Question: Python error when using MEGAHIT assembler
0
gravatar for sratestimon
17 months ago by
sratestimon0 wrote:

Hi Biostars,

I have recently downloaded Megahit and would like to have a try on it.

I have simply enter the following command:

./megahit -r ./example/refExample.fa --k-max 99 --k-min 11

Which I would try to use the example given by Megahit with k-mer of maximum 99 and minimum of 11 to see if it works. However, the returns is as follow:

Traceback (most recent call last):

File "./megahit", line 1143, in module>

sys.exit(main())

File "./megahit", line 1067, in main

get_version()

File "./megahit", line 526, in

get_version

stdout=subprocess.PIPE).communicate()[0].rstrip().decode('utf-8'))

ValueError: invalid literal for int() with base 10: ''

The system base I am using is Window 64bit with cygwin64. I am having python version 2.7.13 from cygwin.

I have tried to search on google and else where, but the results mostly shown are saying that I am defining the variable wrongly.

However, I do no think it is a good way to modify the script by myself as I have no idea on python coding...

Do anyone else have the same experience on this when using Megahit?

Thanks a lot!

assembly megahit python • 548 views
ADD COMMENTlink modified 17 months ago • written 17 months ago by sratestimon0

Is your Python a windows python, or a cygwin python?

You are pushing your luck trying MEGAHIT on cygwin:

MEGAHIT is suitable for 64-bit Linux and MAC OS X.

ADD REPLYlink modified 17 months ago • written 17 months ago by h.mon21k

I should clarify, it is the cygwin-installed python. Thanks for reminding me mon.

So, do you mean that the cygwin-python might not be suitable for megahit?

ADD REPLYlink written 17 months ago by sratestimon0

What I mean is MEGAHIT on cygwin is untested, probably unsupported by the developers. And as few people here use cygwin, few people, if any, will be able to chime in.

If you google for subprocess.PIPE cygwin, you will find a wealth of StackOverflow and blog posts, some of these may help you.

ADD REPLYlink written 17 months ago by h.mon21k

I see ... Ya I know I should probably get a computer with REAL Linux base ... Thanks mon!

ADD REPLYlink written 17 months ago by sratestimon0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1732 users visited in the last hour