search

mdozmorov / genome_runner

Academic Free License v3.0
0 stars 3 forks source link

Broken pipe on low memory machine #67

Closed mdozmorov closed 9 years ago

mdozmorov commented 10 years ago

Tested on 512M Ubuntu. grtk.sh throws a Broken Pipe error that propagates. The script itself contains a warning about memory. Can this be fixed?

ERROR /bin/bash: line 1:  3501 Killed                  tabix -B $tmp <(toBED $2)
awk: write failure (Broken pipe)
awk: close failed on file /dev/stdout (Broken pipe)

gzip: stdout: Broken pipe
/bin/bash: line 1:  3504 Killed                  tabix -B $tmp <(toBED $2)
awk: write failure (Broken pipe)
awk: close failed on file /dev/stdout (Broken pipe)

gzip: stdout: Broken pipe