I ran the following code:
abyss-pe name=Name k=96 in=’read1.fastq read2.fastq’
And I received the following error:
abyss-fixmate: error: The mate pairs of this library are oriented forward-forward (FF), which is not supported by ABySS
The reads I inputted were not mate pairs, and I am not sure if that error message is using legacy terminology from an older version. Regardless, based on this error, I used the following recommendations:
Hi, Michael. ABySS stopping in this situation is intentional. If 2.6 times the number of reads are oriented FF than FR, then the library prep has issues that ABySS will not be able to handle. Better to stop and tell the user. You could omit the paired-end information by using se=reads.fq.gz rather than in=reads.fq.gz.
This, however, did not resolve the missing "contigs.fa" file issue.
I am re-running abyss-pe once again using the following recommendations for how to include merged read files:
abyss-pe name="Name_Merged" k=96 se="merged.fastq read1.fastq read2.fastq"
So, you can feed these 3 files to ABySS and assemble only up to the unitigs stage. Then, continue the assembly into the contigs or scaffold stage using the original read files.
Still not sure why these files aren't automatically going into the contigs stage.
Based on the flow chart found here, it appears that the program stops at the "align reads to contigs" phase, ending with Name-3.fa and the unitigs.fa file.