These are chat archives for dereneaton/ipyrad

9th
Apr 2017
Edgardo M. Ortiz
@edgardomortiz
Apr 09 2017 04:43

Hi @dereneaton @isaacovercast , I have found this bug when trying to assign a popfile in v0.6.11:


 -------------------------------------------------------------
  ipyrad [v.0.6.11]
  Interactive assembly and analysis of RAD-seq data
 -------------------------------------------------------------
  New Assembly: dman-PE
    Error setting parameter 'pop_assign_file'
    'NoneType' object has no attribute '__getitem__'
    You entered: ./popfile.txt

I guess I can run all steps except 7 without this parameter set in the meanwhile, right?

Isaac Overcast
@isaacovercast
Apr 09 2017 06:02
Hey @edgardomortiz , can you post your params file and the pop_assign_file you're trying to use?
Edgardo M. Ortiz
@edgardomortiz
Apr 09 2017 07:11
Thanks @isaacovercast , here it goes:
------- ipyrad params file (v.0.6.11)-------------------------------------------
dman-PE                        ## [0] [assembly_name]: Assembly name. Used to name output directories for assembly steps
./                             ## [1] [project_dir]: Project dir (made in curdir if not present)
                               ## [2] [raw_fastq_path]: Location of raw non-demultiplexed fastq files
                               ## [3] [barcodes_path]: Location of barcodes file
./dman-PE_fastqs/*.fq.gz       ## [4] [sorted_fastq_path]: Location of demultiplexed/sorted fastq files
denovo                         ## [5] [assembly_method]: Assembly method (denovo, reference, denovo+reference, denovo-reference)
                               ## [6] [reference_sequence]: Location of reference sequence file
pairddrad                      ## [7] [datatype]: Datatype (see docs): rad, gbs, ddrad, etc.
CATGC, AATTC                   ## [8] [restriction_overhang]: Restriction overhang (cut1,) or (cut1, cut2)
10                             ## [9] [max_low_qual_bases]: Max low quality base calls (Q<20) in a read
33                             ## [10] [phred_Qscore_offset]: phred Q score offset (33 is default and very standard)
6                              ## [11] [mindepth_statistical]: Min depth for statistical base calling
6                              ## [12] [mindepth_majrule]: Min depth for majority-rule base calling
9999999999                     ## [13] [maxdepth]: Max cluster depth within samples
0.85                           ## [14] [clust_threshold]: Clustering threshold for de novo assembly
0                              ## [15] [max_barcode_mismatch]: Max number of allowable mismatches in barcodes
2                              ## [16] [filter_adapters]: Filter for adapters/primers (1 or 2=stricter)
35                             ## [17] [filter_min_trim_len]: Min length of reads after adapter trim
2                              ## [18] [max_alleles_consens]: Max alleles per site in consensus sequences
96, 101                        ## [19] [max_Ns_consens]: Max N's (uncalled bases) in consensus (R1, R2)
96, 101                        ## [20] [max_Hs_consens]: Max Hs (heterozygotes) in consensus (R1, R2)
4                              ## [21] [min_samples_locus]: Min # samples per locus for output
96, 101                        ## [22] [max_SNPs_locus]: Max # SNPs per locus (R1, R2)
96, 101                        ## [23] [max_Indels_locus]: Max # of indels per locus (R1, R2)
1.0                            ## [24] [max_shared_Hs_locus]: Max # heterozygous sites per locus (R1, R2)
0, 0, 0, 0                     ## [25] [trim_reads]: Trim raw read edges (R1>, <R1, R2>, <R2) (see docs)
0, 0, 0, 0                     ## [26] [trim_loci]: Trim locus edges (see docs) (R1>, <R1, R2>, <R2)
*                              ## [27] [output_formats]: Output formats (see docs)
./popfile.txt                  ## [28] [pop_assign_file]: Path to population assignment file

head popfile.txt
BUX-EO2739    BUX
HYB-EO2244    HYB
HYB-EO2729-1    HYB
HYB-EO2729-2    HYB
HYB-EO2730-1    HYB
HYB-EO2730-2    HYB
M01-EO2338    M01
M01-EO2344    M01
M01-EO2708    M01
M01-EO2709    M01

tail popfile.txt
M11-EO2610    M11
M11-EO2611    M11
SIP-EO2587    SIP
SPE-EO2235    SPE
SPE-EO2242    SPE
SPE-EO2533    SPE
SPE-EO2549    SPE
SPE-EO2627    SPE
SPE-EO2686    SPE
SPE-EO2735    SPE
Isaac Overcast
@isaacovercast
Apr 09 2017 09:44
@edgardomortiz Ah, I see. The population assignment file needs to contain a line specifying the minimum number of samples per population for retaining loci at step 7 (this is really the only thing it is currently used for is per population min sample filtering): http://ipyrad.readthedocs.io/parameters.html?highlight=pop_assign#pop-assign-file
There's an example of what this line should look like in that docs page.