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.