These are chat archives for dereneaton/ipyrad

3rd
Dec 2018
Tonatiuh Ramírez Reyes
@tona30
Dec 03 2018 19:13
Hello!!
I have a problem generating vcf files from an assembly with a reference genome, I get this error: Value error (could not broadcast input array from shape (15) into shape (12). Do you know if it is a mistake of some dependency (eg numpy) ?? or by the parameters used ?? I'm doing the pipeline on a mac. Has someone had that same problem and solved it?
Tonatiuh Ramírez Reyes
@tona30
Dec 03 2018 19:38
Hi @isaacovercast
I have a problem generating vcf files from an assembly with a reference genome, I get this error: Value error (could not broadcast input array from shape (15) into shape (12). Do you know if it is a mistake of some dependency (eg numpy) ?? or by the parameters used ?? I'm doing the pipeline on a mac. Has someone had that same problem and solved it?
Isaac Overcast
@isaacovercast
Dec 03 2018 21:14
What version of ipyrad are you running?
What are your parameters?
Tonatiuh Ramírez Reyes
@tona30
Dec 03 2018 22:21
ipyrad v 0.7.28

pairgbs ## [7] [datatype]: Datatype (see docs): rad, gbs, ddrad, etc.

                           ## [8] [restriction_overhang]: Restriction overhang (cut1,) or (cut1, cut2)

5 ## [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
10000 ## [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
0 ## [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
5, 5 ## [19] [max_Ns_consens]: Max N's (uncalled bases) in consensus (R1, R2)
8, 8 ## [20] [max_Hs_consens]: Max Hs (heterozygotes) in consensus (R1, R2)
4 ## [21] [min_samples_locus]: Min # samples per locus for output
20, 20 ## [22] [max_SNPs_locus]: Max # SNPs per locus (R1, R2)
8, 8 ## [23] [max_Indels_locus]: Max # of indels per locus (R1, R2)
0.5 ## [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)

    [28] [pop_assign_file]: Path to population assignment file

those are my parameters
I did not indicate the parameter 8 because the data no longer have restriction enzyme
@isaacovercast
@isaacovercast

@tona30
ipyrad v 0.7.28
pairgbs ## [7] [datatype]: Datatype (see docs): rad, gbs, ddrad, etc.

                           ## [8] [restriction_overhang]: Restriction overhang (cut1,) or (cut1, cut2)

5 ## [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
10000 ## [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
0 ## [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
5, 5 ## [19] [max_Ns_consens]: Max N's (uncalled bases) in consensus (R1, R2)
8, 8 ## [20] [max_Hs_consens]: Max Hs (heterozygotes) in consensus (R1, R2)
4 ## [21] [min_samples_locus]: Min # samples per locus for output
20, 20 ## [22] [max_SNPs_locus]: Max # SNPs per locus (R1, R2)
8, 8 ## [23] [max_Indels_locus]: Max # of indels per locus (R1, R2)
0.5 ## [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)

    [28] [pop_assign_file]: Path to population assignment file

    those are my parameters
    I did not indicate the parameter 8 because the data no longer have restriction enzyme