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hall-lab / speedseq

A flexible framework for rapid genome analysis and interpretation
MIT License
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sambamba-sort: Cannot open or create file '/dev/stdin' : No such file or directory #126

Open ccario83 opened 6 years ago

ccario83 commented 6 years ago

First of all, awesome tool with a smart design. And easy to compile!

I've been running into the issue where /dev/stdin and /dev/stdout aren't defined, which leads to piping issues. These are normally sym-linked to /dev/stdin -> /proc/self/fd/0 and /dev/stdout -> /proc/self/fd/1 but the system admin for the cluster I'm running speedseq on is unable to create these for technical reasons I won't get into.

Is there a known workaround, or, alternatively, a reason why /proc/self/fd/0 and /proc/self/fd/1 aren't directly accessed?

sambamba-sort: Cannot open or create file '/dev/stdin' : No such file or directory
sambamba-view: Cannot open file `/dev/stdin' in mode `rb' (No such file or directory)
sambamba-sort: Cannot open or create file '/dev/stdin' : No such file or directory
sambamba-view: Cannot open file `/dev/stdin' in mode `rb' (No such file or directory)
samblaster: Version 0.1.22
samblaster: Inputting from stdin
samblaster: Outputting to stdout