Platanus file format error

Question

[singh.naina]

Hi I've tried running

platanus assemble -o plat_errorcorrected -k 60 -f *pair1.fastq *pair2.fastq 2> plat.log

and I get:

Error(2): Read file exception 
Read file is not FASTA/FASTQ format!!

They are fastq format though.'ve trimmed these reads with skewer and corrected using BFC. Reads that were only trimmed and not error corrected were able to be assembled using Platanus and when I tried converting these fastq to fasta, it still would give the same error. These same fastq files were able to be assembled by ABySS. Any advice? Has anyone ever encountered this?

Thanks in advance

[Pierre Lindenbaum]

please, show us the output of the following commands:

head  *pair1.fastq *pair2.fastq

and

file  *pair1.fastq *pair2.fastq

Answer 1

[memory_donk]

Ok so I just had the exact same problem and after losing about half of my hair I figured it out. BFC outputs some letters as lowercase and Platanus doesn't seem to like that. I used a sed one-liner to convert all bases to uppercase and it started running. Obviously only use this on fasta or you could mess with quality scores. Use another command as appropriate to capitalize only sequence line in fastq.

sed -e 's/(.*)/\L\1/' test.fasta > testb.fasta