Asset build output example
Command:
$ refgenie build -c genomes.yaml hg38/fasta --fasta hg38.fa.gzOutput:
Output to: hg38 /Users/mstolarczyk/Desktop/testing/test_genomes /Users/mstolarczyk/Desktop/testing/test_genomes/hg38Removed existing flag: '/Users/mstolarczyk/Desktop/testing/test_genomes/hg38/refgenie_failed.flag'### Pipeline run code and environment:
* Command: `/Library/Frameworks/Python.framework/Versions/3.6/bin/refgenie build -c genomes.yaml hg38/fasta --fasta hg38.fa.gz`* Compute host: MichalsMBP* Working dir: /Users/mstolarczyk/Desktop/testing/test_genomes* Outfolder: /Users/mstolarczyk/Desktop/testing/test_genomes/hg38/* Pipeline started at: (09-17 08:42:19) elapsed: 0.0 _TIME_
### Version log:
* Python version: 3.6.5* Pypiper dir: `/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pypiper`* Pypiper version: 0.12.0dev* Pipeline dir: `/Library/Frameworks/Python.framework/Versions/3.6/bin`* Pipeline version: None
### Arguments passed to pipeline:
* `command`: `build`* `silent`: `False`* `verbosity`: `None`* `logdev`: `False`* `genome_config`: `genomes.yaml`* `recover`: `False`* `config_file`: `/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/refgenie/refgenie.yaml`* `new_start`: `False`* `docker`: `False`* `tags`: `None`* `volumes`: `None`* `outfolder`: `/Users/mstolarczyk/Desktop/testing/test_genomes`* `requirements`: `False`* `genome`: `None`* `asset_registry_paths`: `['hg38/fasta']`* `fasta`: `hg38.fa.gz`* `ensembl_gtf`: `None`* `gencode_gtf`: `None`* `gff`: `None`* `context`: `None`* `refgene`: `None`
----------------------------------------
MissingAssetError: using 'default' as the default tagInputs required to build 'fasta': fastaBuilding asset 'fasta'Target to produce: `/Users/mstolarczyk/Desktop/testing/test_genomes/hg38/fasta/default/build_complete.flag`
> `cp hg38.fa.gz /Users/mstolarczyk/Desktop/testing/test_genomes/hg38/fasta/default/hg38.fa.gz` (38283)<pre></pre>Command completed. Elapsed time: 0:00:01. Running peak memory: 0.002GB. PID: 38283; Command: cp; Return code: 0; Memory used: 0.002GB
> `gzip -d /Users/mstolarczyk/Desktop/testing/test_genomes/hg38/fasta/default/hg38.fa.gz` (38284)<pre></pre>Command completed. Elapsed time: 0:00:09. Running peak memory: 0.002GB. PID: 38284; Command: gzip; Return code: 0; Memory used: 0.001GB
> `samtools faidx /Users/mstolarczyk/Desktop/testing/test_genomes/hg38/fasta/default/hg38.fa` (38285)<pre></pre>Command completed. Elapsed time: 0:00:14. Running peak memory: 0.005GB. PID: 38285; Command: samtools; Return code: 0; Memory used: 0.005GB
> `cut -f 1,2 /Users/mstolarczyk/Desktop/testing/test_genomes/hg38/fasta/default/hg38.fa.fai > /Users/mstolarczyk/Desktop/testing/test_genomes/hg38/fasta/default/hg38.chrom.sizes` (38286)<pre></pre>Command completed. Elapsed time: 0:00:00. Running peak memory: 0.005GB. PID: 38286; Command: cut; Return code: 0; Memory used: 0.001GB
> `touch /Users/mstolarczyk/Desktop/testing/test_genomes/hg38/fasta/default/build_complete.flag` (38288)<pre>psutil.ZombieProcess process still exists but it's a zombie (pid=38288)Warning: couldn't add memory use for process: 38288</pre>Command completed. Elapsed time: 0:00:00. Running peak memory: 0.005GB. PID: 38288; Command: touch; Return code: 0; Memory used: 0GB
> `cd /Users/mstolarczyk/Desktop/testing/test_genomes/hg38/fasta/default; find . -type f -exec md5sum {} \; | sort -k 2 | awk '{print $1}' | md5sum`Default tag for 'hg38/fasta' set to: defaultComputing initial genome digest...Initializing genome...Finished building asset 'fasta'
### Pipeline completed. Epilogue* Elapsed time (this run): 0:10:23* Total elapsed time (all runs): 0:16:17* Peak memory (this run): 0.01 GB* Pipeline completed time: 2019-09-17 08:52:42