Comments (2)
tuliocampos
commented on May 28, 2024
I had the same issue. Seems like the pipeline does not download the file common.py it's supposed to use. I have tried to download (from github) and run the scripts manually, using the calls.tsv.gz (or calls.tsv) file as input. It generates very large svg files that fail to be converted to png when I tried to generate the reports using "snakemake --report report.zip".
from dna-seq-gatk-variant-calling.
matthewthefool
commented on May 28, 2024
I really struggle with this problem rn, have you solved it yet?
from dna-seq-gatk-variant-calling.
Related Issues (20)
- Erro in rule snpeff HOT 1
- README report link served through RawGit will stop working
- snpeff with custom genome database
- Direct output to directory of interest HOT 1
- Which singularity image is used? HOT 1
- Failed to open environment file
- Failed to open environment file mergevcfs HOT 1
- Running without known-variants HOT 3
- Haplotype caller with intervals runs slow HOT 2
- Not executed fastqc for specified inputs HOT 1
- Errors in two rules terminating run HOT 2
- Choice of reference genome HOT 2
- can't set java opts for rule recalibrate_base_qualities
- REMOVE_DUPLICATES is false according to logs in rule mark_duplicates
- VQSR not fully implemented HOT 4
- rule plot_stats fails with "OverflowError: value too large to convert to npy_uint32" HOT 4
- Error tokenizing data. C error: Expected 5 fields in line 4, saw 6 HOT 2
- TypeError in calling.smk rule merge_variants. The bwa mapping stops after creating the indexes files. HOT 7
- Help with dna-seq-gatk-variant-calling
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