Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

mccortex unitigs: "Fatal Error: Couldn't read 'Coverages': expected 4; recieved: 0" #91

Open
karel-brinda opened this issue Sep 11, 2020 · 0 comments

Comments

@karel-brinda
Copy link

  • OS: OS X
  • Version: mccortex=v0.0.3-610-g400c0e3 zlib=1.2.11 htslib=1.8-17-g699ed53 ASSERTS=ON hash=Lookup3 CHECKS=ON k=3..31

Preparation:

wget http://ftp.ebi.ac.uk/pub/software/bigsi/nat_biotech_2018/ctx/ERR145/ERR1458685/cleaned/ERR1458685.ctx.bz2

Error:

$ bzcat -f ERR1458685.ctx.bz2 | mccortex31 unitigs -m 3G -
[11 Sep 2020 13:34:00-ves][cmd] mccortex31 unitigs -m 3G -
[11 Sep 2020 13:34:00-ves][cwd] /private/tmp/~20200911133112
[11 Sep 2020 13:34:00-ves][version] mccortex=v0.0.3-610-g400c0e3 zlib=1.2.11 htslib=1.8-17-g699ed53 ASSERTS=ON hash=Lookup3 CHECKS=ON k=3..31
[11 Sep 2020 13:34:00-ves][memory] 73 bits per kmer
[11 Sep 2020 13:34:00-ves][memory] graph: 2.9GB
[11 Sep 2020 13:34:00-ves][memory] total: 2.9GB of 16GB RAM
[11 Sep 2020 13:34:00-ves] Output in FASTA format to STDOUT
[11 Sep 2020 13:34:00-ves][hasht] Allocating table with 343,932,928 entries, using 2.6GB
[11 Sep 2020 13:34:00-ves][hasht]  number of buckets: 8,388,608, bucket size: 41
[11 Sep 2020 13:34:00-ves][graph] kmer-size: 31; colours: 1; capacity: 343,932,928
[11 Sep 2020 13:34:00-ves][FileFilter] Reading file - [1 src colour]
[11 Sep 2020 13:34:00-ves][GReader] 18,446,744,073,709,551,615 kmers, 16EB filesize
[11 Sep 2020 13:34:02-ves][graph_file_reader.c:364] Fatal Error: Couldn't read 'Coverages': expected 4; recieved: 0; [file: -]
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant