These are chat archives for dereneaton/ipyrad

27th
Mar 2017
Isaac Overcast
@isaacovercast
Mar 27 2017 12:51
@R2C2_Lab_twitter Pushed the new version to conda that fixes your problem.
R2C2.lab
@R2C2_Lab_twitter
Mar 27 2017 12:54
@isaacovercast great, thanks. I’ll try it now
Emily Warschefsky
@ewarschefsky_twitter
Mar 27 2017 15:59
@dereneaton @isaacovercast: since my workaround for the branching trouble didn't pan out, can you please make a fix for the original merging issue I had? I just ran a test dataset in the current version of ipyrad (0.6.11) and the issue happens in this dataset too. Here is the scenario: I want to run two separate datasets through steps 1-5, then merge, and run steps 6-7 together. When I do this, the merging appears successful, but in the end result, all of the samples from one dataset end up with NaN loci in the final assembly (see excerpt from stats file below)
## Final Sample stats summary

                             state  reads_raw  reads_passed_filter  clusters_total  clusters_hidepth  hetero_est  error_est  reads_consens  loci_in_assembly
11H_MI_86_M_casturi_982186A      7    1335965              1332020          534065             30781    0.011143   0.001592          29753               NaN
14G_JFL_501_M_caesia_wanji       7    1496010              1492644          775729             26925    0.005996   0.001521          26265            1835.0
15D_FTG_1_M_sp_Vietnam           7     101792               101524           86561               526    0.008713   0.004157            484             227.0
16H_PA_3_M_quadrifida            7    1443282              1440350          761354             30598    0.010463   0.002188          29311            5215.0
3F_MI_69_Langra_Benarsi          7     798799               796282          457765             10174    0.009939   0.001874           9622               NaN
6C_MI_11_Nam_Doc_Mai             7     603488               599741          301444              9517    0.009598   0.002169           9075               NaN
AA_FS2_M_zeylanica               7    1389807              1386636          686341             26091    0.010716   0.002245          24976            5224.0
AG_K2_M_odorata                  7    1483656              1480362          776665             27873    0.010701   0.002234          26666            5398.0
EA_KRB_4_M_gedebe                7    1210992              1208381          596540             24109    0.008039   0.002289          23186            4688.0
EG_MI_85_M_laurina_1_B4          7    1466982              1463798          621012             28692    0.010336   0.002292          27422            5094.0
GD_KRB_7__M_applanata            7     947622               945449          489710             17949    0.005257   0.001837          17469            1731.0
IB_KRB_6_M_oblongifolia          7     778298               776431          407567             18744    0.006147   0.002045          18266            4692.0
IC_MI_59_M_lalijiwa_G            7    1167782              1164382          563051             20619    0.010808   0.002514          19583            5112.0
KA_CL_1_M_altissima              7    1311074              1308227          679208             26801    0.011753   0.002648          25391            5363.0
LE_CL_3_M_monandra               7    1165246              1162582          604091             20465    0.010302   0.002312          19550            4658.0
NH_PF_2_M_superba                7     968760               966743          475487             21923    0.005540   0.001479          21484            1722.0
OD_PF_25_G_malayana              7    1328115              1325679          819628             21129    0.014327   0.006888          18682             392.0
OF_SBG_13_Boppositifolia         7     761593               759423          396785             19242    0.008445   0.004488          18016            1482.0
PE_PF_22_M_magnifica             7    1546703              1543217          738611             33049    0.010136   0.002069          31838            4926.0
PF_PF_18_M_subsessilifolia       7     523956               522383          306945             10543    0.007914   0.002157          10185            2622.0
QC_FS_3_A_occidentale            7    1410021              1405119          767078             27478    0.007481   0.002589          26320             725.0
QF_SBB_21_M_pedicillata          7    1301507              1298089          692195             25298    0.008222   0.002027          24403            4943.0
RB_SBG_10_M_pajang               7    1169736              1166558          601937             24423    0.006150   0.001849          23731            5046.0
TB_KRP_2_M_minor                 7    1587805              1582043          743501             34009    0.009178   0.001760          32912               NaN
TC_KRB_2_M_similis               7    1755500              1746502          775988             35791    0.011136   0.001937          34347               NaN
TF_KRB_30_M_rufocostata          7    2007780              2001156          839841             34837    0.009375   0.001578          33616               NaN
TG_MI_165_M_griffithii           7    2155304              2148944          865270             39609    0.015266   0.002240          37392               NaN
UC_KRP_17_M_macrocarpa           7    2654845              2641544          947565             43674    0.006830   0.001463          42273               NaN
UG_PF_10_M_gracilipes            7    2893575              2884577          733235             54982    0.007792   0.001226          53708               NaN
XB_SBG_6_M_torquenda             7    1559839              1553874          605809             33272    0.007635   0.001599          32348               NaN
XC_SBG_8_B_macrophylla           7    1161155              1154633          597635             24221    0.010416   0.003702          22571               NaN
XG_FRIM_2_M_foetida              7    1479415              1474907          682479             29457    0.007872   0.001519          28570               NaN
ZA_SBG_7a_M_kemanga              7     825693               823307          426124             14665    0.005250   0.001355          14411               NaN
ZG_SBG_26_M_pentandra            7     823561               821061          451157             14366    0.011119   0.001766          13769               NaN
Emily Warschefsky
@ewarschefsky_twitter
Mar 27 2017 16:47
Regarding the above - I have figured out a solution that seems to be working - if I run steps 1-5, merge, then rerun from step 4 instead of step 6, the output seems to be fine. (In the future I will just run the separate datasets through steps 1-3 instead of 1-5...).