NOVOPlasty
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ndierckx
NOVOPlasty4.3.pl: command not found
Dear all,
I am trying to run NOVOPlasty4.2.pl -c config.txt but Doesn't work. my conda version is 4.13.0. I installed it from Anaconda.org https://anaconda.org/bioconda/novoplasty Also I run it as NOVOPlasty4.13.pl -c again get "command not found"
Best regards
There is no 4.13, so I assume you meant 4.3.1 If you installed 4.3.1 through conda, you should run it like this:
NOVOPlasty4.3.1.pl -c config.txt
Thanks now it works. But now i have error in seed file. Building Hash Table......OK
Subsampled fraction: 0.00 %
Retrieve Seed...BUILD2
INVALID SEED, PLEASE TRY AGAIN WITH A NEW ONE
In Configuration file genome range =12000-18000 while the function is empty in Linux terminal screen ! is it ok?
As previous issue there was problem Id of reads. there are first 2 reads of my data
@A01137:75:H57LCDSX3:1:1101:19696:1000 1:N:0:TGGTGGCA+TTACAGGA NATCAGGCGGAGATGTTTGATGGTGTAGGAAGATCAATTAAGGAGTTGTTGACTATTTTTAATAGGGGGTGCGATTTTCGGATATTGGGTGCCATTATTTGTTGGAGGTTAGAAGGATTATTGTGAGGATTGTGAGAGCGAATGACCCTAA + #FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FF @A01137:75:H57LCDSX3:1:1101:17201:1188 1:N:0:TGGTGGCA+TTACAGGA AACTCAAACACACGAGAACACCTCCTCATAACCCTACACATCATCCCCATACTGACCCTCATTCTAAAACCAGAACTAATCTCAGGGGCCCCTCTATGCTAGTATAGTTTAACCCAAACATTAGATTGTGATTCTAAAAATAGGAGTTCAA + FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFFFFFF @A01137:75:H57LCDSX3:1:1101:12445:1470 1:N:0:TGGTGGCA+TTACAGGA GCCGTAGTCCTTGGAGTTTAGGCCAAGCGGGAATATATGACTTATTTTGTGATTTTTTTGGGAGTTAGTTTTGCATTAGGGGTTTTAGCTGTAGCGTCTAATCCTTCTCCGTATTATGGGGTGGTAGGATTGGTGTTGGCGTCTGTGGCTG
head R2.fastq @A01137:75:H57LCDSX3:1:1101:19696:1000 2:N:0:TGGTGGCA+TTACAGGA TAACACAACACATAACATAACTTTCCCTAAACAGGACCACCTCACAAACTTCTCCTCCTCACTAGGTTACTTCAACCCTCTAGCTCATCGAACTAACCCCACTACCCTCCTCCTCGCAGGACAAAAAATTGCATCTCACCTAATCGACATA + FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF,F: @A01137:75:H57LCDSX3:1:1101:17201:1188 2:N:0:TGGTGGCA+TTACAGGA GAGTAGGGGTGGTAGGATAATTGGGGTGAGAAGGGTAAGAAGTGTCAGTGGTGTAAGAGTGTTTAGGAGTAGTGCTGTCTCCATTACTTTTACTTGGAGTTGCACCAAGATGAATGGCTCCTAAGACCAGTGGATTGCTTTTATCCTTTAA + F:F:FFFFFFFFFFFFFFF:FFFFFFFFFFF,FF:FFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFF @A01137:75:H57LCDSX3:1:1101:12445:1470 2:N:0:TGGTGGCA+TTACAGGA ATCAACAGTAACCGCCACAACCTTTCAAAAATCAACAAATCCCCCCAAAACCACTCCCATAAACACCACCAAAACAAACCCTAACCCATACCCAACCACCCGCCAATTCCCCCAAGCCTCAGGATATGGGTCTGCTGCTAGAGATACAGAA
Hi,
It seems no reads were stored: Subsampled fraction: 0.00 %
In Configuration file genome range =12000-18000 while the function is empty in Linux terminal screen ! is it ok?
No that should not be, so probably also not in the log file? Can you redownload the config file and try again, usually that fixes the issue? And which OS are you using?
Greets