[emboss-dev] Repeated "unknown output format" messages from seqret

Peter Rice pmr at ebi.ac.uk
Mon Aug 10 16:50:19 UTC 2009

Peter wrote:
> Hi all,
> Peter has mentioned supressing repeated error messages (e.g. if
> on converting from Sanger FASTQ to Solexa FASTQ the quality
> scores must be truncated at a maximum of 62). I've got another
> example which is probably going to be more common:
> $ seqret -filter -sformat fastq-sanger -osformat fastq-illuminaa <
> SRR001666_1.fastq | grep "^@SRR" | wc -l
> Error: Unknown output format 'fastq-illuminaa'
> Error: Unknown output format 'fastq-illuminaa'
> Error: unknown output format 'fastq-illuminaa'
> Error: unknown output format 'fastq-illuminaa'
> ...
> I think getting the "unknown output format" message once is enough,
> and 7 million times is overkill ;)

Odd that nobody has spotted that one before. It will be fixed in a
future release.

We will aim to report each message once, and then when the program ends
we can report how many more times the same message was repeated. We hope
to be able to catch several repeated messages because with FASTQ
next-generation data there can indeed be millions of sequences each with
the same error or warning.


Peter Rice

More information about the emboss-dev mailing list