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
I installed parallel, seems to have gotten rid of that error code, however I checked the shell script and it is written for single end not paired end reads so I have changed the parameters to match the paired end reads but no luck. I get a new error:
it's the very same kind of error....