Hi everyone,
I am running yn00 to analyze around 35000 alignments. My codon alignments were generated by pal2nal in PAML input format. When I run the yn00, dn,ds is calculated only for around 300 alignments but not for the rest ~34000 alignments. I tried running these alignments one by one and I get the same error for all of them.
Error in sequence data file: E at 3 seq 1.
Make sure to separate the sequence from its name by 2 or more spaces
I have checked my alignments and they seem to be fine, as in , in multiples of three. It's very confusing as ~200 of them seem to not have this problem although they were all generated by pal2nal. I am attaching a few alignments that did not run. Please help me figure this out. Thank you.
2 642
ENSMUSG00000004821_ENSMUST00000004943_Tmed11_5_108777235_108795363
ATGCAAATTCAGACAATTCTTTTATGTTTTAGCTTTTCATTTTCAGCTGCTTTTTATTTC
CATGCTGGAGAGCGAGAGGAGAAATGTATAATTGAAGACATTCCAAGTGATACATTGATA
ACAGGGACATTCAAGGTACAGCAGTGGGACATAGTCAGACATGACTTCCTTGAATCTGCT
CCTGGCTTAGGAATGTTTGTGACTGTTACAACTAATGATGAGGTATTATTATCCAAGTTA
TATGGTGCACAAGGAACATTCTATTTTACTTCTCATTCATCTGGTGAACACATCATTTGC
TTAGAATCTAATTCTACACAGTTTGTGTCATTTGGAGGAAGTAAGCTGCGCATCCACTTA
GATATTCGAGTTGGAGAACATGACCTTGATGCAGCTATTGTTCAAGCAAAGGATAAAGTT
AATGAAGTAACCTTCAAGCTTCAACATCTAATTGAACAAGTGGAGCAAATACTCAAAGAA
CAAGACTATCAAAGGGACCGTGAAGAAAATTTCCGTATAACCAGTGAAGATACCAATAGA
AATGTTTTATGGTGGGCTTTTGCACAAATATTGATCTTTATCTCAGTTGGAATTTTTCAA
ATGAAACACCTTAAAGATTTCTTCATAGCTAAGAAGCTTGTT
ENSRNOG00000000035_Tmed11_ENSRNOT00000000040_14_1932659_1953305
ATGCAAACTCAGACAATTCTCTTATGTTTCAGTTTTTCCTTTTCAGCTGCTTTTTATTTC
CATGCTGGGGAGCGAGAGGAGAAATGTATAATCGAAGACATTCCAAGTGACACGTTGATA
ACAGGGACATTCAAGATACAGCAGTGGGACATTGGTAGACATGACTTTCTTGAATCTGCT
CCTGGCTTAGGAATGTTTGTGACTGTTACAAACAATGATGAGGTATTATTATCCAAGTTA
TATGGTGCACAAGGGACATTCTATTTTACTTCACACTCATCTGGTGAACACATCATTTGC
TTAGAATCTAATTCTACACAATTTGTGTCATTTGGAGGGAGTAAGCTGCGCATCCACTTA
GATATTCGAGTTGGAGAGCATGACCTTGATGCAGTTATTGTTCAAGCAAAGGACAAAGTT
AATGAAGTAGCCTTCACGCTTCGACATCTAATTGAACAAATTGAACAAATACTCAAAGAA
CAAGACTATCAAAGGGACCGTGAGGAAAATTTCCGTATCACCAGTGAAGATACCAATAGA
AATGTTTTATGGTGGGCTTTCGCACAAATATTAATCTTTATCTCAGTTGGAATTTTTCAA
ATGAAGCACCTTAAAGATTTCTTCATAGCTAAGAAGCTTGTT
Sorry for this format.I couldn't figure out how to attach a file here.
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shreyasibiswas88 •
3 answers
Please show also the headers of the alignments which "are fine" to see if the problem is header length.
I had this error when my input phylip file had between sequence name and sequence tab instead of two spaces. Replacing the tab by two spaces (e.g. in bash via sed 's/\t/ /') fixed the problem - that might be another thing to check.
Hi, have you figured out this problem, I got a same question with you, can you please give me some suggestions about it?
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