(../scripts/rase_test_environments.sh 2>&1) >/dev/null || ../scripts/rase_test_environments.sh
localrules directive specifies rules that are not present in the Snakefile:
test_environments
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 3
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 plot
1 plot_snapshots
1 plot_timeline
1 predict
4
[Mon Feb 25 09:42:26 2019]
rule predict:
input: prediction/.ERR1813536__gono_k18.assign.complete, database/.gono_k18.complete
output: prediction/.ERR1813536__gono_k18.predict.complete
jobid: 2
benchmark: benchmarks/ERR1813536__gono_k18.predict.log
wildcards: pref=ERR1813536, index=gono_k18
priority: 80
mkdir -p "prediction/ERR1813536__gono_k18"
../src/rase/rase_predict.py -t clock -s 1 -p "prediction/ERR1813536__gono_k18/" "database/gono_k18/tree.nw" "database/gono_k18.tsv" "prediction/ERR1813536__gono_k18.bam" > "prediction/ERR1813536__gono_k18.predict_without_flags.tsv"
../src/rase/rase_prediction_add_flags.py "prediction/ERR1813536__gono_k18.predict_without_flags.tsv" > "prediction/ERR1813536__gono_k18.predict.tsv"
rm "prediction/ERR1813536__gono_k18.predict_without_flags.tsv"
touch "prediction/.ERR1813536__gono_k18.predict.complete"
Time t=0h1m: 0 reads and 0 kbps.
Time t=0h1m: 1,203 reads and 12,219 kbps.
Time t=0h1m: 1,203 reads and 12,219 kbps.
Time t=0h1m: 1,204 reads and 12,227 kbps.
Time t=0h1m: 1,736 reads and 17,606 kbps.
Time t=0h1m: 1,737 reads and 17,615 kbps.
Time t=0h1m: 1,966 reads and 19,800 kbps.
Time t=0h1m: 2,963 reads and 29,583 kbps.
Time t=0h1m: 2,964 reads and 29,596 kbps.
Time t=0h1m: 2,965 reads and 29,609 kbps.
Time t=0h1m: 2,966 reads and 29,618 kbps.
Time t=0h1m: 2,967 reads and 29,628 kbps.
Time t=0h2m: 2,967 reads and 29,629 kbps.
Time t=0h2m: 3,970 reads and 39,337 kbps.
Time t=0h2m: 5,053 reads and 50,019 kbps.
Time t=0h2m: 6,511 reads and 64,074 kbps.
Time t=0h2m: 8,002 reads and 78,749 kbps.
Time t=0h2m: 9,328 reads and 91,645 kbps.
Time t=0h2m: 10,796 reads and 106,053 kbps.
Time t=0h2m: 12,414 reads and 121,865 kbps.
Time t=0h2m: 13,750 reads and 134,879 kbps.
Time t=0h2m: 15,191 reads and 148,802 kbps.
Time t=0h2m: 15,191 reads and 148,808 kbps.
Time t=0h2m: 15,191 reads and 148,808 kbps.
Time t=0h2m: 15,633 reads and 152,961 kbps.
Time t=0h2m: 16,602 reads and 162,650 kbps.
Time t=0h2m: 17,235 reads and 168,712 kbps.
Time t=0h2m: 18,097 reads and 177,274 kbps.
Time t=0h2m: 19,252 reads and 188,418 kbps.
Time t=0h2m: 20,251 reads and 198,222 kbps.
Time t=0h2m: 21,659 reads and 211,738 kbps.
Time t=0h2m: 23,108 reads and 225,900 kbps.
Time t=0h2m: 24,627 reads and 240,845 kbps.
Time t=0h2m: 25,936 reads and 253,988 kbps.
Time t=0h2m: 27,439 reads and 269,016 kbps.
Time t=0h2m: 28,675 reads and 281,141 kbps.
Time t=0h2m: 30,200 reads and 295,713 kbps.
Time t=0h2m: 30,201 reads and 295,719 kbps.
Time t=0h2m: 30,223 reads and 295,959 kbps.
Time t=0h2m: 31,382 reads and 307,609 kbps.
Time t=0h2m: 31,554 reads and 309,264 kbps.
Time t=0h2m: 32,970 reads and 323,155 kbps.
Time t=0h2m: 32,971 reads and 323,166 kbps.
Time t=0h2m: 34,056 reads and 333,784 kbps.
Time t=0h2m: 35,608 reads and 349,236 kbps.
Time t=0h2m: 37,198 reads and 364,663 kbps.
Time t=0h2m: 38,910 reads and 381,151 kbps.
Time t=0h2m: 40,545 reads and 397,201 kbps.
Time t=0h2m: 40,546 reads and 397,209 kbps.
Time t=0h2m: 41,071 reads and 402,262 kbps.
Time t=0h3m: 41,238 reads and 403,909 kbps.
OSError: [Errno 5] Input/output error
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "../src/rase/rase_predict.py", line 780, in <module>
main()
File "../src/rase/rase_predict.py", line 774, in main
r.run()
File "../src/rase/rase_predict.py", line 126, in run
f.close()
OSError: [Errno 5] Input/output error
[Mon Feb 25 09:44:40 2019]
Error in rule predict:
jobid: 2
output: prediction/.ERR1813536__gono_k18.predict.complete
RuleException:
CalledProcessError in line 218 of /n/scratch2/kb219/rase-experiments/46_pneumo_negative_control/rase/pipeline/Snakefile:
Command 'set -eo pipefail; mkdir -p "prediction/ERR1813536__gono_k18"
../src/rase/rase_predict.py -t clock -s 1 -p "prediction/ERR1813536__gono_k18/" "database/gono_k18/tree.nw" "database/gono_k18.tsv" "prediction/ERR1813536__gono_k18.bam" > "prediction/ERR1813536__gono_k18.predict_without_flags.tsv"
../src/rase/rase_prediction_add_flags.py "prediction/ERR1813536__gono_k18.predict_without_flags.tsv" > "prediction/ERR1813536__gono_k18.predict.tsv"
rm "prediction/ERR1813536__gono_k18.predict_without_flags.tsv"
touch "prediction/.ERR1813536__gono_k18.predict.complete"' returned non-zero exit status 1.
File "/n/scratch2/kb219/rase-experiments/46_pneumo_negative_control/rase/pipeline/Snakefile", line 218, in __rule_predict
File "/home/kb219/miniconda/envs/rase/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Indexes: ['gono_k18', 'spneumoniae_sparc.k18']
