I am not sure if this question is valid.
I have 4 Fastq files single( 4 samples) end 50 bp reads. I am trying to follow Miseq SOP (http://www.mothur.org/wiki/MiSeq_SOP) which I think may not be appropriate but I made use of reverse.seqs() command as mentioned on this thread: Illumina single-read with index in 2nd sequencing run
I also do not have any Barcode files if any.
I was able to get the make.contigs command to work and this is the result:
[ERROR]: Could not open 18910.num.temp It took 20559 secs to process 219133249 sequences. Group count: P_0_098 38812677 P_1847_3 47203468 No_P_7 36488086 No_P_8 53531374 Total of all groups is 176035605
I saw there was error in between, but I continued.
Command: screen.seqs(fasta=stability.trim.contigs.fasta, group=stability.contigs.groups, summary=stability.trim.contigs.summary, maxambig=0, maxlength=50) Output File Names: stability.trim.contigs.good.summary stability.trim.contigs.good.fasta stability.trim.contigs.bad.accnos stability.contigs.good.groups It took 2053 secs to screen 176035605 sequences.
Command: unique.seqs(fasta=stability.trim.contigs.good.fasta) 126250000 93433220 126251000 93434117 126252000 93435002 126253000 93435907 126254000 93436812 126255000 93437717 126256000 93438597 126257000 93439481 126258000 93440372 126259000 93441265 126260000 93442154 126261000 93443059 Killed
Unfortunately, I was not able to save Logfile and I had saved these outputs by copy pasting to a text file.
I stopped processing the data at this point realizing that it may not be right. Also I found that short reads would cause a problem as mentioned here: Produce too large amount of data when running dist.seqs
My question: is Mothur a right tool for my case or it may not be feasible considering my data.
I am sorry, if this question is very naive and if so please delete it.