Hello --
Was wondering if anyone could help me/has experienced something similar? Abyss appears to have successfully completed a paired-end assembly without reporting any errors but on inspection the final unitig (-3.fa), paired-end contig (-6.fa) and scaffold (-8.fa) files are identical (as confirmed with diff -s). Furthermore, of the intermediate files, those with .path extension (-4.path1, -4.path2, -4.path3, -5.path, -6.path and -7.path) have been created but are empty. It seems the paired-end state of my reads isn't being seen by Abyss, and accordingly the Overlap step has nothing to work with; nevertheless, Abyss reports the composition of my library as PE well enough (>70% of the reads are FR, for instance). This 'unitig/contig/scaffold are the same' issue appears to have occurred before, but its solution (if there was one) wasn't mentioned on this original thread: https://groups.google.com/forum/#!searchin/abyss-users/unitig$20contig$20scaffold/abyss-users/0d-oxhYRHRQ/zRiJsufV1HYJ. Was wondering if anyone knew what the issue might be?
Was wondering if anyone could help me/has experienced something similar? Abyss appears to have successfully completed a paired-end assembly without reporting any errors but on inspection the final unitig (-3.fa), paired-end contig (-6.fa) and scaffold (-8.fa) files are identical (as confirmed with diff -s). Furthermore, of the intermediate files, those with .path extension (-4.path1, -4.path2, -4.path3, -5.path, -6.path and -7.path) have been created but are empty. It seems the paired-end state of my reads isn't being seen by Abyss, and accordingly the Overlap step has nothing to work with; nevertheless, Abyss reports the composition of my library as PE well enough (>70% of the reads are FR, for instance). This 'unitig/contig/scaffold are the same' issue appears to have occurred before, but its solution (if there was one) wasn't mentioned on this original thread: https://groups.google.com/forum/#!searchin/abyss-users/unitig$20contig$20scaffold/abyss-users/0d-oxhYRHRQ/zRiJsufV1HYJ. Was wondering if anyone knew what the issue might be?