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ndierckx / NOVOPlasty

NOVOPlasty - The organelle assembler and heteroplasmy caller
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NOVOPlasty4.3.pl: command not found #193

Open pshtiwan opened 2 years ago

pshtiwan commented 2 years ago

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

ndierckx commented 1 year ago

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

pshtiwan commented 1 year ago

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

ndierckx commented 1 year ago

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