fix: sleep a random time to work around GNU parallel bug (#328)

bihealth · Jan 11, 2023 · 7a02aea · 7a02aea
1 parent 3d045e6
commit 7a02aea
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Showing 7 changed files with 7 additions and 6 deletions.
diff --git a/snappy_wrappers/wrappers/bcftools_call/wrapper.py b/snappy_wrappers/wrappers/bcftools_call/wrapper.py
@@ -125,7 +125,7 @@
 export -f run-shard
 
 # Perform parallel execution
-mkdir -p $TMPDIR/parallel
+(set -x; sleep $(echo "scale=3; $RANDOM/32767*10" | bc)s) # sleep up to 10s to work around bug
 num_threads={snakemake.config[step_config][variant_calling][gatk4_hc_joint][num_threads]}
 cat $TMPDIR/final_intervals.txt \
 | parallel --plain -j $num_threads 'run-shard {{#}} {{}}'

diff --git a/snappy_wrappers/wrappers/gatk3_hc/wrapper.py b/snappy_wrappers/wrappers/gatk3_hc/wrapper.py
@@ -108,7 +108,7 @@
 export -f run-shard
 
 # Perform parallel execution
-mkdir -p $TMPDIR/parallel
+(set -x; sleep $(echo "scale=3; $RANDOM/32767*10" | bc)s) # sleep up to 10s to work around bug
 num_threads={snakemake.config[step_config][variant_calling][gatk3_hc][num_threads]}
 cat $TMPDIR/final_intervals.txt \
 | parallel --plain -j $num_threads 'run-shard {{#}} {{}}'

diff --git a/snappy_wrappers/wrappers/gatk3_ug/wrapper.py b/snappy_wrappers/wrappers/gatk3_ug/wrapper.py
@@ -109,7 +109,7 @@
 export -f run-shard
 
 # Perform parallel execution
-mkdir -p $TMPDIR/parallel
+(set -x; sleep $(echo "scale=3; $RANDOM/32767*10" | bc)s) # sleep up to 10s to work around bug
 num_threads={snakemake.config[step_config][variant_calling][gatk3_ug][num_threads]}
 cat $TMPDIR/final_intervals.txt \
 | parallel --plain -j $num_threads 'run-shard {{#}} {{}}'

diff --git a/snappy_wrappers/wrappers/gatk4_hc/combine_gvcfs/wrapper.py b/snappy_wrappers/wrappers/gatk4_hc/combine_gvcfs/wrapper.py
@@ -110,7 +110,7 @@
 export -f run-shard
 
 # Perform parallel execution
-mkdir -p $TMPDIR/parallel
+(set -x; sleep $(echo "scale=3; $RANDOM/32767*10" | bc)s) # sleep up to 10s to work around bug
 num_threads={snakemake.config[step_config][variant_calling][gatk4_hc_gvcf][num_threads]}
 cat $TMPDIR/final_intervals.txt \
 | parallel --plain -j $num_threads 'run-shard {{#}} {{}}'

diff --git a/snappy_wrappers/wrappers/gatk4_hc/discover/wrapper.py b/snappy_wrappers/wrappers/gatk4_hc/discover/wrapper.py
@@ -113,7 +113,7 @@
 export -f run-shard
 
 # Perform parallel execution
-mkdir -p $TMPDIR/parallel
+(set -x; sleep $(echo "scale=3; $RANDOM/32767*10" | bc)s) # sleep up to 10s to work around bug
 num_threads={snakemake.config[step_config][variant_calling][gatk4_hc_gvcf][num_threads]}
 cat $TMPDIR/final_intervals.txt \
 | parallel --plain -j $num_threads 'run-shard {{#}} {{}}'

diff --git a/snappy_wrappers/wrappers/gatk4_hc/genotype/wrapper.py b/snappy_wrappers/wrappers/gatk4_hc/genotype/wrapper.py
@@ -106,7 +106,7 @@
 export -f run-shard
 
 # Perform parallel execution
-mkdir -p $TMPDIR/parallel
+(set -x; sleep $(echo "scale=3; $RANDOM/32767*10" | bc)s) # sleep up to 10s to work around bug
 num_threads={snakemake.config[step_config][variant_calling][gatk4_hc_gvcf][num_threads]}
 cat $TMPDIR/final_intervals.txt \
 | parallel --plain -j $num_threads 'run-shard {{#}} {{}}'

diff --git a/snappy_wrappers/wrappers/gatk4_hc/joint/wrapper.py b/snappy_wrappers/wrappers/gatk4_hc/joint/wrapper.py
@@ -111,6 +111,7 @@
 export -f run-shard
 
 # Perform parallel execution
+(set -x; sleep $(echo "scale=3; $RANDOM/32767*10" | bc)s) # sleep up to 10s to work around bug
 num_threads={snakemake.config[step_config][variant_calling][gatk4_hc_joint][num_threads]}
 cat $TMPDIR/final_intervals.txt \
 | parallel -j $num_threads 'run-shard {{#}} {{}}'