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dereneaton / ipyrad

Interactive assembly and analysis of RAD-seq data sets
http://ipyrad.readthedocs.io
GNU General Public License v3.0
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problem with merging option on command line #573

Closed jesus-mavarez closed 3 months ago

jesus-mavarez commented 3 months ago

Hi I've been trying to merge two ddRAD libraries in iPyrad but, unless I'm wrong, without success. I started by running option s1 on a first library (Espeletia_1), then again option s1 on a second library (Espeletia _2). And then option m to create a new file, Espeletia, from the merging of the two initial ones. Everything seems to work OK. But when I check this new merged file I see that none of the individuals from the second library had reads that passed the filter (see below).

Do you have an idea about what might be going on?

Thanks in advance Jesús

Summary stats of Assembly Espeletia

             state  reads_raw  reads_passed_filter

annemariana 2 947128 943362 arbelaezii 2 440018 438224 argentea 2 693795 690925 azucarina 1 1138253 0 barclayana 2 2613124 2603714 betancurii 2 2019315 2013509 boyacensis 2 3283039 3270871 brachyaxiantha 2 367765 366800 brassicoidea 2 1009922 1006381 cachaluensis 1 1423092 0 caldasii 1 1134917 0 cayetana 1 3797915 0 chocontana 1 2248113 0 cleefii 1 956079 0 colombiana 1 1805740 0 congestiflora 2 2007420 2001116 conglomerata 1 516603 0 corymbosa 2 2159517 2153151 curialensis_Mo 2 3262190 3248883 curialensis_Pi 2 2368378 2360658 discoidea 1 209145 0 dugandii 1 674698 0 episcopalis 2 1280497 1276227 estanislana 1 216251 0 funckii 1 897898 0 garciae 2 2659343 2649519 glandulosa 2 1106622 1101259 grandiflora_Cg 2 561809 559791 grandiflora_Ru 2 3081000 3069182 grandiflora_Su 2 2792671 2783999 guacharaca 2 1101778 1097202 hartwegiana 1 1616675 0 hirbana 1 3399743 0 incana 2 1898196 1892411 insignis 1 1475116 0 jaramilloi 2 1353394 1348177 ....

isaacovercast commented 3 months ago

Hello, It looks like you did everything right and that the merge worked, but it looks like you ran steps 1 AND 2 on this first assembly. You can see from the stats that all the samples from the second library are in state 1 (which means they completed step 1) and the samples from the first library are in state 2 (which means the completed step 2). You can run step 2 on the merged assembly and it will complete step 2 only for the samples in state 1 (it won't redo step 2 for the samples form the first library).