baoe / flas Goto Github PK

Hello,
I wonder if FLAS will work well with Oxford Nanopore data as well
thanks,
Dario

Hi there,

I was just trying to run FLAS but seem to have problems on my Ubuntu 16.04 system.

As stated in the README i tried:
FLAS input.fasta
but absolutely nothing happens (immediately it finished without an error message or any other message or output).

so I tried the python script:

python3 /opt/FLAS/runFLAS.py PacBio.fastq.gz ✘ 1
File "/opt/FLAS/runFLAS.py", line 109
bronkerbosch1_command = 'bronkerbosch.py ' + temp_dir + '/step1/' + 'allreads.fasta.m4 ' + temp_dir + '/step1/' + 'clique1.txt ' + temp_dir + '/step1/' + 'edge1.txt ' + str(args.c)
^
TabError: inconsistent use of tabs and spaces in indentation

Same when running on the fasta python3 /opt/FLAS/runFLAS.py PacBio.fasta

I would appreciate any hint what this error might mean and how to fix it.

Also, it would be helpful if FLAS would have a .h (help) option), perhaps also a test dataset to see if the application works or not and a little information what the parameters mean. I also was not sure whether the input could be gzipped or has to be unzipped fasta.

Cheers
Eckart

I have been able to install FLAS but when I try to run it, I get a segmentation fault error:

(base) root@b785a137acf8:/# FLAS data/test.fasta
Segmentation fault (core dumped)

Any advice? Thanks!

Please add --help and --version to the FLAS executable with usage and version information.

A new version of MECAT has been released. Is FLAS compatible with MECAT2 or should MECAT be installed?