Error: Unknown format code 'f' for object of type 'str' about cdna_cupcake

[Magdoll]

Hi @lishen,
This error is almost always caused by one of two things:

1. the SAM file was not sorted properly. The sort command should be:

sort -k 3,3 -k 4,4n input.sam > input.sorted.sam

2. The SAM file contains incomplete alignments. This is usually discovered via running the aligner (GMAP, STAR, etc) again and ensuring that the process finished.

If neither fixes the problem, I would need to take a look at the SAM file to know the cause.

Thanks,
--Liz

[lishen]

@Magdoll ,

I converted sam to bam and sorted them using samtools and convert back to sam. I'm sure the sam files are already sorted.

But what do you mean by incomplete alignments? There are unmapped reads, which are at the tail of a sam file with a tag value of 4. Are they the reads that are causing trouble?

[Magdoll]

Hi @lishen,

Sorting using samtools has been known to cause this error. Can you please try:

sort -k 3,3 -k 4,4n input.sam > input.sorted.sam

and see if this problem goes away? Alternatively, you can remove all alignments that are unmapped.

The error shows up because it is expecting all unmapped alignments to either not exist at all, or appear all at the beginning of the SAM file. It's trying to print "r.qCoverage" for an alignment that is unmapped and since it's unmapped r.qCoverage is not a number.

--Liz

[Magdoll]

Closing issue unless noted otherwise.

[rlittman16]

I was using samtools sort, and got this error then I used:
sort -k 3,3 -k 4,4n input.sam > input.sorted.sam
I have the same error.