Hello, I am using Juicer to analyze a HiC data without information on restriction enzyme. The mapping goes successfully. However, the chimeric_sam.awk does not work. Here's the error information.
(-: Align of /home/jib79/hic/2019-NG/juicer/splits/SRR9822212.fastq.sam done successfully
awk: /home/jib79/hic/2019-NG/juicer/scripts/scripts/common/chimeric_sam.awk: line 50: illegal reference to local variable array
awk: /home/jib79/hic/2019-NG/juicer/scripts/scripts/common/chimeric_sam.awk: line 51: illegal reference to local variable array
awk: /home/jib79/hic/2019-NG/juicer/scripts/scripts/common/chimeric_sam.awk: line 164: syntax error at or near [
samtools: /home/jib79/miniconda2/envs/Hicpro/bin/../lib/libtinfow.so.6: no version information available (required by samtools)
samtools: /home/jib79/miniconda2/envs/Hicpro/bin/../lib/libncursesw.so.6: no version information available (required by samtools)
samtools: /home/jib79/miniconda2/envs/Hicpro/bin/../lib/libncursesw.so.6: no version information available (required by samtools)
samtools sort: failed to read header from "-"
***! Failure during chimera handling of /home/jib79/hic/2019-NG/juicer/splits/SRR9822212.fastq
zhangyangfan
commented
2 years ago
Hello, I am using Juicer to analyze a HiC data without information on restriction enzyme. The mapping goes successfully. However, the chimeric_sam.awk does not work. Here's the error information. (-: Align of /home/jib79/hic/2019-NG/juicer/splits/SRR9822212.fastq.sam done successfully awk: /home/jib79/hic/2019-NG/juicer/scripts/scripts/common/chimeric_sam.awk: line 50: illegal reference to local variable array awk: /home/jib79/hic/2019-NG/juicer/scripts/scripts/common/chimeric_sam.awk: line 51: illegal reference to local variable array awk: /home/jib79/hic/2019-NG/juicer/scripts/scripts/common/chimeric_sam.awk: line 164: syntax error at or near [ samtools: /home/jib79/miniconda2/envs/Hicpro/bin/../lib/libtinfow.so.6: no version information available (required by samtools) samtools: /home/jib79/miniconda2/envs/Hicpro/bin/../lib/libncursesw.so.6: no version information available (required by samtools) samtools: /home/jib79/miniconda2/envs/Hicpro/bin/../lib/libncursesw.so.6: no version information available (required by samtools) samtools sort: failed to read header from "-" ***! Failure during chimera handling of /home/jib79/hic/2019-NG/juicer/splits/SRR9822212.fastq