These are chat archives for dereneaton/ipyrad

17th
Feb 2018
Glib Mazepa
@mazepago_twitter
Feb 17 2018 20:29

Hi @isaacovercast @dereneaton I am trying version 0.7.22 on a test dataset of just 2 samples from paired end sequencin and encountered an ERROR 'task_scheme' at the step 1, any guess what could be the cause? All inputs seem to be in order (named like P_01R1.fastq & P_01R2.fastq) as well as the reference_genome.fa and the barcodes, here is the params_file.txt: ------- ipyrad params file (v.0.7.22)-------------------------------------------
17_Feb ## [0] [assembly_name]:
./ ## [1] [project_dir]:

                           ## [2] [raw_fastq_path]: 

./barcodes.txt ## [3] [barcodes_path]:
/home/gmazepa/ul/PelPhylo/home/gmazepa/ul/ipyrad_inputs_test_17_Feb_2018_unassembled_R1_R2/*fastq ## [4] [sorted_fastq_path]:
denovo+reference ## [5] [assembly_method]:
/home/GENOME_Ples_Jose_stitched/Les_Jose.oneline.longer190.stitched.fa ## [6] [reference_sequence]
ddrad ## [7] [datatype]
TGCAGG,CGG ## [8] [restriction_overhang]
5 ## [9] [max_low_qual_bases]
33 ## [10] [phred_Qscore_offset]
6 ## [11] [mindepth_statistical]
6 ## [12] [mindepth_majrule]
10000 ## [13] [maxdepth]
0.90 ## [14] [clust_threshold]
0 ## [15] [max_barcode_mismatch]
0 ## [16] [filter_adapters]
35 ## [17] [filter_min_trim_len]
2 ## [18] [max_alleles_consens]
5, 5 ## [19] [max_Ns_consens]
8, 8 ## [20] [max_Hs_consens]
4 ## [21] [min_samples_locus]
20, 20 ## [22] [max_SNPs_locus]
8, 8 ## [23] [max_Indels_locus]
0.5 ## [24] [max_shared_Hs_locus]
0, 0, 0, 0 ## [25] [trim_reads]
0, 0, 0, 0 ## [26] [trim_loci]

  • [27] [output_formats]

    [28] [pop_assign_file]

Isaac Overcast
@isaacovercast
Feb 17 2018 22:05
@campanam In a denovo assembly the CHROM column of the output vcf indicates which locus each snp is derived from. So you can map 'locus_x' in the vcf to the actual locus in the .loci file.
Isaac Overcast
@isaacovercast
Feb 17 2018 22:12
@mazepago_twitter What version of ipcluster do you have installed? this looks like an ipcluster issue (but an old one): https://github.com/ipython/ipython/issues/3862/
try running python by hand, and then import ipcluster and then print(ipcluster.__version__)
Also if you can try running ipyrad step 1 with the -d flag and post the last few lines of the ipyrad_log.txt file that would be helpful.
you might just try conda install ipcluster -f and see if that pulls down the latest version.