raxmlHPC ERROR: Bad base (A) at site 1 of sequence 1
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matthe...@gmail.com
Dec 28, 2018, 2:33:13 AM12/28/18
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Hello, my raxml raised error, I google a lot and no solutions can fix this, I hope someone know how to fix. Thanks.
Error msg:
My alignment file looks:
My command:
raxmlHPC -s COX1_alignment.phy -n COX1 -m ASC_BINCATX -b 12345 -p 12345 -# 1000ERROR: Bad base (A) at site 1 of sequence 1Printing error context:
161457 ATTATTAGAC GGTTTGAAAG
Problem reading alignment fileMy alignment file looks:
18 161457 ATTATTAGAC GGTTTGAAAG GTTTCGTTTG TGACGTTTGC GGTGATTATA TAGGACAAAT27 ATTATTAGAC GGTTTGAAAG GTTTCGTTTG TGACGTTTGC GGTGATTATA TAGGACAAAT62 ATTATTAGAC GGTTTGAAAG GTTTCGTTTG TGACGTTTGC GGTGATTATA TAGGACAAAT58 ATTATTAGAC GGTTTGAAAG GTTTCGTTTG TGACGTTTGC GGTGATTATA TAGGACAAAT82 ATTATTAGAC GGTTTGAAAG GTTTCGTTTG TGACGTTTGC GGTGATTATA TAGGACAAAT64 ATTATTAGAC GGTTTGAAAG GTTTCGTTTG TGACGTTTGC GGTGATTATA TAGGACAAAT100 ATTATTAGAC GGTTTGAAAG GTTTCGTTTG TGACGTTTGC GGTGATTATA TAGGACAAAT109 ATTATTAGAC GGTTTGAAAG GTTTCGTTTG TGACGTTTGC GGTGATTATA TAGGACAAAT115 ATTATTAGAC GGTTTGAAAG GTTTCGTTTG TGACGTTTGC GGTGATTATA TAGGACAAAT112 ATTATTAGAC GGTTTGAAAG GTTTCGTTTG TGACGTTTGC GGTGATTATA TAGGACAAAT118 ATTATTAGAC GGTTTGAAAG GTTTCGTTTG TGACGTTTGC GGTGATTATA TAGGACAAAT119 ATTATTAGAC GGTTTGAAAG GTTTCGTTTG TGACGTTTGC GGTGATTATA TAGGACAAAT126 ATTATTAGAC GGTTTGAAAG GTTTCGTTTG TGATGTTTGC GGTGATTATA TAGGACAAAT122 ATTATTAGAC GGTTTGAAAG GTTTCGTTTG TGACGTTTGC GGTGATTATA TAGGACAAAT121 ATTATTAGAC GGTTTGAAAG GTTTCGTTTG TGACGTTTGC GGTGATTATA TAGGACAAAT130 ATTATTAGAC GGTTTGAAAG GTTTCGTTTG TGACGTTTGC GGTGATTATA TAGGACAAAT129 ATTATTAGAC GGTTTGAAAG GTTTCGTTTG TGACGTTTGC GGTGATTATA TAGGACAAAT128 ATTATTAGAC GGTTTGAAAG GTTTCGTTTG TGACGTTTGC GGTGATTATA TAGGACAAAT
CATAAGGATA TTGGGACTCT ATATTTTCTT TTTTCTATTT GATCTGGTTT AATAGGAACT CATAAGGATA TTGGGACTTT ATACTTTCTT TTTTCTATTT GATCTGGTTT AATAGGAACT CATAAGGATA TTGGGACTCT ATATTTTCTT TTTTCTATTT GATCTGGTTT AATAGGAACT CATAAGGATA TTGGGACTCT ATACTTTCTT TTTTCTATTT GATCTGGTTT AATAGGAACT CATAAGGATA TTGGGACTTT ATACTTTCTT TTTTCTATTT GATCTGGTTT AATAGGAACT CATAAGGATA TTGGGACTCT ATACTTTCTT TTTTCTATTT GATCTGGTTT AATAGGAACT CATAAGGATA TTGGGACTCT ATACTTTCTT TTTTCTATTT GATCTGGTTT AATAGGAACT
Alexey Kozlov
Dec 28, 2018, 6:35:10 AM12/28/18
to ra...@googlegroups.com
You get this error because you specify binary model (-m
ASC_BINCATX), but your alignment contains DNA data. You should use
nucleotide model instead, e.g. ASC_GTRCATX.
Hope this helps,
Alexey
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matthe...@gmail.com
Dec 29, 2018, 5:02:17 AM12/29/18
to raxml
Thanks.
在 2018年12月28日星期五 UTC+8下午7:35:10，Alexey Kozlov写道：
在 2018年12月28日星期五 UTC+8下午7:35:10，Alexey Kozlov写道：
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