Hi Cornelius,
When I ran the initial build:
mask:
mask_from_end: 8341 # to cover bp 1 - 21562 of the SARS-CoV-2 genome only (= ORF1a/b)
filter:
min_length: 17000 # to allow shorter (partial) genomes
# or alternatively, I tried:
skip_diagnostics: True
I received the following error:
WARNING: more threads requested than there are sequences; falling back to IQ-TREE's `-nt AUTO` mode.
ERROR: Shell exited 2 when running: iqtree -nt AUTO -s results/NYU_rec_Delta-part_testthree/masked_filtered-delim.fasta -m GTR -ninit 2 -n 2 -me 0.05 -ninit 10 -n 4 > results/NYU_rec_Delta-part_testthree/masked_filtered-delim.iqtree.log
Command output was:
ERROR: Alignment must have at least 3 sequences
7 masking sites read from defaults/sites_ignored_for_tree_topology.txt
Building a tree via:
iqtree -nt AUTO -s results/NYU_rec_Delta-part_testthree/masked_filtered-delim.fasta -m GTR -ninit 2 -n 2 -me 0.05 -ninit 10 -n 4 > results/NYU_rec_Delta-part_testthree/masked_filtered-delim.iqtree.log
Nguyen et al: IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies.
Mol. Biol. Evol., 32:268-274. https://doi.org/10.1093/molbev/msu300
ERROR: TREE BUILDING FAILED
Please see the log file for more details: results/NYU_rec_Delta-part_testthree/masked_filtered-delim.iqtree.log
Building original tree took 0.008130550384521484 seconds
[Tue Mar 22 04:34:26 2022]
Error in rule tree:
jobid: 21
output: results/NYU_rec_Delta-part_testthree/tree_raw.nwk
log: logs/tree_NYU_rec_Delta-part_testthree.txt (check log file(s) for error message)
shell:
augur tree --alignment results/NYU_rec_Delta-part_testthree/filtered.fasta --tree-builder-args '-ninit 10 -n 4' --exclude-sites defaults/sites_ignored_for_tree_topology.txt --output results/NYU_rec_Delta-part_testthree/tree_raw.nwk --nthreads 4 2>&1 | tee logs/tree_NYU_rec_Delta-part_testthree.txt
(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
Based on your suggestion, I tried to include a new snakemake rule by:
- creating a my_rule.smk.txt file:
def _get_node_data_by_wildcards(wildcards):
"""Return a list of node data files to include for a given build's wildcards.
"""
# Define inputs shared by all builds.
wildcards_dict = dict(wildcards)
inputs = [
rules.refine.output.node_data,
rules.ancestral.output.node_data,
rules.translate.output.node_data,
rules.rename_emerging_lineages.output.clade_data,
rules.clades.output.clade_data,
rules.recency.output.node_data,
rules.traits.output.node_data,
rules.logistic_growth.output.node_data,
rules.mutational_fitness.output.node_data,
# rules.distances.output.node_data,
rules.calculate_epiweeks.output.node_data,
]
if "run_pangolin" in config and config["run_pangolin"]:
inputs.append(rules.make_pangolin_node_data.output.node_data)
# Convert input files from wildcard strings to real file names.
inputs = [input_file.format(**wildcards_dict) for input_file in inputs]
return inputs
…where I removed the rules.distances line as you suggested (not sure I did it the right way), and also referring to the my_rules.smk.txt file in the builds.yaml file:
custom_rules:
- my_profiles/recomb/my_rules.smk.txt
but I received the following error message:
Error in rule tree:
jobid: 21
output: results/NYU_rec_Delta-part_testfour/tree_raw.nwk
log: logs/tree_NYU_rec_Delta-part_testfour.txt (check log file(s) for error message)
shell:
augur tree --alignment results/NYU_rec_Delta-part_testfour/filtered.fasta --tree-builder-args '-ninit 10 -n 4' --exclude-sites defaults/sites_ignored_for_tree_topology.txt --output results/NYU_rec_Delta-part_testfour/tree_raw.nwk --nthreads 4 2>&1 | tee logs/tree_NYU_rec_Delta-part_testfour.txt
(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
Any thoughts?
Thank you!!