"Failure during chimera handling of" error on CPU version

[G C]

Dear all,

I am stuck with Juicer pipeline obtaining the error "Failure during chimera handling of " and I find it difficult to solve the issue.

I am running the CPU code on a MacBookPro 2019 OS Catalina. The Juicer code is up to date (03/01/2021).

Thanks a lot

[Neva Durand]

Is that the only error message you see? Can you post more information?

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Neva Cherniavsky Durand, Ph.D. | she, her, hers

Assistant Professor |  Molecular and Human Genetics

Aiden Lab | Baylor College of Medicine

www.aidenlab.org

[giaco...@gmail.com]

This is the full error message.

[main] Version: 0.7.17-r1188

[main] CMD: bwa mem -SP5M -t 8 /Users/giacomocorleone/Tools/Juicer/juicer/scripts/references/Homo_sapiens_assembly19.fasta /Users/giacomocorleone/Tools/Juicer/juicer/scripts/splits/IRE-LalB-CTR-001-HIC-CS-080720_R1.fastq.gz /Users/giacomocorleone/Tools/Juicer/juicer/scripts/splits/IRE-LalB-CTR-001-HIC-CS-080720_R2.fastq.gz

[main] Real time: 939.772 sec; CPU: 6537.997 sec

(-:  Align of /Users/giacomocorleone/Tools/Juicer/juicer/scripts/splits/IRE-LalB-CTR-001-HIC-CS-080720.fastq.gz.sam done successfully

awk: calling undefined function and

 input record number 89, file /Users/giacomocorleone/Tools/Juicer/juicer/scripts/splits/IRE-LalB-CTR-001-HIC-CS-080720.fastq.gz.sam

 source line number 298

***! Failure during chimera handling of /Users/giacomocorleone/Tools/Juicer/juicer/scripts/splits/IRE-LalB-CTR-001-HIC-CS-080720.fastq.gz

Thanks

[Neva Durand]

You need to have an updated version of awk / gawk installed on your system (it's not understanding "and")

https://github.com/aidenlab/juicer/issues/9

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