Run_spades error

[kayobianco]

Hi,

I am trying to analyze 3 samples, but ATLAS crashes on the following error:

Building DAG of jobs...
Creating conda environment /media/archaea/UBUNTU-HD/miniconda3/envs/atlasenv/lib/python3.8/site-packages/atlas/workflow/rules/../envs/assembly.yaml...
Downloading and installing remote packages.
Environment for ../../miniconda3/envs/atlasenv/lib/python3.8/site-packages/atlas/workflow/envs/assembly.yaml created (location: ../atlas_database/conda_envs/a1293008546da0884a56f95a1ffd71c1)
Using shell: /usr/bin/bash
Provided cores: 2
Rules claiming more threads will be scaled down.
Singularity containers: ignored
Job stats:
job count min threads max threads

---

DRAM_destill 1 1 1
DRAM_set_db_loc 1 1 1
align 1 2 2
align_reads_to_Genecatalog 3 2 2
align_reads_to_MAGs 3 2 2
align_reads_to_final_contigs 3 2 2
all 1 1 1
all_contigs2bins 1 1 1
all_gtdb_trees 1 1 1
all_prodigal 1 1 1
assembly 1 1 1
assembly_one_sample 3 1 1
bam_2_sam_contigs 3 2 2
binning 1 1 1
build_assembly_report 1 1 1
build_bin_report 1 1 1
build_db_genomes 1 2 2
build_qc_report 1 1 1
calculate_contigs_stats 6 1 1
calculate_insert_size 3 2 2
classify 1 2 2
cluster_genes 1 2 2
combine_bin_stats 1 1 1
combine_bined_coverages_MAGs 1 1 1
combine_contig_stats 1 1 1
combine_coverages_MAGs 1 1 1
combine_egg_nogg_annotations 1 1 1
combine_gene_coverages 1 1 1
combine_insert_stats 1 1 1
combine_read_counts 1 1 1
combine_read_length_stats 1 1 1
combine_taxonomy 1 1 1
concat_annotations 1 1 1
concat_genes 1 1 1
convert_sam_to_bam 6 2 2
dereplication 1 2 2
do_not_filter_contigs 3 1 1
dram_download 1 2 2
filter_genes 1 1 1
finalize_contigs 3 1 1
finalize_sample_qc 3 1 1
gene2genome 1 1 1
gene_subsets 1 1 1
genecatalog 1 1 1
genomes 1 1 1
get_all_bins 1 1 1
get_all_modules 1 1 1
get_bins 3 1 1
get_contigs_from_gene_names 3 1 1
get_metabat_depth_file 3 2 2
get_quality_for_dRep_from_checkm 1 1 1
get_unique_cluster_attribution 3 1 1
identify 1 2 2
merge_checkm 1 1 1
merge_pairs 1 2 2
metabat 3 2 2
parse_clstr_files 1 1 1
pileup 3 2 2
pileup_Genecatalog 3 2 2
pileup_MAGs 3 2 2
predict_genes 3 1 1
qc 1 1 1
rename_contigs 3 2 2
rename_gene_catalog 1 1 1
rename_gene_clusters 1 1 1
rename_genomes 1 1 1
rename_spades_output 3 1 1
run_all_checkm_lineage_wf 1 2 2
run_checkm_lineage_wf 3 2 2
run_checkm_tree_qa 3 1 1
run_spades 3 2 2
write_read_counts 1 1 1
total 128 1 2

[Tue Nov 9 17:25:45 2021]
rule run_spades:
input: tratada/assembly/reads/QC.errorcorr.merged_R1.fastq.gz, tratada/assembly/reads/QC.errorcorr.merged_R2.fastq.gz, tratada/assembly/reads/QC.errorcorr.merged_me.fastq.gz
output: tratada/assembly/contigs.fasta, tratada/assembly/scaffolds.fasta
log: tratada/logs/assembly/spades.log
jobid: 84
benchmark: logs/benchmarks/assembly/spades/tratada.txt
wildcards: sample=tratada
threads: 2
resources: tmpdir=/tmp, mem=16, time=48, mem_mb=16000, time_min=2880

Activating conda environment: /media/archaea/UBUNTU-HD/doutorado/atlas_database/conda_envs/a1293008546da0884a56f95a1ffd71c1
[Tue Nov 9 17:25:45 2021]
Error in rule run_spades:
jobid: 84
output: tratada/assembly/contigs.fasta, tratada/assembly/scaffolds.fasta
log: tratada/logs/assembly/spades.log (check log file(s) for error message)
conda-env: /media/archaea/UBUNTU-HD/doutorado/atlas_database/conda_envs/a1293008546da0884a56f95a1ffd71c1
shell:
rm -f tratada/assembly/pipeline_state/stage_*_copy_files 2> tratada/logs/assembly/spades.log ; spades.py --threads 2 --memory 16 -o tratada/assembly -k 21,33,55,77,99,127 --restart-from last >> tratada/logs/assembly/spades.log 2>&1
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /media/archaea/UBUNTU-HD/doutorado/atlas/.snakemake/log/2021-11-09T172506.723742.snakemake.log

[kuangzhuoran]

Hi！I met the same error, In the log(.../assembly/spades.log)

I see " AttributeError: module 'collections' has no attribute 'Hashable' ",

there may be two problems：

1. I need to install collections module
   'pip install collections' did not work and and there is 'collections' in the default library of python3
2. The names of some scripts are “ collections.py ”
   but i didn't find it

Then I navigate ablab/spades#863, One reply is “Thanks for letting us know! We will consider integrating the fix in the next SPAdes versions.”

[SilasK]

Fixed in atlas v2.8.1 which is in process of being built on conda