Some files wont assemble

[peflanag]

Hi All,

3 of my isolates that I am trying to assemble using unicycler wont assemble. They are paired end Illumina reads. The error I get is

Error: the paired read input files have an unequal number of reads

Any ideas how I can resolve this?

Cheers.

[oschwengers]

Hi, I'm facing the same issue, so this might be related to #188 ? Unfortunately, I have no idea how to solve this. Might be a bug?

[peflanag]

No worries. I might try running spades on my paired end instead of unicycler. It’s just weird that 2 samples ran in my looped script and 3 didn’t!

[oschwengers]

That's exactly what I'm also facing. This unpredictable behavior is rather odd and therefore should be addressed as it might leave some people quite puzzled. Additionally, if Unicycler would allow to incorporate stitched PE reads as SE reads, this might further improve the overall performance...

[Makaode]

Hi, I'm facing the same issue, and I solve the problem.

I found that I had written the wrong code. In the quick usage category, the hybrid assembly is: unicycler -1 short_reads_1.fastq.gz -2 short_reads_2.fastq.gz -l long_reads.fastq.gz -o output_dir

An error occurred when I wrote -1, -2, and -1 as a number. (Error: the paired read input files have an unequal number of reads)

The last one, '-l,' was the small letter of the alphabet, 'L.' (from the 'l'ong read) And then Unicycler goes well.