Make.file truncates 1st line

Hello Patrick and mothur community:

Same issue as reported by bakerdyl Oct 2022. I didn’t follow Patrick’s reply to that post. Here is what I see:
Using mothur v.1.48.0

make.file(inputdir=./, prefix=pgn, type=fastq)
Setting input directories to:
Output File Names:

Here are the first 5 lines of the pgn.files:

pigeons pigeons_exp100_S59_L001_R1_001.fastq pigeons_exp100_S59_L001_R2_001.fastq
pigeons_exp101 pigeons_exp101_S60_L001_R1_001.fastq pigeons_exp101_S60_L001_R2_001.fastq
pigeons_exp102 pigeons_exp102_S61_L001_R1_001.fastq pigeons_exp102_S61_L001_R2_001.fastq
pigeons_exp103 pigeons_exp103_S62_L001_R1_001.fastq pigeons_exp103_S62_L001_R2_001.fastq
pigeons_exp104 pigeons_exp104_S63_L001_R1_001.fastq pigeons_exp104_S63_L001_R2_001.fastq

It seems that mothur is truncating first line, left column. Should say “pigeons_exp100”

many thanks,


Can you replace the _ in your sample names with a different character (probably best to avoid _, -, and .)? That seemed to work on the other thread


Hi Patrick, is removing underscores a temporary fix or is that the recommended solution for the foreseeable future? I use underscores routinely in file and group names given that mothur assigns a special meaning to hyphen. Other mothur programs don’t seem to mind “_” in filenames.

Sorry but that’s unlikely to change any time soon.

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