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populationgenomics / production-pipelines

Genomics workflows for CPG using Hail Batch
MIT License
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Update stripy logging command #759

Closed EddieLF closed 1 month ago

EddieLF commented 1 month ago

Batch job failure message:

+ sed 's/"log_flag_threshold": 1/"log_flag_threshold": -1/' config.json
+ sed 's/"output_json": false/"output_json": true/'
+ sed 's/]/],
"verbose": true/'
sed: -e expression #1, char 6: unterminated `s' command

I asked Claude 3

The issue with the command is in the third sed command. The problem is that the / character is used as the delimiter for the s (substitute) command in sed, but you also have a / character within the replacement string. This confuses sed and causes it to think the command is unterminated. To fix this, you can use a different delimiter for the s command, such as |, which is not present in your replacement string.