Hans

Here is the code I am running and the errors below. ``` docker run --shm-size 2g --rm -u $(id -u):$(id -g) -it -v /Users/hvasquezgross/test_docker/:/data/ xiaolidong/docker-metaerg setup_db.pl -o /data [Wed Mar...

ERROR: : double free or corruption (!prev) and free(): corrupted unsorted chunks

3

Version: diamond v2.1.8.162 installed from bioconda Database: NR downloaded from ncbi 2023/07/28 database was built using the makedb command and providing taxon files. `$diamond makedb --threads 32 --in $db --db...

Assembly running out of memory; tried tuning down minimizer window size and kmer

4

I am working on an assembly for an expected genome size of 2.65Gbp. We have HiC data, and 6 SMRTCells worth of HIFI data (3 from a male, and 3...

Group1 optimization step has been running for 43 days for a genome assembly. I previously used AllHIC for another assembly, and the optimization step took about 2 days. Is there...

agat_sp_extract_sequences.pl Could not open index file but it exists

1

**Describe the bug** When running the command, it gets towards the bottom of the process but then errors saying the it could not open the index file. This is a...

TypeError: read_table() got an unexpected keyword argument 'squeeze'

1

squeeze was deprecated in Pandas 2.0. Is this pipeline still being updated? ```` Building DAG of jobs... InputFunctionException in rule merge_variants in file strabisumus_2025_mito_methyl/dna-seq-gatk-variant-calling_github/workflow/rules/calling.smk, line 64: Error: TypeError: read_table() got...