Asset build output example
Command:
$ refgenie build -c genomes.yaml hg38/fasta --fasta hg38.fa.gz
Output:
Output to: hg38 /Users/mstolarczyk/Desktop/testing/test_genomes /Users/mstolarczyk/Desktop/testing/test_genomes/hg38
Removed 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 tag
Inputs required to build 'fasta': fasta
Building 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: default
Computing 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