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dereneaton / ipyrad

Interactive assembly and analysis of RAD-seq data sets
http://ipyrad.readthedocs.io
GNU General Public License v3.0
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Barcode file not being read, unsure if this is a params issue or a continued formatting error? #436

Closed konradtaube closed 3 years ago

konradtaube commented 3 years ago

Hi, I wanted to try to submit another issue to see if there is something I am doing wrong here with my early on assembly and I believe it is due to my barcode text file but I am not sure.

Here is the error message I am receiving with the following command:

ipyrad -p params-masters-thesis.txt -s 1 -r

ipyrad.assemble.utils.IPyradError: One or more barcodes contain invalid IUPAC nucleotide code characters. Barcodes must contain only characters from this list "RKSYWMCATG". Doublecheck your barcodes file is properly formatted.

My text document, GBS-PstI-barcodes.txt contains the following:

1A CTCTCCAG 1B TAATTG 1C ATCTCGT 1D GACAACT 1E CTCGCAA 1F TGGACACT 1G TGTCAAT 1H TCCTGCT 2A GAACTT 2B ATGCT 2C ATTCCAA 2D GACACACT 2E CGCGT 2F CATACGCG 2G CTATCACT 2H CTGAACCA 3A TCTCCGT 3B TGTACA 3C AAGCAACT 3D ACCGA 3E GTAAG 3F TGATCGCT 3G TGCGG 3H ACTAA 4A GAGGTCCT 4B TAGCTAT 4C CAGCGCAAGA 4D GCTCGCCAT 4E TGTACCAG 4F TGTACGCA 4G TTGGCGCT 4H GTTCACA 5A CATGG 5B ACTACAAT 5C GACTAACT 5D ATGGTGA 5E TATTGCAG 5F ATCTGACT 5G GTCACGA 5H AACGACCACA 6A CGCCTCAT 6B CTTATG 6C TAGAG 6D GGCAT 6E CCGACG 6F TGGTCAAG 6G ACCAAG 6H CCATCCAA 7A GTTCGGT 7B GCCGCAAT 7C CATAAG 7D TTGAGACAG 7E ACCGTCCAT 7F GCGTGCCAGA 7G CCGAT 7H TCCTCCA 8A ACACG 8B CGCAAGA 8C ACACAACA 8D ATATT 8E GTCTCAACG 8F CCGCA 8G TCGTGACAGT 8H AATTG 9A TCCGT 9B TATAAGCAG 9C ATTCA 9D ACATGCCAG 9E TGCCTA 9F AAGGCCAACT 9G ACTCCACG 9H GGTTG A10 TTCTCA B10 CTGCCGT C10 TTCCA D10 GAGCGCT E10 TAATTAA F10 TGTGAGG G10 TGTTGACG H10 TACCT A11 CCAGGA B11 GGATGA C11 ACAGAAT D11 ATACTGAG E11 CTCCAA F11 TTAGGA G11 CCAAGACAGT H11 CATTGA A12 TCATT B12 GAATAGA C12 TTCTG D12 ACCTAA E12 GCGTAG F12 CGTAGCAACA G12 AAGCAGA H12 CAATTGCT

I’m not really sure what the problem could be with the above file, so maybe it’s something in my parameter file? Here are the first few lines of the params file:

masters-thesis ## [0] [assembly_name]: Assembly name. Used to name output directories for assembly steps

analysis-ktaube ## [1] [project_dir]: Project dir (made in curdir if not present)

/home/FM/ktaube/201105_AHLVWJDSXY/McMahan-GBS_S29_L001_R1_001.fastq ## [2] [raw_fastq_path]: Location of raw non-demultiplexed fastq files

/home/FM/ktaube/201105_AHLVWJDSXY/McMahan-GBS_S29_L001_R2_001.fastq ## [2] [raw_fastq_path]: Location of raw non-demultiplexed fastq files

/home/FM/ktaube/201105_AHLVWJDSXY/GBS-PstI-barcodes-idless.txt ## [3] [barcodes_path]: Location of barcodes file

So I have my R1 and R2 both in the raw fastq path for [2], the barcode text file is there in [3], and nothing is in [4]. Any advice or troubleshooting suggestions would be greatly appreciated!

isaacovercast commented 3 years ago

The name of the barcodes file you post here which looks good GBS-PstI-barcodes.txt is not the same as the name of the barcodes file in your params file /home/FM/ktaube/201105_AHLVWJDSXY/GBS-PstI-barcodes-idless.txt, probably still pointing to the old bad barcodes file, no?

isaacovercast commented 3 years ago

These don't seem to be "issues" with ipyrad per se and rather questions about running it, which are much better addressed on our gitter channel: https://gitter.im/dereneaton/ipyrad

If you have questions about installation and running, this is a better place for things like these. Feel free to join the convo over there!