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baoe / FLAS

Fast and High Throughput Algorithm for PacBio Long Read Self-Correction
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unable to run FLAS #1

Open estolle opened 5 years ago

estolle commented 5 years ago

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

KevinBredemeyer commented 4 years ago

Same issue, I assume no progress on this?

ginnamon commented 4 years ago

Hi! Seems that lines 106 and 233 are not well indented. I solved the problem by simply modifying the code. You should re-indent the two lines using the tab (they should be indented as inside "if err != 0:"). Then, try to run FLAS by using the python script: python3 runFLAS.py -raw_reads.fasta-

Anyway, since a recent update of MECAT2, the code doesn't run successfully because module mecat2pw is no more present (it has been modified into mecat2map). We should adapt FLAS script and hope the MECAT functions will be unchanged