Question

[Thierry Gosselin]

Hi Mike,

So I would like to test your pipeline and compare it to what I have with Stacks.

I have 455 individuals.

Will test AdtrRAD with 1 lane

This lane as 48 individuals barcoded (the file is 15GB and compress gz format)

I have put the file in the Data folder

Provided the list of Barcode and Name I would like to have for the individual fq files. This file reside in the Barcodes folder.

I'm using GBS with 2 enzymes (Pst1 and Msp1) so I guess I should run the first part of the pipeline like this:

perl AftrRAD.pl re-TGCAG 

I get this output:

Arguments entered are...

dplexedData     0

P2      ATTAGATC

minParalog      5

Help    0

minIden 90

BarcodePath     Barcodes/

MaxH    90

minQual 20

re      TGCAG

Phred   33

minDepth        5

numIndels       3

stringLength    15

DataPath        Data/

Running AftrRAD...

Recognized 1 data files.

File names are...

 barcode_L06.txt 

The barcodes you entered for data file 1 (file barcode_L06.txt) are...

 CTATTA CTTGCTT AATATGG GCGGAAT TGCAAGGA CCATGGGT GCCAGT ATGAAAG ACGTGTT TAGCGGA TGGTACGT CGCGGAGA GGAAGA AAAAGTT ATTAATT TCGAAGA TCTCAGTG CGTGTGGT GTACTT GAATTCA ATTGGAT TCTGTGA CGCGATAT GCTGTGGA GTTGAA GAACTTG CATAAGT TGCTGGA CGCCTTAT GGATTGGT TAACGA GGACCTA CGCTGAT ACGACTAG AACCGAGA GTGAGGGT TGGCTA GTCGATT CGGTAGA TAGCATGG ACAGGGA TATCGGGA TATTTTT AACGCCT CTACGGA TAGGCCAT ACGTGGTA TTCCTGGA 

The names you entered for data file 1 (file barcode_L06.txt) are...

 EST-GRA-ADU-2013-012 EST-GRA-ADU-2013-013 EST-GRA-ADU-2013-014 EST-GRA-ADU-2013-015 EST-GRA-ADU-2013-016 EST-GRA-ADU-2013-017 EST-GRA-ADU-2013-024 EST-GRA-ADU-2013-025 EST-GRA-ADU-2013-026 EST-GRA-ADU-2013-027 EST-GRA-ADU-2013-028 EST-GRA-ADU-2013-029 EST-GRA-ADU-2013-036 EST-GRA-ADU-2013-037 EST-GRA-ADU-2013-038 EST-GRA-ADU-2013-039 EST-GRA-ADU-2013-040 EST-GRA-ADU-2013-041 EST-GRA-ADU-2013-048 EST-GUL-ADU-2013-001 EST-GUL-ADU-2013-002 EST-GUL-ADU-2013-003 EST-GUL-ADU-2013-004 EST-GUL-ADU-2013-005 EST-GUL-ADU-2013-012 EST-GUL-ADU-2013-013 EST-GUL-ADU-2013-014 EST-GUL-ADU-2013-015 EST-GUL-ADU-2013-016 EST-GUL-ADU-2013-017 EST-GUL-ADU-2013-024 EST-GUL-ADU-2013-025 EST-GUL-ADU-2013-026 EST-GUL-ADU-2013-027 EST-GUL-ADU-2013-028 EST-GUL-ADU-2013-029 EST-GUL-ADU-2013-036 EST-GUL-ADU-2013-037 EST-GUL-ADU-2013-038 EST-GUL-ADU-2013-039 EST-GUL-ADU-2013-040 EST-GUL-ADU-2013-041 EST-GUL-ADU-2013-048 EST-HAY-ADU-2013-001 EST-HAY-ADU-2013-002 EST-HAY-ADU-2013-004 EST-HAY-ADU-2013-005 EST-HAY-ADU-2013-006 

No such file or directory at AftrRAD.pl line 513.

What I'm I doing not correctly ?

Thanks

Thierry

[Mike Sovic]

Hi Thierry,

My first guess is that you need to unzip your data file.  With a .gz file, you should be able to use the gunzip command to do this. Then make sure the name of the unzipped file is exactly the same as the name of the barcode file (which in your case looks like barcodes_L06.txt).  Give this a try and let us know if it still doesn't work.

              Mike