself according to the introduction in the file "INSTALL" (IMonitor-1.4.1/src/INSTALL). The cope was not developed by myself and so i have not the original codes. Sorry about that.
shenxiaotianCNS commented 4 years ago

its working!! thankyou so much