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CDCgov / NCHHSTP-DTBE-Varpipe-WGS

This repository contains an analysis pipeline developed to characterize WGS output
Apache License 2.0
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AttributeError: 'module' object has no attribute 'FullLoader' #1

Closed ybdong919 closed 1 year ago

ybdong919 commented 1 year ago

What type of help do you need?

Please describe how you'd like us to help. $ ./runVarpipeline.sh ls: cannot access _L001_R2_001: No such file or directory ls: cannot access _L001_R1_001: No such file or directory rm: cannot remove ‘_L00’: No such file or directory

../tools/Varpipeline -q A01_R1_001.fastq.gz -r ../tools/ref2.fa -n A01 -q2 A01_R2_001.fastq.gz -a -v

Traceback (most recent call last): File "../tools/Varpipeline", line 97, in args.verbose, ' '.join(sys.argv)) File "/blue/bphl-florida/dongyibo/CDC_TB_pipeline/NCHHSTP-DTBE-Varpipe-WGS/tools/Varpipeline.py", line 76, in init cfg = yaml.load(ymlfile, Loader=yaml.FullLoader) AttributeError: 'module' object has no attribute 'FullLoader' ../tools/Varpipeline -q A04_R1_001.fastq.gz -r ../tools/ref2.fa -n A04 -q2 A04_R2_001.fastq.gz -a -v

Traceback (most recent call last): File "../tools/Varpipeline", line 97, in args.verbose, ' '.join(sys.argv)) File "/blue/bphl-florida/dongyibo/CDC_TB_pipeline/NCHHSTP-DTBE-Varpipe-WGS/tools/Varpipeline.py", line 76, in init cfg = yaml.load(ymlfile, Loader=yaml.FullLoader) AttributeError: 'module' object has no attribute 'FullLoader' ../tools/Varpipeline -q A06_R1_001.fastq.gz -r ../tools/ref2.fa -n A06 -q2 A06_R2_001.fastq.gz -a -v

Traceback (most recent call last): File "../tools/Varpipeline", line 97, in args.verbose, ' '.join(sys.argv)) File "/blue/bphl-florida/dongyibo/CDC_TB_pipeline/NCHHSTP-DTBE-Varpipe-WGS/tools/Varpipeline.py", line 76, in init cfg = yaml.load(ymlfile, Loader=yaml.FullLoader) AttributeError: 'module' object has no attribute 'FullLoader'

reagank commented 1 year ago

This should be resolved with the most recent commit - d396209