These are chat archives for dereneaton/ipyrad

30th
Apr 2017
Edgardo M. Ortiz
@edgardomortiz
Apr 30 2017 18:43

Hi @dereneaton and @isaacovercast, I split this dataset in 6 subsets, and ran steps 1-3 on each subset, then I merged them, but when running step 4 on the merged dataset ipyrad looks for the clustS.gz for the other subsets inside the clust folder of the first one (/scratch/01982/jdpalaci/ddrad/e_PE-86_ipyrad/pana-pe_clust_0.86/ while the other clustS.gz are in panb-pe panc-pe pand-pe etc.)


 -------------------------------------------------------------
  ipyrad [v.0.6.17]
  Interactive assembly and analysis of RAD-seq data
 -------------------------------------------------------------
  loading Assembly: panicum-pe
  from saved path: /scratch/01982/jdpalaci/ddrad/e_PE-86_ipyrad/panicum-pe.json
  host compute node: [48 cores] on nid00874

  Step 4: Joint estimation of error rate and heterozygosity
  [####################] 100%  inferring [H, E]      | 0:00:15  ERROR:ipyrad.assemble.util:  Sample ALI_07-G1_HAL_010 failed with error IOError([Errno 2] No such file or directory: '/scratch/01982/jdpalaci/ddrad/e_PE-86_ipyrad/pana-pe_clust_0.86/ALI_07-G1_HAL_010.clustS.gz')
ERROR:ipyrad.assemble.util:  Sample SEV_04-F_HAL_291 failed with error IOError([Errno 2] No such file or directory: '/scratch/01982/jdpalaci/ddrad/e_PE-86_ipyrad/pana-pe_clust_0.86/SEV_04-F_HAL_291.clustS.gz')
ERROR:ipyrad.assemble.util:  Sample GNZ_27-F_FIL_489 failed with error IOError([Errno 2] No such file or directory: '/scratch/01982/jdpalaci/ddrad/e_PE-86_ipyrad/pana-pe_clust_0.86/GNZ_27-F_FIL_489.clustS.gz')
ERROR:ipyrad.assemble.util:  Sample LBY_03-G1_HAL_195 failed with error IOError([Errno 2] No such file or directory: '/scratch/01982/jdpalaci/ddrad/e_PE-86_ipyrad/pana-pe_clust_0.86/LBY_03-G1_HAL_195.clustS.gz')
ERROR:ipyrad.assemble.util:  Sample GIL_19-F_HAL_164 failed with error IOError([Errno 2] No such file or directory: '/scratch/01982/jdpalaci/ddrad/e_PE-86_ipyrad/pana-pe_clust_0.86/GIL_19-F_HAL_164.clustS.gz')
ERROR:ipyrad.assemble.util:  Sample SOM_03_F_HAL_654 failed with error IOError([Errno 2] No such file or directory: '/scratch/01982/jdpalaci/ddrad/e_PE-86_ipyrad/pana-pe_clust_0.86/SOM_03_F_HAL_654.clustS.gz')
ERROR:ipyrad.assemble.util:  Sample SAP_01_F_HAL_592 failed with error IOError([Errno 2] No such file or directory: '/scratch/01982/jdpalaci/ddrad/e_PE-86_ipyrad/pana-pe_clust_0.86/SAP_01_F_HAL_592.clustS.gz')
ERROR:ipyrad.assemble.util:  Sample HAR_03_F_CAP_711 failed with error IOError([Errno 2] No such file or directory: '/scratch/01982/jdpalaci/ddrad/e_PE-86_ipyrad/pana-pe_clust_0.86/HAR_03_F_CAP_711.clustS.gz')

I fixed it making symbolic links to the clustS in folder pana-pe but I thought you may want to know about this bug.

Ivan Prates
@ivanprates
Apr 30 2017 19:59
Dear @isaacovercast and @dereneaton, I'm running genome-environment association analyses and one key step is to blast and annotate those loci that have SNPs associated with environmental variables. I wrote some R code to do that based on the .loci and .snps.map files produced by ipyrad, but this only works with linked SNPs. I couldn't come up with a way of tracing back to each locus' sequence (in order to blast) from the unlinked SNPs. Would it be possible to include a .u.snps.map as an output of ipyrad, that is, a SNP map of the unlinked SNPs as well? Thanks much!
Deren Eaton
@dereneaton
Apr 30 2017 20:28
@ivanprates yeah, we should be able to do that.
Thanks @edgardomortiz , yeah we should fix that.