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mcveanlab / mccortex

De novo genome assembly and multisample variant calling
https://github.com/mcveanlab/mccortex/wiki
MIT License
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mccortex unitigs: "Fatal Error: Couldn't read 'Coverages': expected 4; recieved: 0" #91

Open karel-brinda opened 3 years ago

karel-brinda commented 3 years ago

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: -]