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qunfengdong / BLCA

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weird sequence #21

Closed qinglong89 closed 5 years ago

qinglong89 commented 5 years ago

Hi Developer,

I had very weird situation met recently: other sequences were classified, but only one OTU sequence was not able to be run through (see the error message below). I pasted this sequence in this new issue. I am not exactly sure about this problem. But looks like several previous posts are related with this similar bug. Is this related with sequence pattern???

BLCA package was installed in August 2018.

$blastn -version blastn: 2.7.1+ Package: blast 2.7.1, build Oct 18 2017 19:57:24

$ muscle -version MUSCLE v3.8.31 by Robert C. Edgar

$ python /home/qinglong/programs/BLCA/2.blca_main.py -i 3908.fa -r /home/qinglong/programs/BLCA/db/16SMicrobial.ACC.taxonomy -q /home/qinglong/programs/BLCA/db/16SMicrobial -o 3908.txt ################################################################## blastdbcmd is located in your PATH! muscle is located in your PATH!

Fasta file read in!! Reading in taxonomy information! .... blastn is located in your PATH! Running blast!! Blastn Finished!! Read in blast output! Traceback (most recent call last): File "/home/qinglong/softwares/BLCA/2.blca_main.py", line 355, in outout.write(le+":"+max(lexsum,key=lexsum.get)+";"+str(max(lexsum.values()))+";") ValueError: max() arg is an empty sequence ###################################################################

OTU_3908 ATTAGGCCAGCTACTGTCTGTTCGAGCCTGTGCTAGGTCAGACGCAGAGAGGTTGATCTC GGGTGACGAGCGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAA CTACTGGAAACGGTAGCTAATACCGCATAATGTCGCAAGACCAAAGTGGGGGACCTTCGG GCCTCATGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACC TAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGG TCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGC AGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAA GGCGATAAGGTTAATAACCTTGTCGATTGACGTTACCCGCAGAAGAAGCACCGGCTAACT CCGTG

Thanks.

Qinglong

qunfengdong commented 5 years ago

Hi Qinglong:

Could you please try it with the latest version of BLCA? The version in 2018 has been improved.

Qunfeng

On Wed, Jul 24, 2019 at 4:43 PM qinglong89 notifications@github.com wrote:

Hi Developer,

I had very weird situation met recently: other sequences were classified, but only one OTU sequence was not able to be run through (see the error message below). I pasted this sequence in this new issue. I am not exactly sure about this problem. But looks like several previous posts are related with this similar bug. Is this related with sequence pattern???

BLCA package was installed in August 2018.

$blastn -version blastn: 2.7.1+ Package: blast 2.7.1, build Oct 18 2017 19:57:24

$ muscle -version MUSCLE v3.8.31 by Robert C. Edgar

$ python /home/qinglong/programs/BLCA/2.blca_main.py -i 3908.fa -r /home/qinglong/programs/BLCA/db/16SMicrobial.ACC.taxonomy -q /home/qinglong/programs/BLCA/db/16SMicrobial -o 3908.txt ################################################################## blastdbcmd is located in your PATH! muscle is located in your PATH!

Fasta file read in!! Reading in taxonomy information! .... blastn is located in your PATH! Running blast!! Blastn Finished!! Read in blast output! Traceback (most recent call last): File "/home/qinglong/softwares/BLCA/2.blca_main.py", line 355, in

outout.write(le+":"+max(lexsum,key=lexsum.get)+";"+str(max(lexsum.values()))+";") ValueError: max() arg is an empty sequence ###################################################################

OTU_3908 ATTAGGCCAGCTACTGTCTGTTCGAGCCTGTGCTAGGTCAGACGCAGAGAGGTTGATCTC GGGTGACGAGCGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAA CTACTGGAAACGGTAGCTAATACCGCATAATGTCGCAAGACCAAAGTGGGGGACCTTCGG GCCTCATGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACC TAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGG TCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGC AGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAA GGCGATAAGGTTAATAACCTTGTCGATTGACGTTACCCGCAGAAGAAGCACCGGCTAACT CCGTG

Thanks.

Qinglong

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