what should i put for scaffolds_iteration_3.p in stitch.py

marbl / SALSA

SALSA: A tool to scaffold long read assemblies with Hi-C data

MIT License

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what should i put for scaffolds_iteration_3.p in stitch.py #95

Closed anjiyuan closed 4 years ago

anjiyuan commented 4 years ago

i tried to stitch unitigs.fasta file using

python2 stitch.py -c xxx.contigs.fasta -u xxx.unitigs.fasta -p scaffolds_iteration_3.p -o output_scaffold_stitched_3p.fasta I got error:

Traceback (most recent call last): File "/home/an/bin/SALSA/SALSA-master/stitch.py", line 29, in scaffolds = pickle.load(open(args.pickle,'r')) IOError: [Errno 2] No such file or directory: 'scaffolds_iteration_3.p'

if i create an empty file scaffolds_iteration_3.p, i still got error EOFError.

thanks anji

skoren commented 4 years ago

Did your code run for 3 iterations? The 3.p is just an example in the readme. What is the content of your folder where you ran salsa?