nchernia
commented
3 years ago This is very strange. Have you looked at the output files in the splits directory?
On Fri, Jul 16, 2021 at 1:10 PM Lattesnow @.***> wrote:
Hey, I processed the test data and my shallow sequencing data. The results seem to be okay. But for my deep seq data it always give this failure during chimera handling. I update my gawk and all the other dependencies but still getting this.
[main] CMD: bwa mem -SP5M -t 64 reference/hg38gatk.fastq /mnt/d/HiC/JU/juicer/CPU/splits/deep3_L001_R1_001.fastq /mnt/d/HiC/JU/juicer/CPU/splits/deep3_L001_R2_001.fastq [main] Real time: 30224.177 sec; CPU: 1084536.297 sec (-: Align of /mnt/d/HiC/JU/juicer/CPU/splits/deep3_L001_001.fastq.sam done successfully awk: /mnt/d/HiC/JU/juicer/scripts/common/chimeric_blacklist.awk:357: (FILENAME=/mnt/d/HiC/JU/juicer/CPU/splits/deep3_L001_001.fastq.sam FNR=2209126524) fatal: print to "/mnt/d/HiC/JU/juicer/CPU/splits/deep3_L001_001.fastq_norm.txt" failed: Invalid argument ***! Failure during chimera handling of /mnt/d/HiC/JU/juicer/CPU/splits/deep3_L001_001.fastq
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/aidenlab/juicer/issues/232, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAK2EWYENLJX4QUSU4RVNH3TYBRWVANCNFSM5AP6DDRQ .
-- Neva Cherniavsky Durand, Ph.D. | she, her, hers Assistant Professor | Molecular and Human Genetics Aiden Lab | Baylor College of Medicine www.aidenlab.org
Lattesnow
Xinxin0314
Hey, I processed the test data and my shallow sequencing data. The results seem to be okay. But for my deep seq data it always give this failure during chimera handling. I update my gawk and all the other dependencies but still getting this.
[main] CMD: bwa mem -SP5M -t 64 reference/hg38gatk.fastq /mnt/d/HiC/JU/juicer/CPU/splits/deep3_L001_R1_001.fastq /mnt/d/HiC/JU/juicer/CPU/splits/deep3_L001_R2_001.fastq [main] Real time: 30224.177 sec; CPU: 1084536.297 sec (-: Align of /mnt/d/HiC/JU/juicer/CPU/splits/deep3_L001_001.fastq.sam done successfully awk: /mnt/d/HiC/JU/juicer/scripts/common/chimeric_blacklist.awk:357: (FILENAME=/mnt/d/HiC/JU/juicer/CPU/splits/deep3_L001_001.fastq.sam FNR=2209126524) fatal: print to "/mnt/d/HiC/JU/juicer/CPU/splits/deep3_L001_001.fastq_norm.txt" failed: Invalid argument ***! Failure during chimera handling of /mnt/d/HiC/JU/juicer/CPU/splits/deep3_L001_001.fastq