OSError: [Errno 2] No such file or directory

[Nuturetree]

hello， my genome has 13 chromosomes, when I run this program, I get that err information.

File "/public/home/xhhuang/softW/anaconda2/envs/sci/lib/python2.7/site-packages/sci-0.1-py2.7.egg/sci/utils.py", line 63, in run_LINE
tOutput = _LaunchJob(command)

File "/public/home/xhhuang/softW/anaconda2/envs/sci/lib/python2.7/site-packages/sci-0.1-py2.7.egg/sci/utils.py", line 23, in _LaunchJob
stderr=subprocess.PIPE)
File "/public/home/xhhuang/softW/anaconda2/envs/sci/lib/python2.7/subprocess.py", line 394, in init
errread, errwrite)
File "/public/home/xhhuang/softW/anaconda2/envs/sci/lib/python2.7/subprocess.py", line 1047, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

[poflawless]

@Nuturetree,

Did you solved this issue? I have faced the same error now.

Best Wishes,

[Nuturetree]

no, I can not solved this problem At 2022-07-21 16:05:44, "poflawless" ***@***.***> wrote: @Nuturetree, Did you solved this issue? I have faced the same error now. Best Wishes, — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>

[yuz12012]

hello， my genome has 13 chromosomes, when I run this program, I get that err information.

File "/public/home/xhhuang/softW/anaconda2/envs/sci/lib/python2.7/site-packages/sci-0.1-py2.7.egg/sci/utils.py", line 63, in run_LINE
tOutput = _LaunchJob(command)

File "/public/home/xhhuang/softW/anaconda2/envs/sci/lib/python2.7/site-packages/sci-0.1-py2.7.egg/sci/utils.py", line 23, in _LaunchJob stderr=subprocess.PIPE) File "/public/home/xhhuang/softW/anaconda2/envs/sci/lib/python2.7/subprocess.py", line 394, in init errread, errwrite) File "/public/home/xhhuang/softW/anaconda2/envs/sci/lib/python2.7/subprocess.py", line 1047, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory

I failed to reproduce the problem. I suspect that the issue is caused by different operating system settings. I would suggest ppl use the docker container which is specifically built for such problems.

[Nuturetree]

I guess sci can support the chromosome less than 23 (human) 在 2022-07-22 03:29:24，"yuz12012" ***@***.***> 写道： hello， my genome has 13 chromosomes, when I run this program, I get that err information. File "/public/home/xhhuang/softW/anaconda2/envs/sci/lib/python2.7/site-packages/sci-0.1-py2.7.egg/sci/utils.py", line 63, in run_LINE tOutput = _LaunchJob(command) File "/public/home/xhhuang/softW/anaconda2/envs/sci/lib/python2.7/site-packages/sci-0.1-py2.7.egg/sci/utils.py", line 23, in _LaunchJob stderr=subprocess.PIPE) File "/public/home/xhhuang/softW/anaconda2/envs/sci/lib/python2.7/subprocess.py", line 394, in init errread, errwrite) File "/public/home/xhhuang/softW/anaconda2/envs/sci/lib/python2.7/subprocess.py", line 1047, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory I failed to reproduce the problem. I suspect that the issue is caused by different operating system settings. I would suggest ppl use the docker container which is specifically built for such problems. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>

[Simple53]

I have the same problem. My genome also have chromosomes more than 23. Have you guys figured it out?

[Simple53]

I want to try the docker container, but got the following warnings:

INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
Getting image source signatures
Copying blob 75f829a71a1c done  
Copying blob 0be0a38615de done  
Copying blob 3fcbf7af1349 done  
Copying blob 14411072679d done  
Copying blob ef072ab87ab5 done  
Copying blob 857cb289ef57 done  
Copying config 6777ebf2e6 done  
Writing manifest to image destination
Storing signatures
2023/06/08 20:59:26  info unpack layer: sha256:75f829a71a1c5277a7abf55495ac8d16759691d980bf1d931795e5eb68a294c0
2023/06/08 20:59:27  warn rootless{usr/bin/newgidmap} ignoring (usually) harmless EPERM on setxattr "security.capability"
2023/06/08 20:59:27  warn rootless{usr/bin/newuidmap} ignoring (usually) harmless EPERM on setxattr "security.capability"
2023/06/08 20:59:27  warn rootless{usr/bin/ping} ignoring (usually) harmless EPERM on setxattr "security.capability"
2023/06/08 20:59:28  warn rootless{usr/sbin/arping} ignoring (usually) harmless EPERM on setxattr "security.capability"
2023/06/08 20:59:28  warn rootless{usr/sbin/clockdiff} ignoring (usually) harmless EPERM on setxattr "security.capability"
2023/06/08 20:59:30  info unpack layer: sha256:0be0a38615de325daa1d7ee1095c41e240e2dc0ec63ae9f472feb92229b2ce53
2023/06/08 21:00:23  warn rootless{usr/bin/ssh-agent} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/06/08 21:00:23  warn rootless{usr/bin/staprun} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/06/08 21:00:28  warn rootless{usr/libexec/openssh/ssh-keysign} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/06/08 21:00:33  info unpack layer: sha256:3fcbf7af1349e85a55bc595340bcd049506191d8d6033ea6b7cdde3d054dc701
2023/06/08 21:00:48  info unpack layer: sha256:14411072679d95e648aba312f23b5256206fbfc8c05376fe97c4b336816072d1
2023/06/08 21:01:21  info unpack layer: sha256:ef072ab87ab544062a11baf08a18f6b7124fbcac391a8327187a82e5a9965af0
2023/06/08 21:01:21  info unpack layer: sha256:857cb289ef57c1f0f35d8c4c2be73da827a4396cd271eda7f327d3068127035d

[Nuturetree]

no | | 黄鲜晖 | | ***@***.*** | ---- Replied Message ---- | From | ***@***.***> | | Date | 6/8/2023 21:19 | | To | ***@***.***> | | Cc | ***@***.***> , ***@***.***> | | Subject | Re: [LabShengLi/sci] OSError: [Errno 2] No such file or directory (Issue #8) | I have the same problem. My genome also have chromosomes more than 23. Have you guys figured it out? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>

[yuz12012]

I want to try the docker container, but got the following warnings:

INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
Getting image source signatures
Copying blob 75f829a71a1c done  
Copying blob 0be0a38615de done  
Copying blob 3fcbf7af1349 done  
Copying blob 14411072679d done  
Copying blob ef072ab87ab5 done  
Copying blob 857cb289ef57 done  
Copying config 6777ebf2e6 done  
Writing manifest to image destination
Storing signatures
2023/06/08 20:59:26  info unpack layer: sha256:75f829a71a1c5277a7abf55495ac8d16759691d980bf1d931795e5eb68a294c0
2023/06/08 20:59:27  warn rootless{usr/bin/newgidmap} ignoring (usually) harmless EPERM on setxattr "security.capability"
2023/06/08 20:59:27  warn rootless{usr/bin/newuidmap} ignoring (usually) harmless EPERM on setxattr "security.capability"
2023/06/08 20:59:27  warn rootless{usr/bin/ping} ignoring (usually) harmless EPERM on setxattr "security.capability"
2023/06/08 20:59:28  warn rootless{usr/sbin/arping} ignoring (usually) harmless EPERM on setxattr "security.capability"
2023/06/08 20:59:28  warn rootless{usr/sbin/clockdiff} ignoring (usually) harmless EPERM on setxattr "security.capability"
2023/06/08 20:59:30  info unpack layer: sha256:0be0a38615de325daa1d7ee1095c41e240e2dc0ec63ae9f472feb92229b2ce53
2023/06/08 21:00:23  warn rootless{usr/bin/ssh-agent} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/06/08 21:00:23  warn rootless{usr/bin/staprun} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/06/08 21:00:28  warn rootless{usr/libexec/openssh/ssh-keysign} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/06/08 21:00:33  info unpack layer: sha256:3fcbf7af1349e85a55bc595340bcd049506191d8d6033ea6b7cdde3d054dc701
2023/06/08 21:00:48  info unpack layer: sha256:14411072679d95e648aba312f23b5256206fbfc8c05376fe97c4b336816072d1
2023/06/08 21:01:21  info unpack layer: sha256:ef072ab87ab544062a11baf08a18f6b7124fbcac391a8327187a82e5a9965af0
2023/06/08 21:01:21  info unpack layer: sha256:857cb289ef57c1f0f35d8c4c2be73da827a4396cd271eda7f327d3068127035d

I have the same problem. My genome also have chromosomes more than 23. Have you guys figured it out?

Hi all,

I think the issue is: Line is not found if you are not in the /sci dir.

please run the script in the correct directory.

[Simple53]

Thanks@yuz12012! I have succesfully run the scripts in the sci/ dir.
During the process I faced annother err:

LINE/line: error while loading shared libraries: libgsl.so.25: cannot open shared object file: No such file or directory

But I figured it out by add the gsl path to $LD_LIBRARY_PATH.

export LD_LIBRARY_PATH=/path/to/gsl/lib:$LD_LIBRARY_PATH