I am running the metawrap pipeline. I have 206 samples that I first concatenated them in 10 groups (A_case, A_control, B_case, B_control, C_case, C_control, D_case, D_control, E_case and E_control), and later into one big paired fastq file as shown below:
cat A_case*1.fastq > A_case_1.fastq & cat A_case*2.fastq > A_case_2.fastq cat A_control*1.fastq > A_control_1.fastq & cat B_control*2.fastq > B_control_2.fastq
And so on....
Then combined all:
cat *1.fastq > ALL_READS_1.fastq and cat *2.fastq > ALL_READS_2.fastq
Using these ALL_READS fastq files, I ran assembly, binning, bin refinement and abundance modules using metawrap pipeline. However, during the abundance module, it says "There were 1 samples detected" (I was expecting it to be 10 samples) and it generated abundance for only one sample. So, why metawrap is treating all the reads as one? even though I had 10 different groups?
Please help to solve this issue.
Many thanks in advance!