Concatenation error generates empty mapping files

[arachloroptera]

When I run the following to create a map:

/home/miniconda3/envs/lotus2/share/lotus2-2.21-0/lotus2 -create_map 01_map

An empty mapping file is created accompanied by the following message:

Use of uninitialized value $first in concatenation (.) or string at /home/miniconda3/envs/lotus2/share/lotus2-2.21-0/lotus2 line 5667. common prefix Map is 01_map Please check that all files required are present in map 01_map. Use of uninitialized value $pathPre in concatenation (.) or string at /home/miniconda3/envs/lotus2/share/lotus2-2.21-0/lotus2 line 5756.

The corresponding lines are:

5667: print "$first common prefix\n";

5756: print "==========================\nTo start analysis:\nlotus2 -m $ofile -i $pathPre/ -o [outdir] [further parameters if desired]\n==========================\n";

I am not familiar enough with Perl to fully understand what is going on, but I am curuious as to why there would be any issue with the script itself when I did not edit in in any way. Am I missing something in terms of my input? I have run this from the input directory containing 100 files (R1 and R2 of 50 samples) in fastq format.

[ozkurt]

Hi, thanks for reporting the issue. You need to define the input dir to your fastq files: perl lotus2 -create_map 01_map -i $INPUTdir

Hope this helps. Ezgi

[arachloroptera]

Thank you so much for the quick response. I thought it was taking the current directory as input by default. Thank you for clarifying!