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cytham / nanovar

Structural variant caller for low-depth long-read sequencing data
GNU General Public License v3.0
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Error: windowmasker obinary failed #58

Closed adbeggs closed 1 year ago

adbeggs commented 1 year ago

Hello

Thanks for the great tool. I'm trying to run the pipeline, after succesfully installing with conda and coming up against the error below.

It's a ONT R9.4.1 BAM aligned to GRCh38

Thanks!

Andrew

[30/03/2023 14:34:49] - INFO - Initialize NanoVar log file
[30/03/2023 14:34:49] - INFO - Version: NanoVar-1.4.1
[30/03/2023 14:34:49] - INFO - Command: /rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/nanovar/bin/nanovar -t 24 -f hg38 --cnv hg38 HB3062combined.sorted.bam /rds/homes/b/beggsa/beggsa-clinicalnanopore/genomes/grch38/genome.fa nanovar_sample -x ont
[30/03/2023 14:34:50] - INFO - Input file: HB3062combined.sorted.bam
[30/03/2023 14:34:50] - INFO - Read type: ont
[30/03/2023 14:34:50] - INFO - Reference genome: /rds/homes/b/beggsa/beggsa-clinicalnanopore/genomes/grch38/genome.fa
[30/03/2023 14:34:50] - INFO - Working directory: nanovar_sample
[30/03/2023 14:34:50] - INFO - Model: /rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/nanovar/lib/python3.9/site-packages/nanovar/model/ANN.E100B400L3N12-5D0.4-0.2SGDsee11_het_gup_v1.h5
[30/03/2023 14:34:50] - INFO - Filter file: hg38
[30/03/2023 14:34:50] - INFO - Minimum number of reads for calling a breakend: 2
[30/03/2023 14:34:50] - INFO - Minimum SV len: 25
[30/03/2023 14:34:50] - INFO - Mapping percent for split-read: 0.05
[30/03/2023 14:34:50] - INFO - Length buffer for clustering: 50
[30/03/2023 14:34:50] - INFO - Score threshold: 1.0
[30/03/2023 14:34:50] - INFO - Homozygous read ratio threshold: 0.75
[30/03/2023 14:34:50] - INFO - Heterozygous read ratio threshold: 0.35
[30/03/2023 14:34:50] - INFO - Number of threads: 24

[30/03/2023 14:34:50] - INFO - Total number of reads in FASTQ/FASTA: -

[30/03/2023 14:34:50] - INFO - NanoVar started
[30/03/2023 14:35:09] - DEBUG - Genome filter BED passed
[30/03/2023 14:35:09] - INFO - Input BAM file, skipping minimap2 alignment
[30/03/2023 14:35:09] - DEBUG - Make blast index skipped
[30/03/2023 14:35:09] - DEBUG - Windowmasker counts skipped
[30/03/2023 14:35:09] - INFO - Windowmasker binary
[30/03/2023 14:35:09] - DEBUG - reading counts...
[30/03/2023 14:35:09] - DEBUG - Error: (Exception::creation failure) unrecognized unit counts format
[30/03/2023 14:35:09] - DEBUG - Error: (Exception::creation failure) could not create a unit counts container
[30/03/2023 14:35:09] - DEBUG - Error: (106.16) Application's execution failed (Exception::creation failure) could not create a unit counts container
[30/03/2023 14:35:09] - CRITICAL - Error: windowmasker obinary failed
cytham commented 1 year ago

Hi @adbeggs, sorry for the delayed response. Looks like some corrupted windowmasker files. Can you please try to run with the --force parameter to rerun the entire pipeline?