Question: Platanus file format error
0
gravatar for singh.naina
3.2 years ago by
singh.naina0 wrote:

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

assembly software error • 1.5k views
ADD COMMENTlink modified 2.8 years ago by memory_donk290 • written 3.2 years ago by singh.naina0

please, show us the output of the following commands:

head  *pair1.fastq *pair2.fastq

and

file  *pair1.fastq *pair2.fastq
ADD REPLYlink written 3.2 years ago by Pierre Lindenbaum124k
0
gravatar for memory_donk
2.8 years ago by
memory_donk290
Australia
memory_donk290 wrote:

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

ADD COMMENTlink written 2.8 years ago by memory_donk290
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1936 users visited in the last hour