These are chat archives for dereneaton/ipyrad

8th
May 2018
Isaac Overcast
@isaacovercast
May 08 2018 15:10
@insectnate can you paste in your params file here?
@insectnate Also, what happens if you just try to run step 1?
@frogsicles_twitter Yeah, step 6 is currently a pretty significant bottleneck, especially for people with really big datasets or walltime limits. We have a good idea of how to parallelize the limiting substep in step 6, but unfortunately it's a pretty big chunk of work, so it's kind of on the back burner. Is there any way you can get more wall time? Sorry I don't really have a better idea for you at this point.
@insectnate Also, can you re-run your ipyrad command with the -d flag and email me the ipyrad_log.txt file:
ipyrad -p ipyrad_params -s 12 -d
Nathan Jones
@insectnate
May 08 2018 21:03
I get the same error running just ipyrad -p ipyrad_params -s 1 -c 8

Params file. ------- ipyrad params file (v.0.5.15)-------------------------------------------
ipyrad_params ## [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

/media/ddRADseq_1/samples_all_PE ## [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.
catg, aatt ## [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 0.97 ## [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 (5'>, <3') applies same to pairs (see docs)
0, 0, 0, 0 ## [26] [trim_loci]: Trim locus edges (see docs) (R1>, <R1, R2>, <R2)
p, s, v ## [27] [output_formats]: Output formats (see docs)

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

log file for ipyrad -p pyrad_params -s 12 -d -c 8 -------------------------------------------------------------
ipyrad [v.0.7.24]

Interactive assembly and analysis of RAD-seq data

Begin run: 2018-05-08 16:01
Using args {'preview': False, 'force': False, 'threads': 2, 'results': False, 'quiet': False, 'merge': None, 'ipcluster': None, 'cores': 8, 'params': 'ipyrad_params', 'branch': None, 'steps': '1', 'debug': True, 'new': None, 'download': None, 'MPI': False}
Platform info: ('Linux', desktop', '3.13.0-144-generic', '#193-Ubuntu SMP Thu Mar 15 17:03:53 UTC 2018', 'x86_64')2018-05-08 16:01:22,496 pid=29503 [init.py] INFO debugging turned off