extendedFrags_fastqc.html" does not exist or is empty #1
Description
Script launch failed.
My data are paired end 16S data ( illumina V3-V5)
myData/
1001_R1.fastq 1082_R2.fastq 1222_R1.fastq 2006_R2.fastq 2060_R1.fastq 2120_R2.fastq 2178_R1.fastq 2309_R2.fastq 2375_R1.fastq 3025_R2.fastq 3089_R1.fastq 3143_R2.fastq 3209_R1.fastq
1001_R2.fastq 1086_R1.fastq 1222_R2.fastq 2007_R1.fastq 2060_R2.fastq 2122_R1.fastq 2178_R2.fastq 2311_R1.fastq 2375_R2.fastq 3026_R1.fastq 3089_R2.fastq 3145_R1.fastq 3209_R2.fastq
1003_R1.fastq 1086_R2.fastq 1230_R1.fastq 2007_R2.fastq 2061_R1.fastq 2122_R2.fastq 2179_R1.fastq 2311_R2.fastq 2378_R1.fastq 3026_R2.fastq 3092_R1.fastq 3145_R2.fastq 3210_R1.fastq
1003_R2.fastq
After running :
Minimum read length [--minreadlength]= 35
Minimum phred quality [--minphred]= 20
Minimum allowed percentage of correctly called nucleotides [--minphredperc]= 80
Minimum number of mistach for the filtering [--NbMismatchMapping]= 1
Filtering databases= human phi
# OTU process:
Dereplication is in full length mode
Minimum length of an amplicon [--minampliconlength]= 64
Minimum size of an OTU for singleton removal [--minotusize]= 4
Chimera filtering is in de novo mode
Clustering is performed with vsearch
# 16S/18S annotation
Identity threshold with vsearch [--identityThreshold]= 0.75
Conserved position for alignment[--conservedPosition]= 0.5
Tree generated in fast mode with FastTree
* Start analysis
* Start working on reads
* 1/188 - Quality control with Fastqc
* File "/mydata/result//reads//1001.extendedFrags_fastqc.html" does not exist or is empty !