Closed jiangqiuqiuu closed 1 year ago
Hi Qiuyu,
Not sure what has changed, but my guess is that pixy is having trouble with your chromosome column (formatted with |
characters). That might not be supported, I'll have to take a look into that.
Also, just FYI, the --bypass_invariant_check
option should basically never be used for real data (hence the warning). The calculations will be way off in most cases.
Cheers,
Kieran
Hi Kieran,
Thank you for your response! Could you suggest any solutions to this problem here? I appreciate your help!
Cheers Qiuyu
Hi Qiuyu,
I won't be able to change anything on my end until after Christmas, but you could try stripping the "|quiver|pilon-snap-gene-0.22-mRNA-1" from each of your contig identifiers.
Perhaps something like:
zcat your.vcf.gz | sed 's/|.*|.*//g' | bgzip -c > your.new.vcf.gz
tabix your.new.vcf.gz
Hi Qiuyu, did you find a solution for your issue? If not, feel free to reopen this issue.
Hi, I am trying to run pixy on my laptop with the cmd:
pixy --stats pi dxy fst --vcf populations.snps_sorted.vcf.gz --population sel_ariz.list --window_size 10000 --bypass_invariant_check yes
,The error msg was: `[pixy] pixy 1.2.7.beta1 [pixy] See documentation at https://pixy.readthedocs.io/en/latest/
[pixy] Validating VCF and input parameters... [pixy] Checking write access...OK [pixy] Checking CPU configuration...OK [pixy] Checking for invariant sites...WARNING [pixy] EXTREME WARNING: --bypass_invariant_check is set to 'yes'. Note that a lack of invariant sites will result in incorrect estimates. [pixy] Checking chromosome data...OK [pixy] Checking intervals/sites...OK [pixy] Checking sample data...OK [pixy] All initial checks past!
[pixy] Preparing for calculation of summary statistics: pi, dxy, fst [pixy] Using Weir and Cockerham (1984)'s estimator of FST. [pixy] Data set contains 11 population(s), 2913 chromosome(s), and 100 sample(s) [pixy] Window size: 10000 bp
[pixy] Started calculations at 23:34:26 on 2022-12-09 [pixy] Using 1 out of 8 available CPU cores
[pixy] Processing chromosome/contig maker-Contig264|quiver|pilon-snap-gene-0.22-mRNA-1... /bin/sh: quiver: command not found /bin/sh: pilon-snap-gene-0.22-mRNA-1: command not found IndexError: list index out of range`
I am not sure what's going on here as I ran pixy successfully last time...
Here is a part of the vcf file I was trying to inout:
maker-Contig264|quiver|pilon-snap-gene-0.22-mRNA-1 861 7:111:- C T . PASS NS=80;AF=0.288 GT:DP:AD:GQ:GL ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. 0/1:69:45,24:40:-46.13,0,-105.31 1/1:117:0,117:40:-326.73,-34.94,0 ./.:.:.:.:. 0/0:161:161,0:40:0,-48.61,-450.69 0/0:22:22,0:40:-0,-6.87,-61.98 1/1:20:0,20:40:-55.47,-5.81,-0 0/0:26:25,1:40:-0,-5.27,-67.57 0/1:111:49,62:40:-139.78,0,-103.89 0/0:2:2,0:13:-0.06,-0.92,-6.1 0/1:43:20,23:40:-51.15,0,-43.21 1/1:11:0,11:38:-30.31,-3.11,-0 0/1:21:3,18:29:-43.77,-0,-2.28 0/1:70:30,40:40:-90.58,0,-63.07 1/1:78:0,78:40:-217.67,-23.23,0 0/1:94:43,51:40:-114.13,0,-92.21 ./.:.:.:.:. 0/1:5:2,3:40:-6.63,-0,-4.29 1/1:17:0,17:40:-47.09,-4.91,-0 1/1:18:0,18:40:-49.88,-5.21,-0 0/1:23:5,18:40:-43.17,-0,-7.27 ./.:.:.:.:. 0/1:26:8,18:40:-42.27,0,-14.76 0/1:15:6,9:40:-20.4,-0,-12.47 1/1:83:0,83:40:-231.65,-24.73,0 1/1:13:0,12:40:-33.1,-3.41,-0 0/1:143:55,87:40:-200.39,0,-111.35 1/1:124:0,124:40:-346.31,-37.05,0 1/1:221:0,220:40:-614.77,-65.88,0 ./.:.:.:.:. 0/1:103:57,45:40:-94.95,0,-128.96 0/0:19:19,0:40:-0,-5.97,-53.59 0/0:20:20,0:40:-0,-6.27,-56.38 0/0:15:15,0:40:-0,-4.76,-42.4 0/0:29:29,0:40:-0,-8.97,-81.55 0/0:14:14,0:40:-0,-4.46,-39.61 0/0:88:87,0:40:-0,-26.39,-243.75 0/0:127:127,0:40:0,-38.4,-355.61 0/0:20:19,0:40:-0,-5.97,-53.59 0/0:14:13,1:22:-0.01,-1.68,-34.02 0/0:11:11,0:40:-0,-3.56,-31.22 ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. 0/0:67:67,0:40:0,-20.38,-187.82 0/0:199:199,0:40:-0,-60.03,-556.95 0/0:54:54,0:40:-0,-16.48,-151.46 0/0:25:25,0:40:-0,-7.77,-70.37 0/0:307:307,0:40:0,-92.46,-858.97 0/0:616:611,4:40:0,-173.78,-1697.91 0/0:89:88,0:40:0,-26.69,-246.54 0/0:189:189,0:40:0,-57.02,-528.99 0/0:58:57,0:40:0,-17.38,-159.85 0/0:107:106,0:40:0,-32.09,-296.88 0/0:2:2,0:13:-0.06,-0.92,-6.1 0/0:140:140,0:40:0,-42.31,-391.96 0/1:73:34,38:40:-84.38,0,-73.65 ./.:.:.:.:. ./.:.:.:.:. 0/1:137:66,71:40:-157.14,0,-143.62 ./.:.:.:.:. ./.:.:.:.:. 0/0:4:4,0:20:-0.01,-1.48,-11.66 0/0:29:29,0:40:-0,-8.97,-81.55 0/0:97:96,0:40:0,-29.09,-268.92 0/0:55:55,0:40:0,-16.78,-154.26 0/0:131:131,0:40:0,-39.6,-366.79 0/0:60:60,0:40:0,-18.28,-168.24 0/0:357:354,0:40:0,-106.58,-990.41 0/0:258:255,0:40:0,-76.84,-713.56 0/0:57:57,0:40:0,-17.38,-159.85 0/0:11:11,0:40:-0,-3.56,-31.22 0/0:263:263,0:40:0,-79.25,-735.93 0/0:167:167,0:40:0,-50.42,-467.47 ./.:.:.:.:. 0/0:56:56,0:40:0,-17.08,-157.06 0/0:45:44,0:40:-0,-13.47,-123.5 0/0:32:32,0:40:-0,-9.87,-89.94 0/0:27:27,0:40:-0,-8.37,-75.96 ./.:.:.:.:. 0/0:55:54,0:40:0,-16.48,-151.46 0/0:48:48,0:40:-0,-14.68,-134.69 0/0:36:36,0:40:-0,-11.07,-101.13 0/0:17:17,0:40:-0,-5.36,-47.99 0/1:16:3,13:40:-31.29,-0,-3.78 0/1:79:62,17:40:-23.55,0,-149.85 0/0:4:4,0:20:-0.01,-1.48,-11.66 0/0:7:7,0:30:-0,-2.36,-20.03 1/1:25:2,23:23:-58.28,-1.73,-0.01 1/1:26:0,26:40:-72.25,-7.61,-0 1/1:154:0,154:40:-430.2,-46.06,0 1/1:295:0,295:40:-824.5,-88.4,-0 1/1:100:0,100:40:-279.19,-29.84,0 0/0:131:131,0:40:0,-39.6,-366.79
And here is the pop file: sel_ariz.txt
Thank you for your help! Qiuyu