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Simulate integrations and score results
I am not able to import a fasta with the singularity flag.
Works fine with the conda flag.
I used the human GRCh38 chromosome 1 as host and the HBV_NC_003977.2 as virus.
snakemake --snakefile Snakefile --configfile test/config/HBVhuman.yml --use-singularity --cores 1
Config:
# conduct multiple experiments
# each experiment has multiple conditions, which have different parameteres
# within each experiment, use all possible combinations of all parameters ('conditions')
# and perform a number of replicates of each condition
HBVhumanChr1:
### experiment parameters ###
out_directory: "/home/bready/Workspace/data/out/" # root directory for output
replicates: 2 # number of replicates for each condition (combination of parameters)
### parameters for integration simulation (python script) ###
# fasta files to use for simulating integrations
# and names for each
hosts:
"human" : "/home/bready/Workspace/data/references/GRCh38_human_chr1.fna"
viruses:
"HBV" : "/home/bready/Workspace/data/references/HBV_NC_003977_2.fasta"
# random seed for first replicate - will be incremented on successive replicates
# use the same seed for the python script and ART
initial_seed: 12345
seed_increment: 123
# number of integrations to perform
int_num:
- 10
min_sep:
- 50
epi_num:
- 0
# probabilities
p_whole:
- 0.5
min_len:
- 50
p_rearrange:
- 0.1
p_delete:
- 0.1
lambda_split:
- 1
p_overlap:
- 0.2
p_gap:
- 0.2
lambda_junction:
- 1
p_host_deletion:
- 0.2
lambda_host_deletion:
- 20
### parameters for read simulation (art) ###
read_len:
- 150
# fold coverage (-f)
fcov:
- 10
# mean fragment length (-m)
frag_len:
- 250
- 500
# fragment length standard deviation (-s)
frag_std:
- 30
# sequencing system profile for art-illumna
seq_sys:
- "MSv3"
Error message:
(intvi) bready@Bready-Desktop:~/Workspace/intvi_simulation$ snakemake --snakefile Snakefile --configfile test/config/HBVhuman.yml --use-singularity --cores 1
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Conda environments: ignored
Job counts:
count jobs
1 all
4 annotate_reads
4 art
4 convert
4 simulate_integrations
1 write_summary
18
[Wed Nov 18 13:59:07 2020]
rule simulate_integrations:
input: /home/bready/Workspace/data/references/GRCh38_human_chr1.fna, /home/bready/Workspace/data/references/HBV_NC_003977_2.fasta
output: /home/bready/Workspace/data/out/HBVhumanChr1/sim_ints/cond1.rep0.fa, /home/bready/Workspace/data/out/HBVhumanChr1/sim_ints/cond1.rep0.int-info.tsv, /home/bready/Workspace/data/out/HBVhumanChr1/sim_ints/cond1.rep0.epi-info.tsv
jobid: 9
wildcards: outpath=/home/bready/Workspace/data/out, exp=HBVhumanChr1, samp=cond1.rep0
resources: mem_mb=1765, time=2:00:00, nodes=1
Activating singularity image /home/bready/Workspace/intvi_simulation/.snakemake/singularity/c567d0aedeec996de62affb41dc79c42.simg
INFO: Convert SIF file to sandbox...
initialising a new Events object
importing host fasta
Traceback (most recent call last):
File "scripts/insert_virus.py", line 1880, in <module>
main(argv[1:])
File "scripts/insert_virus.py", line 113, in main
seqs = Events(args.host, args.virus, seed=args.seed, verbose = True, min_len = args.min_len)
File "scripts/insert_virus.py", line 161, in __init__
raise OSError("Could not open host fasta")
OSError: Could not open host fasta
INFO: Cleaning up image...
[Wed Nov 18 13:59:09 2020]
Error in rule simulate_integrations:
jobid: 9
output: /home/bready/Workspace/data/out/HBVhumanChr1/sim_ints/cond1.rep0.fa, /home/bready/Workspace/data/out/HBVhumanChr1/sim_ints/cond1.rep0.int-info.tsv, /home/bready/Workspace/data/out/HBVhumanChr1/sim_ints/cond1.rep0.epi-info.tsv
shell:
python3 scripts/insert_virus.py --host /home/bready/Workspace/data/references/GRCh38_human_chr1.fna --virus /home/bready/Workspace/data/references/HBV_NC_003977_2.fasta --ints /home/bready/Workspace/data/out/HBVhumanChr1/sim_ints/cond1.rep0.fa --int_info /home/bready/Workspace/data/out/HBVhumanChr1/sim_ints/cond1.rep0.int-info.tsv --epi_info /home/bready/Workspace/data/out/HBVhumanChr1/sim_ints/cond1.rep0.epi-info.tsv --int_num 10 --epi_num 0 --min-sep 50 --min-len 50 --p_whole 0.5 --p_rearrange 0.1 --p_delete 0.1 --lambda_split 1 --p_overlap 0.2 --p_gap 0.2 --lambda_junction 1 --p_host_deletion 0.2 --lambda_host_deletion 20 --seed 12468 --verbose
(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: /home/bready/Workspace/intvi_simulation/.snakemake/log/2020-11-18T135907.106881.snakemake.log
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