Hello - I am trying to analyze my sequencing data and am having trouble with the demultiplex step of Fast-GBS, which utilizes Sabre. The problem appears to be with the demultiplex step. I used paired-end sequencing method so I have two barcode files. Because of this I have named them barcodes_FLOW1_1 and barcodes_FLOW1_2 and set the lanes to two lanes, although the MiSeq only has one flow cell and one lane. The sequence data is names FLOW1_1.fq.gz and FLOW1_2.fq.gz. I have used just the 5’-3’ sequence as there is no other place to put the second adapter sequence. I have checked the names of the files and all appears to be fine, I removed the .txt from the file name as instructed.
The error shown on terminal is:
Demultiplex with Sabre ./fastgbs.sh: line 213: parallel: command not found !!! There is a problem with the demultiplex step with sabre for !!! Check the names given to the sequences and barcode files
Here is the parameters I have set:
; FLOWCELL INFORMATION FLOWCELL=FLOW1 ; LANES INFORMATION FLOW1_LANES=1 2 ; SEQUENCING TECHNOLOGY: ILLUMINA IONTORRENT TECHNOLOGY=ILLUMINA ; SEQUENCE TYPE (PAIRED_END OR SINGLE-END): PE SE SEQTYP=PE ; NAME OF THE REFERENCE GENOME FILES REFGEN=adzukireferencegenome.fasta ; SEQUENCE USED FOR ADAPTOR RECOGNITION (THE COMPLETE ADAPTOR SEQUENCE IS ; AGATCGGAAGAGCGGG) ADAP=CACGACGCTCTTCCGATCT ; MINIMUM READ LENGTH TO KEEP READLEN=50 ; NUMBER OF PARALLEL PROCESS FOR BWA BWAPAR=2 ; NUMBER OF THREAD FOR EACH BWA PROCESS BWATHR=4 ; MAXIMUM NUMBER OF CORES THAT COULD BE ALLOWED BY YOUR COMPUTER FOR THIS ANALYSIS ; SHOULD BE EQUAL TO: BWAPAR X BWATHR NBCOR=8 ; NAME OF FILE CONTAINING LOG LOGFILE=logfile_fastgbs.log ; NAME OF FILE CONTAINING LIST OF S1.BAM FILE FOR PLATYPUS ANALYSIS BAMLIST=List_bam ; FOR PLATYPUS: Minimum number of supporting reads required before a ; variant candidate will be considered (equivalent to minDP in vcftools) MINREADS=2 ; PLATYPUS LOGFILE LOGPLAT=FastGBS_platypus_log.txt ; PLATYPUS OUTPUT VCF FILE OUTPLAT=FastGBS_platypus ; VCFTOOLS filtering: --max-missing 0.2 MAXMIS=0.2