trim.seqs segfault

mothur bugs
#1

I’ve been unsuccessful in using the trim.seqs command on all but a very limited number of my sequences. It segfaults pretty much right away.

This can be reproduced 100% of the time using the following E. coli 16S sequence:

>gi|86278349|gb|DQ360844.1| Escherichia coli strain ATCC 25922 16S ribosomal RNA gene, partial sequence
AGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGA
AGCAGCTTGCTGCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGG
GATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTC
TTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAAAGGCTCACCTAGGCGACGATCCCT
AGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAG
TGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAACCATGCCGCGTGTATGAAGAAGGCCTTCGGGTT
GTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAG
AAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGG
GCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAGCTGCATC
TGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGAT
CTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGA
GCAAACAGGATTAGATACCTGGTAGTCCACGCCGTAAACGATGTCGACCTGGAGGTTGTGCCCTGAGGCG
AGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAA
TTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGT
CTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGC
TGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCC
AGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGT
CATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCACACAAAGAGAAGCGATCTCGCGA
GAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGA
ATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCAC
ACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTC
ATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTT

with the oligos file:

#Bac8F
forward AGAGTTTGATCCTGGCTCAG

#Bac1492R
reverse GGTTACCTTGTTACGACTT

and the command:

trim.seqs(fasta=ecoli.fasta, oligos=ecoli.oligos)

Tested OSX and Linux 64-bit 1.18.1 builds.

#2

Thanks for bringing this to our attention. The problem occurs because #Bac8F just has a line return after it and so mothur reads through the next line. This will be fixed in the next version. Also, I noticed that in the oligos file sample you gave contains spaces separating the forward type and the primer. This will cause mothur to get confused, and should be either a tab or one space.