Hi, I am using this the --make_annotaion preprocessing to run a multiple samples TE detecting,but after I ran out the --make_annotation,then I use -1 -2 to add sample,and find a repeat annotation step for relocate2 and other steps,which means RepeatMasker is progressed multiple times for every sample. Cound you help me? Below is my annotaion step code :
nohup python3 ~/software/mcclintock/mcclintock.py -c ref/TElib.fa -r ref/C.auratus.chromosome_20210819.fasta -p 80 -o output_template_all/ --serial --keep_intermediate all --make_annotations > logs/make_annotation.log &
Then I add a sample for resume:
nohup python3 ~/software/mcclintock/mcclintock.py -r ref/C.auratus.chromosome_20210819.fasta -c ref/TElib.fa -1 input_fastq/bc17_1.fastq.gz -2 input_fastq/bc17_2.fastq.gz -p 40 -m relocate,TEMP,ngs_te_mapper -o ./output_template_all/ --resume > logs/bc17_template.log &
I find RepeatMasker and bwa index steps were re-run ,could you please tell me why? Thanks
Best wishes!
Hi, I am using this the --make_annotaion preprocessing to run a multiple samples TE detecting,but after I ran out the --make_annotation,then I use -1 -2 to add sample,and find a repeat annotation step for relocate2 and other steps,which means RepeatMasker is progressed multiple times for every sample. Cound you help me? Below is my annotaion step code :
Then I add a sample for resume:
I find RepeatMasker and bwa index steps were re-run ,could you please tell me why? Thanks
Best wishes!