adriantich
commented
3 years ago Hi!
Thanks for contacting me.
Since many names refer to size/count/reads depending on the input format, I designed DnoisE to run whatever the name is. However, now I see that it was not done for the fasta_ouput line. I'll fix it now and tell you when it's done! I'll also modify to accept both upper and lower case letters and combined.
Thank again!
Adrià
On 16/4/21 13:58, SanniH wrote:
Hi!
I tried to run the DnoiSE.py with my own fasta file of dereplicated, non-chimeric ESVs, but unfortunately I got an error after about 45min, and was hoping you might be able to help?
The error I get:
Traceback (most recent call last): File "DnoisE/src/DnoisE.py", line 467, in denoised_ratio_d[i]['sequence'].upper() + "\n") KeyError: 'count'
I run DnoiSE on a remote server through a shell script, and my fasta is formatted as requested following your paper and the repo, although there was no mention of whether all bases must be as capitals so I have a mix.
$ head UTILA_DSE.fasta
uniq1;size=62441; TTATTCTACATACCCTGCTAGTGCTTATTTATCAACTGATTTAATAATCTTTTCATTACATTTAGCCGGTGCTAGTTCTATATTGTCTTCAATAAATTTTATTATAACAGTTTTTATGTTGCCTATAAattcttctttttctttttttcaatatcctttatttatagtagctcaaattactgtttcttttttATTATTAATATCTTTACCTGTTTTAGCCGCTGCTATTACTATGTTACTTTTTGATCGTAATTTCAACACTTCttttttttCCAATTATTTGGGTGGTGATGCTCTTCTTTATCAACATTTATTT uniq2;size=24836; TTTGAGTAGTGTTCAAGCTCATTCAGGTCCTTCTGTGGATTTGGCTATTTTTAGCCTTCATTTGTCCGGGGCAGCATCTATTATGGGTTCGATTAATTTCATTACAACAATTATTAATATGCGACCGGGAGGAATGGGAATGCATCGTTTGCCGCTATTTGTATGGGCAGTTTTGCTAACCGCAATTCTATTGTTGCTTTCTCTTCCTGTTTTGGCTGGGGGTATTACTATGTTGTTGACTGACCGAAATTTTAACACTACCTTTTTTGATCCCGCTGGAGGAGGAGACCCTGTTCTTTATCAACACCTATTT ...My file was generated using PEAR for PE merging, and VSEARCH for length filtering and dereplication, and the resulting fasta contains ~44K unique sequences, single line, with length ranging from 303-323 (COI Leray fragment). I attached the fasta I used here.
The command I used for running DnoiSE was this: $ python3 DnoisE/src/DnoisE.py -i UTILA_DSE.fasta -o Utila -c 20
Any help would be appreciated as I am very keen to see how this compares to my previously generated data using dada2!
UTILA_DSE.zip https://github.com/adriantich/DnoisE/files/6324683/UTILA_DSE.zip
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SanniH
Hi!
I tried to run the DnoiSE.py with my own fasta file of dereplicated, non-chimeric ESVs, but unfortunately I got an error after about 45min, and was hoping you might be able to help?
The error I get:
Traceback (most recent call last): File "DnoisE/src/DnoisE.py", line 467, in
denoised_ratio_d[i]['sequence'].upper() + "\n")
KeyError: 'count'
I run DnoiSE on a remote server through a shell script, and my fasta is formatted as requested following your paper and the repo, although there was no mention of whether all bases must be as capitals so I have a mix.
$ head UTILA_DSE.fasta
My file was generated using PEAR for PE merging, and VSEARCH for length filtering and dereplication, and the resulting fasta contains ~44K unique sequences, single line, with length ranging from 303-323 (COI Leray fragment). I attached the fasta I used here.
The command I used for running DnoiSE was this: $ python3 DnoisE/src/DnoisE.py -i UTILA_DSE.fasta -o Utila -c 20
Any help would be appreciated as I am very keen to see how this compares to my previously generated data using dada2!
UTILA_DSE.zip