chimeric_sam.awk

[xueqinerer]

Hi,
When I run juicer.sh, there is an error. The error is as follows:
awk: /data/xueqin/Project/test/test_analyses/test_genome/hic/GPA202407536/2_HQData/juicer/scripts/common/chimeric_sam.awk: line 50: illegal reference to local variable array
awk: /data/xueqin/Project/test/test_Geome_analyses/test_genome/hic/GPA202407536/2_HQData/juicer/scripts/common/chimeric_sam.awk: line 51: illegal reference to local variable array
awk: /data/xueqin/Project/test/test_Geome_analyses/test_genome/hic/GPA202407536/2_HQData/juicer/scripts/common/chimeric_sam.awk: line 164: syntax error at or near [
samtools sort: failed to read header from "-".

How can I solve this error problem? Thank you.

[SidG13]

Hi, if you look at this issue, you need to make sure you're using gawk and not awk. I used an alias to use gawk instead of awk and it worked.