Errors in running

[taowis]

Hi,

When I run "../tools/bin/bpipe run -p EXOME_TARGET="SCA8_region.bed" ../pipelines/STRetch_exome_pipeline.groovy *.fastq.gz" for testing, it return such errors: File "/opt/STRetch/tools/miniconda/envs/STR/lib/python3.7/site-packages/Bio/Alphabet/init.py", line 21, in "Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the molecule_type as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information." ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the molecule_type as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information. ERROR: stage STR_locus_counts failed: Command in stage STR_locus_counts failed with exit status = 1 : ...... STRPATH=$PATH; PATH=/opt/STRetch/tools/bin:$PATH; /opt/STRetch/tools/bin/python /opt/STRetch/scripts/identify_locus.py --bam 11_L001_R1.STRdecoy.bam --bed /opt/STRetch/reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed --output 11_L001_R1.STRdecoy.locus_counts ;PATH=$STRPATH

ERROR: stage STR_locus_counts failed: Command in stage STR_locus_counts failed with exit status = 1 :

[hdashnow]

Hi, would you mind confirming which version of STRetch you are running? Within the STRetch directory type git log and check the most recent commit message. The latest is currently Feb 25 2021

I believe this bug was fixed in the most recent version: https://github.com/Oshlack/STRetch/commit/c5345e5dea4adfde790befb9903ec2d81ed5b2c1

[Jolleboll]

Hello, I also get this error with the latest release (0.4.0). Perhaps it's time for a new release? :P

I fetched the latest commit (dd35b85e3bd0f6c58f6e76ec9e5a47ab0e98987c) and the error is fixed. FYI.