These are chat archives for dereneaton/ipyrad

17th
May 2018
ClaudiaPaetzold
@ClaudiaPaetzold
May 17 2018 14:44
Hi! I was wondering how the statisics of step 6 are calculated. Especially regarding the number of clusters and singletons. Are these clusters those originating in step 3 or as a result from step 5 when clustering the consensus sequences? In any case, are the values averaged or summed up across samples? Thank you. Cheers Claudia
leclearnm
@leclearnm
May 17 2018 17:04
Hi @dereneaton
I am not sure if this is an ipyrad problem or not, but I am trying to run both ipyrad and tetrad through a cluster and coming up with the same issue. Can't tell if it something wrong on the software end (I just updated to the latest version) or with our facility, so I am checking here first.
ls5 nleclear@nid00016: /scratch/03530/nleclear/jatropha/ultimate/fw-full-4a $ tetrad -s jat-FW140-85.snps.phy -b 100 -c 24 -o 85m4
Thu May 17 11:56:57 2018: [unset]:_pmi_alps_get_apid:alps response not OKAY
Thu May 17 11:56:57 2018: [unset]:_pmi_init:_pmi_alps_init returned -1
[Thu May 17 11:56:57 2018] [c0-0c0s4n0] Fatal error in PMPI_Init_thread: Other MPI error, error stack:
MPIR_Init_thread(525): 
MPID_Init(225).......: channel initialization failed
MPID_Init(598).......:  PMI2 init failed: 1 
aborting job:
Fatal error in PMPI_Init_thread: Other MPI error, error stack:
MPIR_Init_thread(525): 
MPID_Init(225).......: channel initialization failed
MPID_Init(598).......:  PMI2 init failed: 1
Deren Eaton
@dereneaton
May 17 2018 18:03
@leclearnm hmm, seems like a strange error. Tetrad shouldn't try using MPI unless you specify the --MPI flag....
Hi @ClaudiaPaetzold, the number of clusters in step 6 comes from clustering all of the consensus sequences created in step 5. Their is only one number for the data set because the data come from all samples. Of those clusters, the number that are singletons is also shown. These are typically not included in downstream analyses since they contain no evolutionary information (there is no other sequence to compare them to).
leclearnm
@leclearnm
May 17 2018 18:18
@dereneaton it doesn't give me the error when I run tetrad on my laptop on the same data with the same commands. Seems like it must be an issue on our end of things. I'll check with them, thanks for the quick response