These are chat archives for dereneaton/ipyrad

4th
Oct 2016
LinaValencia85
@LinaValencia85
Oct 04 2016 20:38

Hi, I have been running PYRAD for the past six months and I am now moving to IPYRAD. I have succesfully run IPYRAD with my data set, but realized that I was loosing 30% of the reads on step 2, so decided to trim both the cutsites and the last 10bp of the reads as they were low quality. I am now trying to run iPYRAD again and I am getting this error in s2: Step 2: Filtering reads
[####################] 100% processing reads | 0:02:17

Encountered an error, see ./ipyrad_log.txt.
IndexError(tuple index out of range)

Any ideas of what is going on? Thanks!
Deren Eaton
@dereneaton
Oct 04 2016 20:40
Hi @LinaValencia85, can you paste in your params file here.
LinaValencia85
@LinaValencia85
Oct 04 2016 20:42
This message was deleted

nwm ## [0] [assembly_name]: Assembly name. Used to name
./ ## [1] [project_dir]: Project dir (made in curdir if not p

                                     ## [2] [raw_fastq_path]: Location of raw non-d
                                     ## [3] [barcodes_path]: Location of barcodes file

../trimmed_deML/*.fq.gz ## [4] [sorted_fastq_path]: Location of
denovo ## [5] [assembly_method]: Assembly method (denovo,

                                     ## [6] [reference_sequence]: Location of reference 

pairddrad ## [7] [datatype]: Datatype (see docs): rad, gbs, ddrad,
CATGC, AATT ## [8] [restriction_overhang]: Restriction overhang
14 ## [9] [max_low_qual_bases]: Max low quality base 33 ## [10] [phred_Qscore_offset]: phred Q score offset
6 ## [11] [mindepth_statistical]: Min depth for statistical
6 ## [12] [mindepth_majrule]: Min depth for majority-
10000 ## [13] [maxdepth]: Max cluster depth within samples
0.90 ## [14] [clust_threshold]: Clustering threshold for de
0 ## [15] [max_barcode_mismatch]: Max number of
1 ## [16] [filter_adapters]: Filter for adapters/primers (1
30 ## [17] [filter_min_trim_len]: Min length of reads after 2 ## [18] [max_alleles_consens]: Max alleles
8, 8 ## [19] [max_Ns_consens]: Max N's (uncalled bases) in
12, 12 ## [20] [max_Hs_consens]: Max Hs (heterozygotes) in
97 ## [21] [min_samples_locus]: Min # samples per locus fo
30, 30 ## [22] [max_SNPs_locus]: Max # SNPs per locus (R1, R2)
12, 12 ## [23] [max_Indels_locus]: Max # of indels per locus
0.5 ## [24] [max_shared_Hs_locus]: Max # heterozygous sites

                              ## [25] [edit_cutsites]: Edit cut-sites (R1, R2) (see docs)

4, 4, 4, 4 ## [26] [trim_overhang]: Trim overhang (see docs) (R1>,

  • [27] [output_formats]: Output formats (see docs)

    ## [28] [pop_assign_file]: Path to population assignment 
LinaValencia85
@LinaValencia85
Oct 04 2016 20:48
@LinaValencia85 I just realized that I specified a cut site, when I actually deleted it from the read. Is that maybe the issue?
Deren Eaton
@dereneaton
Oct 04 2016 20:48
So you trimmed your data in other software before starting with ipyrad?
LinaValencia85
@LinaValencia85
Oct 04 2016 20:49
Yes, I trimmed my data with BBduk and demultiplexed in deML
Deren Eaton
@dereneaton
Oct 04 2016 20:53
Are you using the latest version of ipyrad (v.0.4.1)?
LinaValencia85
@LinaValencia85
Oct 04 2016 20:53
yup ipyrad 0.4.1
Deren Eaton
@dereneaton
Oct 04 2016 20:55
I have an idea of what the problem might be. I'm trying to replicate it now.
LinaValencia85
@LinaValencia85
Oct 04 2016 21:01
ok thanks!
Deren Eaton
@dereneaton
Oct 04 2016 21:33
@LinaValencia85 it is a little hard to tell from the print out, but it looks like you have an empty argument for param 25. The default is 0,0 and if it was empty that would raise an error like the one you printed. Could that be it?
LinaValencia85
@LinaValencia85
Oct 04 2016 21:35
Well before I had 4, 4, 4, 4 which was the param I was using before trimming cut sites, and I still got that error. I could try with 0,0 and see if it works.
Deren Eaton
@dereneaton
Oct 04 2016 21:35
try setting 25 to 0,0 and 26 to 0,0,0,0.
LinaValencia85
@LinaValencia85
Oct 04 2016 21:36
ok, should i also delete the cut sites on param #8?
Deren Eaton
@dereneaton
Oct 04 2016 21:38
They will have no effect on step 2 with your current settings (filter_adapters=1)
but, in step 7 the length of the cutsites will be trimmed from both reads at their ends.
LinaValencia85
@LinaValencia85
Oct 04 2016 21:39
ok , I will try like this and see if it work. Thanks!
Deren Eaton
@dereneaton
Oct 04 2016 21:39
so if you think you've removed them and don't want ipyrad to try to filter the cut sites at all then yes, you can leave that line blank.
Thanks, I'll try to add a more informative error message for that problem.
LinaValencia85
@LinaValencia85
Oct 04 2016 21:42
Also I wanted to ask you if its possible to do merge in s3 or s4?
Deren Eaton
@dereneaton
Oct 04 2016 21:45
I believe so, but @edgardomortiz raised an issue about this the other day that I haven't had time to investigate yet.