juicer 2.0 can't use my fastq.gz files

[Nick Jeffery]

Hello, 

I am not sure what is wrong with my input for juicer but I am thinking there's an issue with my directory structure. I am running on a CPU with 80 cores in my juicer directory, the following line of code and the error messages. I tried making a symbolic link of my fastq files into splits but it just tells me the fastq files exist already. Can anyone help me figure out this issue?

~/juicer$ ./scripts/juicer.sh -d /home/mcrg/juicer -p references/sizes.genome -y restriction_sites/CrabGenome_Arima.txt -z references/CrabGenome.fasta -t 40 -D /home/mcrg/juicer
(-: Looking for fastq files...fastq files exist
---  Using already created files in /home/mcrg/juicer/splits

(-: Aligning files matching /home/mcrg/juicer/fastq/*_R*.fastq*
 to genome references/CrabGenome.fasta with no fragment delimited maps.
gzip: /home/mcrg/juicer/splits/*_R1*.fastq.gz: No such file or directory
Running command bwa mem -SP5M -t 40 -R @RG\tID:**\tSM:HiC_sample\tPL:ILM\tLB:HiC_library references/CrabGenome.fasta /home/mcrg/juicer/splits/*_R1*.fastq.gz /home/mcrg/juicer/splits/*_R2*.fastq.gz > /home/mcrg/juicer/splits/**.fastq.gz.sam
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[E::main_mem] fail to open file `/home/mcrg/juicer/splits/*_R1*.fastq.gz'.
***! Alignment of /home/mcrg/juicer/splits/*_R1*.fastq.gz /home/mcrg/juicer/splits/*_R2*.fastq.gz failed.

[Olga Dudchenko]

Do your fastq files match the _R1* _R2* format? It looks like you might have file naming issues. -Olga