Are you using the latest version of samtools and HTSlib? If not, please specify.
(run samtools --version)
samtools 1.10
Please describe your environment.
- OS (run
uname -sr on Linux/Mac OS or wmic os get Caption, Version on Windows)
- machine architecture (run
uname -m on Linux/Mac OS or wmic os get OSArchitecture on Windows)
- compiler (run
gcc --version or clang --version)
Linux 3.10.0-957.27.2.el7.x86_64
Please specify the steps taken to generate the issue, the command you are running and the relevant output.
When accessing a file on CEPH storage using the S3 protocol, samtools fails on longer paths. I haven't determined yet whether the root cause is the length of the path string, or the depth of nesting. I figured I would check here if this is a known issue before diving too deep into debugging, as I can solve the problem in the short term by moving the data to a location with shorter paths. I'll need to resolve this eventually though.
Are you using the latest version of samtools and HTSlib? If not, please specify.
(run
samtools --version)samtools 1.10Please describe your environment.
uname -sron Linux/Mac OS orwmic os get Caption, Versionon Windows)uname -mon Linux/Mac OS orwmic os get OSArchitectureon Windows)gcc --versionorclang --version)Linux 3.10.0-957.27.2.el7.x86_64Please specify the steps taken to generate the issue, the command you are running and the relevant output.
When accessing a file on CEPH storage using the S3 protocol, samtools fails on longer paths. I haven't determined yet whether the root cause is the length of the path string, or the depth of nesting. I figured I would check here if this is a known issue before diving too deep into debugging, as I can solve the problem in the short term by moving the data to a location with shorter paths. I'll need to resolve this eventually though.