### Pipeline run code and environment:
* Command: `/home/mjs5kd/.local/bin/refgenie build hg19_cdna/salmon_index`
* Compute host: udc-ba25-17
* Working dir: /sfs/qumulo/qproject/shefflab/deploy/rg.databio.org_full/rg.databio.org
* Outfolder: /project/shefflab/deploy/rg.databio.org_full/genomes/data/fc77e33fa26398662380748a62ab6279dab2a637256acd89/salmon_index/default/_refgenie_build/
* Pipeline started at: (04-08 16:06:05) elapsed: 0.0 _TIME_
### Version log:
* Python version: 3.6.6
* Pypiper dir: `/sfs/qumulo/qhome/mjs5kd/.local/lib/python3.6/site-packages/pypiper`
* Pypiper version: 0.12.1
* Pipeline dir: `/sfs/qumulo/qhome/mjs5kd/.local/bin`
* Pipeline version: None
### Arguments passed to pipeline:
* `asset_registry_paths`: `['hg19_cdna/salmon_index']`
* `assets`: `None`
* `command`: `build`
* `config_file`: `refgenie.yaml`
* `docker`: `False`
* `files`: `None`
* `genome`: `None`
* `genome_config`: `None`
* `genome_description`: `None`
* `logdev`: `False`
* `new_start`: `False`
* `outfolder`: `/project/shefflab/deploy/rg.databio.org_full/genomes/data`
* `params`: `None`
* `recipe`: `None`
* `recover`: `False`
* `requirements`: `False`
* `silent`: `False`
* `skip_read_lock`: `False`
* `tag_description`: `None`
* `verbosity`: `None`
* `volumes`: `None`
----------------------------------------
Target to produce: `/project/shefflab/deploy/rg.databio.org_full/genomes/data/fc77e33fa26398662380748a62ab6279dab2a637256acd89/salmon_index/default/_refgenie_build/fc77e33fa26398662380748a62ab6279dab2a637256acd89_salmon_index__default.flag`
> `salmon index -t /project/shefflab/deploy/rg.databio.org_full/genomes/data/fc77e33fa26398662380748a62ab6279dab2a637256acd89/fasta/default/fc77e33fa26398662380748a62ab6279dab2a637256acd89.fa -i /project/shefflab/deploy/rg.databio.org_full/genomes/data/fc77e33fa26398662380748a62ab6279dab2a637256acd89/salmon_index/default -k 31 -p 8` (23098)
[33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
Version Info: Could not resolve upgrade information in the alotted time.
Check for upgrades manually at https://combine-lab.github.io/salmon
[2021-04-08 16:06:06.012] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.
[2021-04-08 16:06:06.012] [jLog] [info] building index
out : /project/shefflab/deploy/rg.databio.org_full/genomes/data/fc77e33fa26398662380748a62ab6279dab2a637256acd89/salmon_index/default
[2021-04-08 16:06:06.015] [puff::index::jointLog] [info] Running fixFasta
[Step 1 of 4] : counting k-mers
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000415118], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000434970], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000448914], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000604642], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000603326], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000604950], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000603077], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000605284], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000604446], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000603693], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000603935], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000604102], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000604838], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000390591], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000454908], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000439842], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000390567], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000452198], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000390569], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000437320], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000390571], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000390572], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000450276], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000390574], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000390575], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000431870], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000390578], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000451044], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000390580], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000390581], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000431440], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000390583], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000390584], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000390585], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000430425], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000454691], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000390588], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000414852], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000390590], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000604319], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000603768], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000604592], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000605864], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000603644], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000603804], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000604055], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000603618], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000603316], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000605850], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000603007], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000605143], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000603340], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000603359], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000604735], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000603379], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000604309], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000604234], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000603739], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000604564], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000603303], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000605430], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000605685], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000603725], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000605709], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.029] [puff::index::jointLog] [warning] Entry with header [ENST00000604111], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.130] [puff::index::jointLog] [warning] Entry with header [ENST00000489969], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.409] [puff::index::jointLog] [warning] Entry with header [ENST00000551948], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:06.447] [puff::index::jointLog] [warning] Entry with header [ENST00000550409], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:08.001] [puff::index::jointLog] [warning] Entry with header [ENST00000595481], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:08.534] [puff::index::jointLog] [warning] Entry with header [ENST00000552580], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:09.025] [puff::index::jointLog] [warning] Entry with header [ENST00000598624], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:09.384] [puff::index::jointLog] [warning] Entry with header [ENST00000602572], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:09.776] [puff::index::jointLog] [warning] Entry with header [ENST00000548090], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:10.478] [puff::index::jointLog] [warning] Entry with header [ENST00000437226], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:10.632] [puff::index::jointLog] [warning] Entry with header [ENST00000417283], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:10.632] [puff::index::jointLog] [warning] Entry with header [ENST00000465958], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:10.860] [puff::index::jointLog] [warning] Entry with header [ENST00000594394], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:10.965] [puff::index::jointLog] [warning] Entry with header [ENST00000552241], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:10.998] [puff::index::jointLog] [warning] Entry with header [ENST00000598940], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:12.715] [puff::index::jointLog] [warning] Entry with header [ENST00000552194], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:13.632] [puff::index::jointLog] [warning] Entry with header [ENST00000518246], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:13.634] [puff::index::jointLog] [warning] Entry with header [ENST00000605343], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:13.850] [puff::index::jointLog] [warning] Entry with header [ENST00000473810], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:13.882] [puff::index::jointLog] [warning] Entry with header [ENST00000606517], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:13.883] [puff::index::jointLog] [warning] Entry with header [ENST00000543745], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:13.925] [puff::index::jointLog] [warning] Entry with header [ENST00000573437], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:14.021] [puff::index::jointLog] [warning] Entry with header [ENST00000579054], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:14.038] [puff::index::jointLog] [warning] Entry with header [ENST00000603775], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:06:14.084] [puff::index::jointLog] [warning] Removed 12985 transcripts that were sequence duplicates of indexed transcripts.
[2021-04-08 16:06:14.084] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag
[2021-04-08 16:06:14.143] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides
[2021-04-08 16:06:14.143] [puff::index::jointLog] [info] Clipped poly-A tails from 1401 transcripts
wrote 167220 cleaned references
[2021-04-08 16:06:16.635] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2021-04-08 16:06:18.949] [puff::index::jointLog] [info] ntHll estimated 100826112 distinct k-mers, setting filter size to 2^31
Threads = 8
Vertex length = 31
Hash functions = 5
Filter size = 2147483648
Capacity = 2
Files:
/project/shefflab/deploy/rg.databio.org_full/genomes/data/fc77e33fa26398662380748a62ab6279dab2a637256acd89/salmon_index/default/ref_k31_fixed.fa
--------------------------------------------------------------------------------
Round 0, 0:2147483648
Pass Filling Filtering
1 73 164
2 67 0
True junctions count = 665162
False junctions count = 998367
Hash table size = 1663529
Candidate marks count = 7808426
--------------------------------------------------------------------------------
Reallocating bifurcations time: 0
True marks count: 5143432
Edges construction time: 2611
--------------------------------------------------------------------------------
Distinct junctions = 665162
allowedIn: 15
Max Junction ID: 768114
seen.size():6144921 kmerInfo.size():768115
approximateContigTotalLength: 72596465
counters for complex kmers:
(prec>1 & succ>1)=38809 | (succ>1 & isStart)=685 | (prec>1 & isEnd)=713 | (isStart & isEnd)=75
contig count: 994041 element count: 131267297 complex nodes: 40282
# of ones in rank vector: 994040
[2021-04-08 16:55:14.915] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2021-04-08 16:55:14.915] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory /project/shefflab/deploy/rg.databio.org_full/genomes/data/fc77e33fa26398662380748a62ab6279dab2a637256acd89/salmon_index/default
size = 131267297
-----------------------------------------
| Loading contigs | Time = 15.281 ms
-----------------------------------------
size = 131267297
-----------------------------------------
| Loading contig boundaries | Time = 7.5416 ms
-----------------------------------------
Number of ones: 994040
Number of ones per inventory item: 512
Inventory entries filled: 1942
994040
[2021-04-08 16:55:15.162] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2021-04-08 16:55:15.170] [puff::index::jointLog] [info] contig count for validation: 994040
[2021-04-08 16:55:15.542] [puff::index::jointLog] [info] Total # of Contigs : 994040
[2021-04-08 16:55:15.542] [puff::index::jointLog] [info] Total # of numerical Contigs : 994040
[2021-04-08 16:55:15.603] [puff::index::jointLog] [info] Total # of contig vec entries: 5131470
[2021-04-08 16:55:15.603] [puff::index::jointLog] [info] bits per offset entry 23
[2021-04-08 16:55:15.859] [puff::index::jointLog] [info] Done constructing the contig vector. 994041
[2021-04-08 16:55:16.511] [puff::index::jointLog] [info] # segments = 994040
[2021-04-08 16:55:16.511] [puff::index::jointLog] [info] total length = 131267297
[2021-04-08 16:55:16.566] [puff::index::jointLog] [info] Reading the reference files ...
[2021-04-08 16:55:17.855] [puff::index::jointLog] [info] positional integer width = 27
[2021-04-08 16:55:17.856] [puff::index::jointLog] [info] seqSize = 131267297
[2021-04-08 16:55:17.856] [puff::index::jointLog] [info] rankSize = 131267297
[2021-04-08 16:55:17.856] [puff::index::jointLog] [info] edgeVecSize = 0
[2021-04-08 16:55:17.856] [puff::index::jointLog] [info] num keys = 101446097
[Building BooPHF] 0.582% elapsed: 0 min 0 sec remaining: 0 min 17 sec
[Building BooPHF] 0.688% elapsed: 0 min 0 sec remaining: 0 min 17 sec
[Building BooPHF] 0.743% elapsed: 0 min 0 sec remaining: 0 min 17 sec
[Building BooPHF] 0.79 % elapsed: 0 min 0 sec remaining: 0 min 16 sec
[Building BooPHF] 0.88 % elapsed: 0 min 0 sec remaining: 0 min 16 sec
[Building BooPHF] 0.906% elapsed: 0 min 0 sec remaining: 0 min 16 sec
[Building BooPHF] 0.843% elapsed: 0 min 0 sec remaining: 0 min 16 sec
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[Building BooPHF] 99.6 % elapsed: 0 min 17 sec remaining: 0 min 0 sec
[Building BooPHF] 99.8 % elapsed: 0 min 17 sec remaining: 0 min 0 sec
[Building BooPHF] 99.7 % elapsed: 0 min 17 sec remaining: 0 min 0 sec
[Building BooPHF] 99.8 % elapsed: 0 min 17 sec remaining: 0 min 0 sec
[Building BooPHF] 100 % elapsed: 0 min 17 sec remaining: 0 min 0 sec
[2021-04-08 16:55:35.268] [puff::index::jointLog] [info] mphf size = 63.3658 MB
[2021-04-08 16:55:35.268] [puff::index::jointLog] [info] chunk size = 16408413
[2021-04-08 16:55:35.268] [puff::index::jointLog] [info] chunk 0 = [0, 16408413)
[2021-04-08 16:55:35.268] [puff::index::jointLog] [info] chunk 1 = [16408413, 32816826)
[2021-04-08 16:55:35.268] [puff::index::jointLog] [info] chunk 2 = [32816826, 49225239)
[2021-04-08 16:55:35.268] [puff::index::jointLog] [info] chunk 3 = [49225239, 65633652)
[2021-04-08 16:55:35.268] [puff::index::jointLog] [info] chunk 4 = [65633652, 82042065)
[2021-04-08 16:55:35.268] [puff::index::jointLog] [info] chunk 5 = [82042065, 98450490)
[2021-04-08 16:55:35.268] [puff::index::jointLog] [info] chunk 6 = [98450490, 114858903)
[2021-04-08 16:55:35.268] [puff::index::jointLog] [info] chunk 7 = [114858903, 131267267)
[2021-04-08 16:56:00.078] [puff::index::jointLog] [info] finished populating pos vector
[2021-04-08 16:56:00.078] [puff::index::jointLog] [info] writing index components
[2021-04-08 16:56:01.864] [puff::index::jointLog] [info] finished writing dense pufferfish index
[2021-04-08 16:56:01.934] [jLog] [info] done building index
for info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000
Bitarray 531550656 bits (100.00 %) (array + ranks )
final hash 0 bits (0.00 %) (nb in final hash 0)
Command completed. Elapsed time: 0:49:56. Running peak memory: 0.605GB.
PID: 23098; Command: salmon; Return code: 0; Memory used: 0.605GB
> `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/fc77e33fa26398662380748a62ab6279dab2a637256acd89/salmon_index/default/_refgenie_build/fc77e33fa26398662380748a62ab6279dab2a637256acd89_salmon_index__default.flag` (1481)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.605GB.
PID: 1481; Command: touch; Return code: 0; Memory used: 0.001GB
Asset digest: 271fdab58efc5b58a0310594c08f7f42
Default tag for 'fc77e33fa26398662380748a62ab6279dab2a637256acd89/salmon_index' set to: default
### Pipeline completed. Epilogue
* Elapsed time (this run): 0:49:58
* Total elapsed time (all runs): 0:49:56
* Peak memory (this run): 0.6054 GB
* Pipeline completed time: 2021-04-08 16:56:03
Finished building 'salmon_index' asset
Created alias directories:
- /project/shefflab/deploy/rg.databio.org_full/genomes/alias/hg19_cdna/salmon_index/default