File "/usr/local/opt/anaconda/lib/python2.7/site-packages/ipyrad-0.1.71-py2.7.egg/ipyrad/assemble/cluster_across.py", line 427, in singlecat
icatg[iloc] = catarr[iloc, :icatg[iloc].shape[1], :]
raise TypeError("Can't broadcast %s -> %s" % (target_shape, count))
TypeError: Can't broadcast (4, 4) -> (1, 150, 4)
//
. Easy fix.
sim_rad
data and randomly sticking them into the mt genome from the mouse. Good enough for government work, but randomly some of the simulated fragments overlap enough so that bedtools merges them, in which case they are joined as one cluster and then muscle tries to align them with obvious consequences.
denovo
i'll start testing refmapping. should be interesting. you in idayho?
1C_0 TGTTTCCTAGACGGGAGATCATC-----TGAAATTCGGTT-TTATCCTTGACCTGGTGCCACCGCCTCAATCTCTTGATTTCAGACCAAAAGAA
1D_0 TGTTTCCTAGACGGGAGTTCATCNNNNNTGAAATTCGGTTNTTATCCTTGACCTGGTGCCACCGCCTCAATCTCTTGATTTCAGACCAAAAGAA
2E_0 GGTTTCCTAGACGGGAGTTCATC----NTGAAATTCGGTTNTTATCCTTGACCTGGTGCCACCGCCTCAATCTCTTGATTTCAGACCAAAAGAA
2G_0 TGTTTCCTAGACGGGAGTTCATCNNNNNTGAAATTCGGTTNTTATCCTTGACCTGGTGCCACCGCCTCAATCTCTTGATTTCAGACCAAAAGAA
3I_0 TGTTTCCAAGACGGGAGTTCATCNNNNNTGAAATTCGGTTNTTATCCTTGACCTGGTGCCACCGCCTCAATCTCTTGATTTCAGACCAAAAGAA
// - - - |
1B_0 TCGTGATGGTGCTGACTCAATTGGTACTCTGGCACGAT-----TATGCCGCATAGCACCACCCGTGCCGGATTGGCACCGNNNNNNNNNACAAGTGTTAGGC
1C_0 TCGTGATGGTGCTGACTCAATTGGTACTCTGGCACGAT-----TATGCCGCATAGCACCACCCGTGCCGGATTGGCACCGNNNNNNNNNACAAGTGTTAGGC
2G_0 TCGTGATGGTGCTGACTCAATTGGTACTCTGGCACGAT-----TATGCCGCATAGCACCACCCGTGCCGGATTGGCACCGNNNNNNNNNACAAGTGTTAGGC
3I_0 TCGTGATGGTGCTGACTCAATTGGTACTCTGGCACGATNNNNNTATGCCGCATAGCACCACCCGTGCCGGATTGGCACCG-----NNNNACAAGTGTTAGGC
// |
sim_mt_genome
that isn't so much of a shit show. It has 24 sequences inserted from sim_rad_test_r1_
so that none are overlapping, no high indels errors even at low clustering thresholds.