pick_de_novo_otus.py -i sample1/forward_fasta/f.fna -o sample1/forward_fasta/otus
ValueError: An empty fasta file was provided. Did the alignment complete sucessfully? Did PyNAST discard all sequences due to too-stringent minimum length or minimum percent ID settings?
All sequences are around 260 bp. I think this error is due to the fact that the sequences identifiers in the file is not correct as I did not run split_libraries.py. In the documentation I found following: "The sequence identifiers in this file should be of the form <sample_id>_<unique_seq_id>"
In my sample1/forward_fasta/f.fna there is not sample id as for each sample I have its own folder. Is it a requirement to have a sample id in the identifier? If yes, could it be the reason why I do not get the clusters?
/forward_fasta/f.fna looks as follows:
@M04070:53:000000000-AUCFU:1:1101:21310:2043 1:N:0:102
TATTGGAGCTGGAATTACCGCGGCTGCTGGCACTAGACTTGCCCTCCAATGGATCTTCGTTAAAGGATTTAAAGTGGACTCATTCCAATTACAGGACCTCGAAAGAGTCCTGTATTGGTATGTTTCATCACTACCTCCTTGGGTCGGGAGTGGGTAATTTGCATGCCTGCTGCCTTCCTTGAATGTGGTATCCATTTCTCAGGCTCCCTCTACAGTATTCAACCCTGATTCCCCATCACCCGTGGTCACCATGGTAGGCACAG
+
GGGGGGGGGGGGGGGGEFGEGDCFGCEG<CC,FFCE9EFF<FFGGGG8<EEE9FGGGG@FGF7<A98EEGFC9CC,5,EFGCFFFE9EFGCEFCFDFGFGCC,+><EFGFG9FFFGD9F,CFFGFGCFG9FGDFFGGGGGC8AFF7>C+CCCCGGE,EFG9F9E9DFF9FGBFGGGFGGG7,,>>DDFGC,5DCFC@:@,,,*0;CDGG<F8C>8++=C+4+;;>G54ACFACA40=36CDB8(0>A;AE4?23@9*4<<:4(
@M04070:53:000000000-AUCFU:1:1101:19674:2260 1:N:0:102
TATTGGAGCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATTGTTCCTCGTTAAGGGATTTAAATTGTACTCATTCCAATTACAAGACCCAAAAGAGCCCTGTATCAGTATTTATTGTCACTACCTCCCCGTGTCGGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAATAGAACCCTAATTCCCCGTTACCCGTTGATACCATGGTAGGCCACTAT
+
GGGGGGGGGGGGGGGGGGGGGGGGGGDGFFGGGGGGGGGGFGGEGGGGGGGGGGGGGGGGGGGGGG?FFGGGGGGFGGGGGGGGGGGGGGGGFGCGGGGGCFFGFGGGGGGGGGGGGGGGAE?FGGGGGFGGGGFGGGGGGGFGEG:EFGGCFEG8EFAFGGGGGGGGGGGGGG7EGGGGGDDFCFGFGGGGGGGCFGGGCFD*;ECFFFGGGG*85=>FGGGAFGFF=@=?GFEFFFFGB>)8FFFFF???<AF4>?8??FB)
@M04070:53:000000000-AUCFU:1:1101:22694:2710 1:N:0:102
TATTGGAGCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAGGGATTTAGATTGTACTCATTCCAATTACCAGACTCATAGAGCCCGGTATTGTTATTTATTGTCACTACCTCCCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAATCGAACCCTTATTCCCCGTTACCCGTTGAAACCATGGTAGGCCTCTAT
Attached is the log file from dynast_aligned_seqs
add_qiime_labels.py -m mapping_radtags.txt -i forward_fasta -c InputFileName -o forward_fasta/combined_sample_fastapick_de_novo_otus.py -i forward_fasta/combined_sample_fasta/combined_seqs.fna -o forward_fasta/combined_sample_fasta/otus