thanks for your reply.
I rectified that issue by changing few parameters.
Now, I am facing issue with the below command:
mothur > screen.seqs(fasta=/scratch/sathya/HM2_Analysis/fileList.paired.trim.contigs.good.unique.align, count=/scratch/sathya/HM2_Analysis/fileList.paired.trim.contigs.good.count_table, summary=/scratch/sathya/HM2_Analysis/fileList.paired.trim.contigs.good.unique.summary, start=1, optimize=end)
error message:
IC1 because all sequences have been removed.
Removing group: IC10 because all sequences have been removed.
Removing group: IC11 because all sequences have been removed.
Removing group: IC12 because all sequences have been removed.
Removing group: IC13 because all sequences have been removed.
Removing group: IC14 because all sequences have been removed.
Removing group: IC15 because all sequences have been removed.
Removing group: IC16 because all sequences have been removed.
Removing group: IC17 because all sequences have been removed.
Removing group: IC18 because all sequences have been removed.
Removing group: IC19 because all sequences have been removed.
Removing group: IC2 because all sequences have been removed.
Removing group: IC20 because all sequences have been removed.
Removing group: IC21 because all sequences have been removed.
Removing group: IC22 because all sequences have been removed.
Removing group: IC23 because all sequences have been removed.
Removing group: IC24 because all sequences have been removed.
Removing group: IC25 because all sequences have been removed.
Removing group: IC26 because all sequences have been removed.
Removing group: IC27 because all sequences have been removed.
Removing group: IC28 because all sequences have been removed.
filter.seqs(fasta=fileList.paired.trim.contigs.good.unique.good.align, vertical=T, trump=.)
mothur > filter.seqs(fasta=fileunique.good.align, vertical=T, trump=.)
Using 18 processors.
[ERROR]:
mothur> fileList.paired.trim.contigs.good.unique.good.align is blank. Please correct.
Error in reading your fastafile, at position -1. Blank name.
Creating Filter…
[ERROR]:
mothur> fileList.paired.trim.contigs.good.unique.good.align is blank. Please correct.
kindly help in this case.
i don’t know how to proceed further if the file is blank.
thanks!
SS