Hi all,
I have a problem with scaffolding using Abyss. I have paired end data and mate pair data. First I performed a paired end assembly, which worked fine. When I ran another assembly exactly the same but including the mate pair data, it did not improve. I ran the last few steps again using the following command:
abyss-map -v -j20 -l39 -k25 mate_pair_reads_R1 mate_pair_reads_R2 assembly-6.fa | abyss-fixmate -v -h mp1-6.hist | sort -snk3 -k4 | DistanceEst --dot -v -j20 -k25 -l39 -s200 -n3 -o mp1-6.dist.dot mp1-6.hist
And this is the result I am getting:
Mapped 59132142 of 59432904 reads (99.5%)
Mapped 53446089 of 59432904 reads uniquely (89.9%)
Read 59432904 alignments
Mateless 59432904 100%
Unaligned 0
Singleton 0
FR 0
RF 0
FF 0
Different 0
Total 59432904
error: the histogram `mp1-6.hist' is empty
abyss-scaffold -k63 -s200 -n3 -g assembly-6.path1.dot assembly-6.dot mp1-6.dist.dot > assembly-6.path1
abyss-scaffold: ../Graph/AdjIO.h:104: std::istream& read_adj(std::istream&, ContigGraph<G>&, BetterEP) [with Graph = DirectedGraph<Length, DistanceEst>, BetterEP = BetterDistanceEst]: Assertion `in' failed.
I have checked the orientation of the mate pair reads and it is F - R, just like the paired end reads. Does anyone have any idea what may cause this type of problem? I would really appreciate some help!
I have a problem with scaffolding using Abyss. I have paired end data and mate pair data. First I performed a paired end assembly, which worked fine. When I ran another assembly exactly the same but including the mate pair data, it did not improve. I ran the last few steps again using the following command:
abyss-map -v -j20 -l39 -k25 mate_pair_reads_R1 mate_pair_reads_R2 assembly-6.fa | abyss-fixmate -v -h mp1-6.hist | sort -snk3 -k4 | DistanceEst --dot -v -j20 -k25 -l39 -s200 -n3 -o mp1-6.dist.dot mp1-6.hist
And this is the result I am getting:
Mapped 59132142 of 59432904 reads (99.5%)
Mapped 53446089 of 59432904 reads uniquely (89.9%)
Read 59432904 alignments
Mateless 59432904 100%
Unaligned 0
Singleton 0
FR 0
RF 0
FF 0
Different 0
Total 59432904
error: the histogram `mp1-6.hist' is empty
abyss-scaffold -k63 -s200 -n3 -g assembly-6.path1.dot assembly-6.dot mp1-6.dist.dot > assembly-6.path1
abyss-scaffold: ../Graph/AdjIO.h:104: std::istream& read_adj(std::istream&, ContigGraph<G>&, BetterEP) [with Graph = DirectedGraph<Length, DistanceEst>, BetterEP = BetterDistanceEst]: Assertion `in' failed.
I have checked the orientation of the mate pair reads and it is F - R, just like the paired end reads. Does anyone have any idea what may cause this type of problem? I would really appreciate some help!