This parameter is only valid if chip.use_bwa_mem_for_pe and FASTQs are paired-ended.
This parameter defaults to 70 (as mentioned in bwa's manual).
This parameter controls the threshold for read length of bwa mem for paired ended dataset. The pipeline automatically determines sample's read length from a (merged) FASTQ R1 file. If such read length is shorter than this threshold then pipeline automatically switches back to bwa aln instead of bwa mem. If you FASTQ's read length is < 70 and you still want to use bwa mem then try to reduce this parameter.
Added input parameters:
chip.bowtie2_use_local_mode--localtobowtie2command line, which will override the default--end-to-endmode ofbowtie2.chip.bwa_mem_read_len_limitchip.use_bwa_mem_for_peand FASTQs are paired-ended.70(as mentioned in bwa's manual).bwa memfor paired ended dataset. The pipeline automatically determines sample's read length from a (merged) FASTQ R1 file. If such read length is shorter than this threshold then pipeline automatically switches back tobwa alninstead ofbwa mem. If you FASTQ's read length is <70and you still want to usebwa memthen try to reduce this parameter.Conda environemnt
tbbin the environment, which will possibly fix thebowtie2andmambaconflicting library issue.