Error while running "multiple_join_paired_end.py"
multiple_join_paired_ends.py -i input_R1_R2/ -o joined_reads
ValueError: Invalid filename found for splitting on input for file /path/to/my/samples/input_R1_R2/SampleA_L001_R1_001.fastq.gz, check input read1_indicator and read2_indicator parameters as well.
QIIME searches for "R1" and "R2" in sample filename, but is confused to fine it also in the directory name
rename directory such that it does not contain "R1" or "R2" (also remove multiple "R1" in sample-filename)
multiple_join_paired_ends.py -i input_unpaired_reads/ -o joined_reads