Step 4: VsearchOUT.fa error

[Anoop Anand Malik]

Dear Aurthur,

I am trying to build a mock reference using Vsearch, where earlier it was Usearch. Please find the attached file in which I am facing the same error (Vsearch error) despite of trying it several time while changing the Lib.fq.gz  combinations.

Please guide me on this. The GBS-SNP-CROP-4.pl used in this pipeline was latest which was updated two months ago.

Thanks and regards

Anoop

India

[iago...@gmail.com]

Dear Aloop, very sorry for your troubles!  It looks like we have a typo in the example command lines for Script 4 in the User Manual!  The -db argument needs to be followed by a number.  In the sample command line, it is immediately followed by the -min argument, which is what is causing the problem.  Simplest solution is to follow -db with the number of genotypes being used for Mock Reference construction.  For example, if you are using only the single most read-abundant genotype, your command should be:

shashi_bhushan_tripathi@SBT:~/PTCMB/GBS-SNP-CROP-POLYGO/Polygo_Complete_Ananlysis/parsed/demultiplexed$ perl GBS-SNP-CROP-4.pl -vs /usr/local/bin/vsearch -d SE -b barcodesID.txt -t 10 -cl consout -p 0.01 -id 0.93 -db 1 -min 32 -MR POLYGO.MR

I hope that helps,

Iago

[iago...@gmail.com]

Also sorry for the typo in your name, Anoop!  I hope the pipeline proves useful for your research,

Iago

On Sunday, September 8, 2019 at 11:26:16 AM UTC-4, Anoop Anand Malik wrote: