Running different snakemake rules in parallel - snakemake

Question

I show below a pseudocode version of my snakefile. Snakemake rule A creates the input files for Snakemake rule B2 and I would like to run Snakemake rules B1 and B2 at the same time but am not having success. I can run this snakefile successfully on very small data without a problem (although the Snakemake rules B1 and B2 do not run in parallel) but once I give it larger data it fails to create the output for Snakemake rule B1. The commands between Snakemake rule B1 and B2 use the same program but have different arguments and input files so I didn't think they should be in the same rule.
rule all:
input: file_A_out, file_B1_out, file_B2_out, file_C_out
rule A:
input: file_A_in
output: file_A_out
log: file_A_log
shell: 'progA {input} --output {output}'
rule B1:
input: file_B1_in
output: file_B1_out
group: 'groupB'
log: file_B1_log
shell: 'progB {input} -x 100 -o {output}'
rule B2:
input: file_A_out
output: file_B2_out
group: 'groupB'
log: file_B2_log
shell: 'progB {input} -x 1 --y -o {output}'
rule C:
input: file_B1_out, file_B2_out
output: file_C_out
log: file_C_log
shell: 'progC {input[0]} {input[1]} -o {output}'
I thought using group to group the rules would indicate to Snakemake that the two rules can be ran at once. To execute snakemake I run nohup snakemake --cores 16 > log.txt 2>&1 & however, it only successfully runs rule B2 while the output of rule B1 is deemed corrupted. I have seen solutions on running one rule in parallel but what about running different rules in parallel?
Error in rule B1:
jobid: 2
input: 'file_B1_in'
output: 'file_B1_out'
log: 'file_B1_log'
(check log file(s) for error details)
shell: 'progB {input} -x 100 -o {output}'
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Removing output files of failed job B1 since they might be corrupted:
file_B1_out
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

Answer 1

The snakefile below runs rules A, B1, and B2 in parallel then runs rule C, as expected. Maybe there is something you are not showing us?
# Make dummy input files
touch file_A_in file_B1_in
# Run pipeline
snakemake -p -j 10
The snakefile:
rule all:
input: 'file_A_out', 'file_B1_out', 'file_B2_out', 'file_C_out'
rule A:
input: 'file_A_in'
output: 'file_A_out'
shell: 'sleep 10; echo {input} > {output}'
rule B1:
input: 'file_B1_in'
output: 'file_B1_out'
shell: 'sleep 10; echo {input} > {output}'
rule B2:
input: 'file_A_in'
output: 'file_B2_out'
shell: 'sleep 10; echo {input} > {output}'
rule C:
input: 'file_B1_out', 'file_B2_out'
output: 'file_C_out'
shell: 'sleep 10; echo {input[0]} {input[1]} > {output}'