paired-end are not recognized

[yeroslaviz]

thanks for a great script. Unfortunately, I'm having troubles executing it.

I have two samples in PE format. These are the four files:

$ ll /home/yeroslaviz/poolFolders/pool-bcfngs/fastq_files/P891/conc.fastq/
total 2207785
drwxr-xr-x 2 yeroslaviz b_cox         0 Jan 14 13:40 ./
drwxr-xr-x 2 yeroslaviz b_cox         0 Jan 13 12:37 ../
-rwxr-xr-x 1 yeroslaviz b_cox 537679844 Dec 20 16:48 Dam_TaDa-P891_n1_read1.fastq.gz*
-rwxr-xr-x 1 yeroslaviz b_cox 574549405 Dec 20 16:48 Dam_TaDa-P891_n1_read2.fastq.gz*
-rwxr-xr-x 1 yeroslaviz b_cox 556999936 Dec 20 16:48 grain_TaDa-P891_n1_read1.fastq.gz*
-rwxr-xr-x 1 yeroslaviz b_cox 591520683 Dec 20 16:48 grain_TaDa-P891_n1_read2.fastq.gz*

The command I'm using the execute the script

perl damidseq_pipeline-1.6/damidseq_pipeline \
     --gatc_frag_file=${basis}/GATC_fragments_files/Dmel_BDGP6.GATC.gff.gz \
     --bowtie2_genome_dir=/home/yeroslaviz/poolFolders/pool-bcfngs/genomes/Dme.BDGP6.28/bowtie2.4.4Index/Dmel.BDGP6.46 \
     --datadir /home/yeroslaviz/poolFolders/pool-bcfngs/fastq_files/P891/conc.fastq/   

throws an error at the beginning of the script

damidseq_pipeline v1.6
Copyright 2013-24, Owen Marshall


*** Reading GATC file ***
  Sorting ...

*** Reading data files ***
   not paired.  Assuming SE sequencing ...
:
	/home/yeroslaviz/poolFolders/pool-bcfngs/fastq_files/P891/conc.fastq/

Error: no Dam control sample detected!
Please use include a filename starting with 'Dam', or specify the Dam control file to use with the --dam=[filename] switch

I'm not sure, how to make the script recognize that these are paired-end files. Why aren't the read1 and read2 enough of a pattern to see that?
Also, I do have the files beginning with Dam, so why do I get this message?

thanks

Assa

[yeroslaviz]

I managed to run it, when I put everything in the same folder. I think there is a problem in the script with the --datadir parameter. But now it worked for me.