Open dipingxian431 opened 6 months ago
It shows errors as following:
/data/Mingchao/dowload_data/Monopogen/Monopogen_testout/Script/runGermline_chr20.sh: line 1: /home/mingchao/Linux_file/Monopogen/Monopogen/apps/samtools: Permission denied /data/Mingchao/dowload_data/Monopogen/Monopogen_testout/Script/runGermline_chr20.sh: line 1: /home/mingchao/Linux_file/Monopogen/Monopogen/apps/bcftools: Permission denied /data/Mingchao/dowload_data/Monopogen/Monopogen_testout/Script/runGermline_chr20.sh: line 1: /home/mingchao/Linux_file/Monopogen/Monopogen/apps/bcftools: Permission denied /data/Mingchao/dowload_data/Monopogen/Monopogen_testout/Script/runGermline_chr20.sh: line 1: /home/mingchao/Linux_file/Monopogen/Monopogen/apps/bgzip: Permission denied
Could you set execute permission on /home/mingchao/Linux_file/Monopogen/Monopogen/apps/*? For example chmod g+x
Thank you so much for the reply!
I tried to execute the permission by using chmod g+x /home/mingchao/Linux_file/Monopogen2/Monopogen/apps/*
before:
(Variants) mingchao@JS-Lambda-Vector:~/Linux_file/Monopogen2/Monopogen/apps$ ll
total 41076
drwxrwxr-x 2 mingchao mingchao 4096 Apr 7 22:23 ./
drwxrwxr-x 9 mingchao mingchao 4096 Apr 7 21:59 ../
-rw-rw-r-- 1 mingchao mingchao 1939857 Apr 7 21:59 bcftools
-rw-rw-r-- 1 mingchao mingchao 300906 Apr 7 21:59 beagle.08Feb22.fa4.jar
-rw-rw-r-- 1 mingchao mingchao 330554 Apr 7 21:59 beagle.27Jul16.86a.jar
-rw-rw-r-- 1 mingchao mingchao 631018 Apr 7 21:59 bgzip
-rw-rw-r-- 1 mingchao mingchao 100800 Apr 7 21:59 gzip
-rw-rw-r-- 1 mingchao mingchao 12784 Apr 7 21:59 java
-rw-rw-r-- 1 mingchao mingchao 68192 Apr 7 21:59 libbz2.so.1.0
-rw-rw-r-- 1 mingchao mingchao 3152968 Apr 7 21:59 libcrypto.so.1.0.0
-rw-rw-r-- 1 mingchao mingchao 64528 Apr 7 21:59 libdeflate.so
-rw-rw-r-- 1 mingchao mingchao 17389398 Apr 7 21:59 picard.jar
-rw-rw-r-- 1 mingchao mingchao 2911966 Apr 7 21:59 samtools
-rw-rw-r-- 1 mingchao mingchao 683232 Apr 7 21:59 tabix
-rw-rw-r-- 1 mingchao mingchao 14444639 Apr 7 21:59 vcftools
After:
(Variants) mingchao@JS-Lambda-Vector:~/Linux_file/Monopogen2/Monopogen/apps$ ll
total 41076
drwxrwxr-x 2 mingchao mingchao 4096 Apr 7 22:23 ./
drwxrwxr-x 9 mingchao mingchao 4096 Apr 7 21:59 ../
-rw-rwxr-- 1 mingchao mingchao 1939857 Apr 7 21:59 bcftools*
-rw-rwxr-- 1 mingchao mingchao 300906 Apr 7 21:59 beagle.08Feb22.fa4.jar*
-rw-rwxr-- 1 mingchao mingchao 330554 Apr 7 21:59 beagle.27Jul16.86a.jar*
-rw-rwxr-- 1 mingchao mingchao 631018 Apr 7 21:59 bgzip*
-rw-rwxr-- 1 mingchao mingchao 100800 Apr 7 21:59 gzip*
-rw-rwxr-- 1 mingchao mingchao 12784 Apr 7 21:59 java*
-rw-rwxr-- 1 mingchao mingchao 68192 Apr 7 21:59 libbz2.so.1.0*
-rw-rwxr-- 1 mingchao mingchao 3152968 Apr 7 21:59 libcrypto.so.1.0.0*
-rw-rwxr-- 1 mingchao mingchao 64528 Apr 7 21:59 libdeflate.so*
-rw-rwxr-- 1 mingchao mingchao 17389398 Apr 7 21:59 picard.jar*
-rw-rwxr-- 1 mingchao mingchao 2911966 Apr 7 21:59 samtools*
-rw-rwxr-- 1 mingchao mingchao 683232 Apr 7 21:59 tabix*
-rw-rwxr-- 1 mingchao mingchao 14444639 Apr 7 21:59 vcftools*
I also test them by using /home/mingchao/Linux_file/Monopogen2/Monopogen/apps/samtools
the output still permission denied:-bash: /home/mingchao/Linux_file/Monopogen2/Monopogen/apps/samtools: Permission denied
.
Same as another one:
(Variants) mingchao@JS-Lambda-Vector:~/Linux_file/Monopogen2/Monopogen/apps$ ./gzip -h
-bash: ./gzip: Permission denied
What should I do next?
Thank you so much!
Could you try chmod u+x ./*.
Using g+x only allows the group not the owner with the executing permission.
Thank you for the reply!
I tried hmod u+x ./*. But new questions come.
(base) mingchao@JS-Lambda-Vector:~/Linux_file/Monopogen2/Monopogen/apps$ ./bcftools
./bcftools: error while loading shared libraries: libdeflate.so: cannot open shared object file: No such file or directory
(base) mingchao@JS-Lambda-Vector:~/Linux_file/Monopogen2/Monopogen/apps$ ./samtools
./samtools: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory
And I can not use sudo apt-get install libncurses5
to install.
Do you have some other suggestions?
Thank you!
I also test other apps. It looks like all of them cannot be right run now.
(base) mingchao@JS-Lambda-Vector:~/Linux_file/Monopogen2/Monopogen/apps$ ./beagle.08Feb22.fa4.jar
-bash: ./beagle.08Feb22.fa4.jar: cannot execute binary file: Exec format error
(base) mingchao@JS-Lambda-Vector:~/Linux_file/Monopogen2/Monopogen/apps$ ./bgzip
./bgzip: error while loading shared libraries: libdeflate.so: cannot open shared object file: No such file or directory
(base) mingchao@JS-Lambda-Vector:~/Linux_file/Monopogen2/Monopogen/apps$ ./libbz2.so.1.0
Segmentation fault (core dumped)
Hi, I am running Germline, after successfully running preProcess. I met a few problems. First, when I ran germline, the output showed that I didn't have Java. So, I installed Java using
conda install bioconda::java-jdk
. After that, I rerun it. the output showed that no bam.bai file. So, I used thesamtools index
to add the bai file. Then re-run Germine with the following command.The job still cannot run correctly. The output file only has chr20.gl.vcf.gz and the size is 0. But at the end of the report shows "Monopogen.py Success! See instructions above."
The Monopogen_testout files:
The output report:
Any guidance to resolve this would be helpful.
Thank you so much!