Re: Phylophlan error

Nicola Segata

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Oct 4, 2015, 4:35:47 PM10/4/15

to Naseer Sangwan, phylophl...@googlegroups.com

Hi Naseer,

thanks for getting in touch. I'm forwarding your message to the PhyloPhlAn user group, as I think they can help you with the problem....

thanks

Nicola

On Sat, Oct 3, 2015 at 4:25 AM Naseer Sangwan <nikki101...@gmail.com> wrote:

Hello Nicola,

how are you?

i was trying to use Phylophlan on 80 draft genomes (assigning taxonomy)

./phylophlan.py -u all_protein_seqs --nproc 24

and it produced the following error

data/all_protein_seqs/Pair_1_Genome2.b6o generated!
All usearch runs performed!
Traceback (most recent call last):
File "./phylophlan.py", line 793, in <module>
gens2prots(inps, projn)
File "./phylophlan.py", line 311, in gens2prots
assert vv not in prots2ups
AssertionError

Any idea whats wrong here

Thanks for the help

Naseer

--
Post-Doctoral Research Associate
Biosciences Division (BIO)
Argonne National Laboratory
9700 South Cass Avenue,
Bldg. 202, Room. No B317
Argonne, IL 60439, U.S.A.
email: nikki101...@gmail.com
contact: (630) 854 7656

Malte Rühlemann

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Oct 5, 2015, 7:20:14 AM10/5/15

to PhyloPhlAn-users, nikki101...@gmail.com, nicola...@unitn.it

Hi,

i have had this error before and if I remember correctly it was due to multiple fasta headers with the same id. did you rename your sequences after ORF prediction?

Malte

SJ Park

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Dec 5, 2018, 4:00:59 AM12/5/18

to PhyloPhlAn-users

good!!!! Malte.

thanks. your reply, finally, seriously helpful to me. thanks!!!!!

2015년 10월 5일 월요일 오후 8시 20분 14초 UTC+9, Malte Rühlemann 님의 말:

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