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.
Problem:
QIIME searches for "R1" and "R2" in sample filename, but is confused to fine it also in the directory name
/path/to/my/samples/input_R1_R2/C1-A10_S24_L001_R1_001.fastq.gz
Solution:
rename directory such that it does not contain "R1" or "R2" (also remove multiple "R1" in sample-filename)
/path/to/my/samples/input_unpaired_reads/C1-A10_S24_L001_R1_001.fastq.gz
multiple_join_paired_ends.py -i input_unpaired_reads/ -o joined_reads