pcr.seqs bug in 1.34.1

mothur bugs
1

Bonsoir

pcr.seqs does not work for me anymore. I am using the following command:

pcr.seqs(fasta=pr2.fasta, taxonomy=pr2.tax, oligos=Oligos_V4_Chlo.txt, pdiffs=0, keepdots=F, processors=8)

With version 1.33.3 I was able to trim to the V4 region of the 18S rRNA gene and with version 1.34.1 nothing happens…

Before pcr.seqs

JN207865.1.848_U
ATTCCAGCTCCAATAGCGTATATTTAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCGGGTGGGCGTTAGCGGTCCGGCTCT
GCTGTGTACTGCTAGTGCCTATCTTTCTGTCGGGGACGGGCTCTTGGGCTTCATTGTCCGGGACTCGGAGTCGACGTGGTTACTT
TGAGTAAATTAGAGTGTTCAAAGCAAGCGTTCGCTGTGAATACATTAGCATGGAATAACACGATAGGACTCTGGCTTATCTTGTTG
GTCTGTAAGACCGGAGTAATGATTAAGAGGGACAGTCGGGGGCATTCGTATTTCATTGTCAGAGGTGAAATTCTTGGATTTATGA
AAGACGAACTTCTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATTAGATACCG
TCGTAGTCTCAACCATAAACGATGCCGACTAGGGATTGGCAGGTGTTTCGTTGATGACCCTGCCAGCACCTTATGAGAAATCAAAG
TTTTTGGGTTCCGGGGGGAGTATGGTCGCAAGGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGCGTGGAGCCTGCG
GCTTAATTTGACTCAACACGGGGAAACTTACCAGGTCCAGACACGGGGAGGATTGACAGATTGAGAGCTCTTTCTTGATTCTGTG
GGTGGTGGTGCATGGCCGGTTCTTAGTTGGTGGGTTGCCTTGTCAGGTTGATTCCGGTAACGAACGAGACCTCAGCCTGCTAAA
TAGTCACGGCTACTTTTTTGTAGCCGTCCGACTTCTTANAGGGACTATTGTCGTTTAGGCAATGGAAGTGTGAGGCAATAA

After pcr.seqs 1.33.3

FM205834.1.1779_U
AGCTCCAATAGCGTATATTTAAGTTGCTGCAGTTAAAAAGCTCGTAGTTGGATTTCGGGTGGGGCCTGCCGGTCCGCCGTTTCGG
TGTGCACTGGCAGGGCCCACCTTGTTGCCGGGGACGGGCTCCTGGGCTTCACTGTCCGGGACTCGGAGTCGGCGCTGTTACTTT
GAGTAAATTAGAGTGTTCAAAGCAGGCCTACGCTCTGAATACATTAGCATGGAATAACACGATAGGACTCTGGCCTATCCTGTTGG
TCTGTAGGACCGGAGTAATGATTAAGAGGGACAGTCGGGGGCATTCGTATTTCATTGTCAGAGGTGAAATTCTTGGATTTATGAA
AGACGAACTACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAAC

After pcr.seqs 1.34.1

JN207865.1.848_U
ATTCCAGCTCCAATAGCGTATATTTAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCGGGTGGGCGTTAGCGGTCCGGCTCT
GCTGTGTACTGCTAGTGCCTATCTTTCTGTCGGGGACGGGCTCTTGGGCTTCATTGTCCGGGACTCGGAGTCGACGTGGTTACTT
TGAGTAAATTAGAGTGTTCAAAGCAAGCGTTCGCTGTGAATACATTAGCATGGAATAACACGATAGGACTCTGGCTTATCTTGTTG
GTCTGTAAGACCGGAGTAATGATTAAGAGGGACAGTCGGGGGCATTCGTATTTCATTGTCAGAGGTGAAATTCTTGGATTTATGA
AAGACGAACTTCTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATTAGATACCG
TCGTAGTCTCAACCATAAACGATGCCGACTAGGGATTGGCAGGTGTTTCGTTGATGACCCTGCCAGCACCTTATGAGAAATCAAAG
TTTTTGGGTTCCGGGGGGAGTATGGTCGCAAGGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGCGTGGAGCCTGCG
GCTTAATTTGACTCAACACGGGGAAACTTACCAGGTCCAGACACGGGGAGGATTGACAGATTGAGAGCTCTTTCTTGATTCTGTG
GGTGGTGGTGCATGGCCGGTTCTTAGTTGGTGGGTTGCCTTGTCAGGTTGATTCCGGTAACGAACGAGACCTCAGCCTGCTAAA
TAGTCACGGCTACTTTTTTGTAGCCGTCCGACTTCTTANAGGGACTATTGTCGTTTAGGCAATGGAAGTGTGAGGCAATAA

2

Could you post the contents of your oligos file?

3

Here is the file

#Type Sequence Sequence Name
primer CCAGCASCYGCGGTAATTCC CTTCGAGCCCCCAACTTTC V4_Chlo

PS. There is a TAB between the two primers (not clearly seen on the screen depending on the magnification)

CCAGCASCYGCGGTAATTCC
CTTCGAGCCCCCAACTTTC

4

Thanks for bringing this to our attention. I will release an update to fix it later. In the meantime, you can work around it by entering your oligos file as follows:

forward CCAGCASCYGCGGTAATTCC
reverse CTTCGAGCCCCCAACTTTC

Kindly,
Sarah

5

Thanks a lot… Daniel

6

I released version 1.34.3 which includes the fix for this.