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Error with Upper Bound Assembly

Open MartaBenegas opened this issue 3 years ago • 0 comments

Dear QUAST team,

I'm running QUAST v 5.2.0 inside a docker and testing it with the test data. I haven't managed to generate the Upper Bound Assembly:

root@246f1e3d414e:/data# python3 /quast/quast.py contigs_1.fasta contigs_2.fasta -r reference.fasta.gz --upper-bound-assembly --mp1 reads1.fastq.gz --mp2 reads2.fastq.gz -o output/
WARNING: Python locale settings can't be changed
/quast/quast.py contigs_1.fasta contigs_2.fasta -r reference.fasta.gz --upper-bound-assembly --mp1 reads1.fastq.gz --mp2 reads2.fastq.gz -o output/

Version: 5.2.0, 3d87c606

System information:
  OS: Linux-5.15.0-56-generic-x86_64-with-glibc2.29 (linux_64)
  Python version: 3.8.10
  CPUs number: 12

Started: 2022-12-23 11:01:11

Logging to /data/output/quast.log
NOTICE: Maximum number of threads is set to 3 (use --threads option to set it manually)

CWD: /data
Main parameters: 
  MODE: default, threads: 3, min contig length: 500, min alignment length: 65, min alignment IDY: 95.0, \
  ambiguity: one, min local misassembly length: 200, min extensive misassembly length: 1000

Reference:
  /data/reference.fasta.gz ==> reference

2022-12-23 11:01:12
Generating Upper Bound Assembly...
Compiling BWA (details are in /quast/quast_libs/bwa/make.log and make.err)
Compiling BEDtools (details are in /quast/quast_libs/bedtools/make.log and make.err)
Compiling Minimap2 (details are in /quast/quast_libs/minimap2/make.log and make.err)
Downloading red (file: Red)...
 0.0% of 4468453 bytes
 1.0% of 4468453 bytes
 2.0% of 4468453 bytes
[....]
98.0% of 4468453 bytes
 98.0% of 4468453 bytes
 99.0% of 4468453 bytes
red successfully downloaded!
  Insert size, which will be used for Upper Bound Assembly: auto
  Pre-processing reads...
  Running BWA for reference...
  Done.
  Sorting SAM-file for reference...
  Calculating reads coverage...
  Running repeat masking tool...

ERROR!   Failed to create Upper Bound Assembly, see log for details: /data/output/upper_bound_assembly/upper_bound_assembly.log
[the rest ends correctly]

upper_bound_assembly.log file:

Could not remove: /data/output/upper_bound_assembly/tmp/tmp_red
Invalid State Exception.
The number of states must be positive.
terminate called after throwing an instance of 'exception::InvalidStateException'
  what():  The number of states must be positive.
the default background order: 5.
Using the default threshold: 2.
Calculating GC content ...
Using the default half width: 20 based on the GC content of 52.07

List of final parameters: 
-frm: 2
-gau: 20
-gnm: /data/output/upper_bound_assembly/tmp/tmp_red
-len: 12
-min: 5
-ord: 5
-rpt: /data/output/upper_bound_assembly/tmp
-thr: 2

Deleting pre-existing files under /data/output/upper_bound_assembly/tmp


Stage 1: Building the table ...
Counting k-mers in /data/output/upper_bound_assembly/tmp/tmp_red/reference.fa ...
Processing 0 keys out of 16777216
Processing 10000000 keys out of 16777216
Enrichment view is ready.


Stage 2: Calculating the percentage ...
Calculating the percentage in: /data/output/upper_bound_assembly/tmp/tmp_red/reference.fa ...
The percentage is 100


Stage 3: Training ...
The number of states is: -2147483648

Any help would be appreciated!

MartaBenegas avatar Dec 23 '22 10:12 MartaBenegas