search

affinis / SMTa

Spatial meta-transcriptome analysis pipeline
4 stars 1 forks source link

awk error with ./run_SMTa_test.sh and microperc.sh #5

Open ebarrozo opened 1 year ago

ebarrozo commented 1 year ago

When running ./run_SMTa_test.sh on the tinytest data or microperc.sh on my own spaceranger outputs I get the following error

awk: line 1: syntax error at or near ,

Are there errors in the samtools awk commands on lines 68 and 70 in the microperc.sh script?

affinis commented 1 year ago

sorry for that, no error occured on our server, I think that may be a bug caused by different Linux distribution, are you runing it on MAC OS or Centos? or it may be an issue of awk. The linux description of our server is Ubuntu 20.04.2 LTS, and the awk version is GNU Awk 5.0.1, API: 2.0 (GNU MPFR 4.0.2, GNU MP 6.2.0). Hope these could help you