### Pipeline run code and environment:
* Command: `/home/mjs5kd/.local/bin/refgenie build hg38_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/9a02d64909100f146272f8e16563178e9e93c218b1126ff9/salmon_index/default/_refgenie_build/
* Pipeline started at: (04-08 16:05:35) 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`: `['hg38_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/9a02d64909100f146272f8e16563178e9e93c218b1126ff9/salmon_index/default/_refgenie_build/9a02d64909100f146272f8e16563178e9e93c218b1126ff9_salmon_index__default.flag`
> `salmon index -t /project/shefflab/deploy/rg.databio.org_full/genomes/data/9a02d64909100f146272f8e16563178e9e93c218b1126ff9/fasta/default/9a02d64909100f146272f8e16563178e9e93c218b1126ff9.fa -i /project/shefflab/deploy/rg.databio.org_full/genomes/data/9a02d64909100f146272f8e16563178e9e93c218b1126ff9/salmon_index/default -k 31 -p 8` (22831)
[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 16:05:35.469] [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 16:05:35.469] [jLog] [info] building index
out : /project/shefflab/deploy/rg.databio.org_full/genomes/data/9a02d64909100f146272f8e16563178e9e93c218b1126ff9/salmon_index/default
[2021-04-08 16:05:35.472] [puff::index::jointLog] [info] Running fixFasta
[Step 1 of 4] : counting k-mers
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000631435.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000415118.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000448914.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000434970.2], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000632684.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000439842.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000390567.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000452198.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000390569.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000437320.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000390571.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000390572.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000390574.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000390575.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000431870.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000450276.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000390578.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000451044.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000390580.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000390581.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000431440.2], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000390583.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000633210.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000603693.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000604838.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000604446.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000604102.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000603935.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000632524.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000633009.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000634070.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000632963.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000633030.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000633765.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000632619.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000631871.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000633010.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000633159.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000632968.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000632473.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000631884.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000632859.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000631895.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000634154.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000632609.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000632911.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000633504.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000632304.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000632542.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000633968.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000634085.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000633353.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000631803.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000390584.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.482] [puff::index::jointLog] [warning] Entry with header [ENST00000390585.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.482] [puff::index::jointLog] [warning] Entry with header [ENST00000430425.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.482] [puff::index::jointLog] [warning] Entry with header [ENST00000454691.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.482] [puff::index::jointLog] [warning] Entry with header [ENST00000390588.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.482] [puff::index::jointLog] [warning] Entry with header [ENST00000414852.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.482] [puff::index::jointLog] [warning] Entry with header [ENST00000390590.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.482] [puff::index::jointLog] [warning] Entry with header [ENST00000390591.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.482] [puff::index::jointLog] [warning] Entry with header [ENST00000454908.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.482] [puff::index::jointLog] [warning] Entry with header [ENST00000604642.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.482] [puff::index::jointLog] [warning] Entry with header [ENST00000603326.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.482] [puff::index::jointLog] [warning] Entry with header [ENST00000604950.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.482] [puff::index::jointLog] [warning] Entry with header [ENST00000603077.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.482] [puff::index::jointLog] [warning] Entry with header [ENST00000605284.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:36.177] [puff::index::jointLog] [warning] Entry with header [ENST00000629250.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:36.802] [puff::index::jointLog] [warning] Entry with header [ENST00000632054.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:37.153] [puff::index::jointLog] [warning] Entry with header [ENST00000437226.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:39.029] [puff::index::jointLog] [warning] Entry with header [ENST00000626807.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:41.767] [puff::index::jointLog] [warning] Entry with header [ENST00000417283.5], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:41.767] [puff::index::jointLog] [warning] Entry with header [ENST00000465958.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:43.743] [puff::index::jointLog] [warning] Entry with header [ENST00000632342.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:43.744] [puff::index::jointLog] [warning] Entry with header [ENST00000518246.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:43.921] [puff::index::jointLog] [warning] Entry with header [ENST00000543745.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:43.944] [puff::index::jointLog] [warning] Entry with header [ENST00000473810.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:44.105] [puff::index::jointLog] [warning] Entry with header [ENST00000579054.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:44.116] [puff::index::jointLog] [warning] Entry with header [ENST00000603775.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:44.236] [puff::index::jointLog] [warning] Entry with header [ENST00000573437.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:44.251] [puff::index::jointLog] [warning] Entry with header [ENST00000634174.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:44.259] [puff::index::jointLog] [warning] Removed 11698 transcripts that were sequence duplicates of indexed transcripts.
[2021-04-08 16:05:44.259] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag
[2021-04-08 16:05:44.355] [puff::index::jointLog] [info] Replaced 5 non-ATCG nucleotides
[2021-04-08 16:05:44.355] [puff::index::jointLog] [info] Clipped poly-A tails from 1439 transcripts
wrote 177412 cleaned references
[2021-04-08 16:05:47.703] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2021-04-08 16:05:50.376] [puff::index::jointLog] [info] ntHll estimated 108822814 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/9a02d64909100f146272f8e16563178e9e93c218b1126ff9/salmon_index/default/ref_k31_fixed.fa
--------------------------------------------------------------------------------
Round 0, 0:2147483648
Pass Filling Filtering
1 78 183
2 75 0
True junctions count = 735544
False junctions count = 1282287
Hash table size = 2017831
Candidate marks count = 9985239
--------------------------------------------------------------------------------
Reallocating bifurcations time: 1
True marks count: 6356421
Edges construction time: 2730
--------------------------------------------------------------------------------
Distinct junctions = 735544
allowedIn: 18
Max Junction ID: 841960
seen.size():6735689 kmerInfo.size():841961
approximateContigTotalLength: 77652820
counters for complex kmers:
(prec>1 & succ>1)=47693 | (succ>1 & isStart)=728 | (prec>1 & isEnd)=811 | (isStart & isEnd)=77
contig count: 1102893 element count: 142900026 complex nodes: 49309
# of ones in rank vector: 1102892
[2021-04-08 16:57:20.748] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2021-04-08 16:57:20.749] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory /project/shefflab/deploy/rg.databio.org_full/genomes/data/9a02d64909100f146272f8e16563178e9e93c218b1126ff9/salmon_index/default
size = 142900026
-----------------------------------------
| Loading contigs | Time = 15.541 ms
-----------------------------------------
size = 142900026
-----------------------------------------
| Loading contig boundaries | Time = 8.2593 ms
-----------------------------------------
Number of ones: 1102892
Number of ones per inventory item: 512
Inventory entries filled: 2155
1102892
[2021-04-08 16:57:21.019] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2021-04-08 16:57:21.028] [puff::index::jointLog] [info] contig count for validation: 1102892
[2021-04-08 16:57:21.474] [puff::index::jointLog] [info] Total # of Contigs : 1102892
[2021-04-08 16:57:21.474] [puff::index::jointLog] [info] Total # of numerical Contigs : 1102892
[2021-04-08 16:57:21.544] [puff::index::jointLog] [info] Total # of contig vec entries: 6373539
[2021-04-08 16:57:21.544] [puff::index::jointLog] [info] bits per offset entry 23
[2021-04-08 16:57:21.879] [puff::index::jointLog] [info] Done constructing the contig vector. 1102893
[2021-04-08 16:57:22.642] [puff::index::jointLog] [info] # segments = 1102892
[2021-04-08 16:57:22.642] [puff::index::jointLog] [info] total length = 142900026
[2021-04-08 16:57:22.705] [puff::index::jointLog] [info] Reading the reference files ...
[2021-04-08 16:57:24.389] [puff::index::jointLog] [info] positional integer width = 28
[2021-04-08 16:57:24.389] [puff::index::jointLog] [info] seqSize = 142900026
[2021-04-08 16:57:24.389] [puff::index::jointLog] [info] rankSize = 142900026
[2021-04-08 16:57:24.389] [puff::index::jointLog] [info] edgeVecSize = 0
[2021-04-08 16:57:24.389] [puff::index::jointLog] [info] num keys = 109813266
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[Building BooPHF] 100 % elapsed: 0 min 20 sec remaining: 0 min 0 sec
[2021-04-08 16:57:44.417] [puff::index::jointLog] [info] mphf size = 68.5921 MB
[2021-04-08 16:57:44.417] [puff::index::jointLog] [info] chunk size = 17862504
[2021-04-08 16:57:44.417] [puff::index::jointLog] [info] chunk 0 = [0, 17862504)
[2021-04-08 16:57:44.417] [puff::index::jointLog] [info] chunk 1 = [17862504, 35725008)
[2021-04-08 16:57:44.417] [puff::index::jointLog] [info] chunk 2 = [35725008, 53587534)
[2021-04-08 16:57:44.417] [puff::index::jointLog] [info] chunk 3 = [53587534, 71450054)
[2021-04-08 16:57:44.417] [puff::index::jointLog] [info] chunk 4 = [71450054, 89312558)
[2021-04-08 16:57:44.417] [puff::index::jointLog] [info] chunk 5 = [89312558, 107175062)
[2021-04-08 16:57:44.417] [puff::index::jointLog] [info] chunk 6 = [107175062, 125037580)
[2021-04-08 16:57:44.417] [puff::index::jointLog] [info] chunk 7 = [125037580, 142899996)
[2021-04-08 16:58:11.814] [puff::index::jointLog] [info] finished populating pos vector
[2021-04-08 16:58:11.814] [puff::index::jointLog] [info] writing index components
[2021-04-08 16:58:13.958] [puff::index::jointLog] [info] finished writing dense pufferfish index
[2021-04-08 16:58:14.028] [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 575391872 bits (100.00 %) (array + ranks )
final hash 0 bits (0.00 %) (nb in final hash 0)
Command completed. Elapsed time: 0:52:39. Running peak memory: 0.324GB.
PID: 22831; Command: salmon; Return code: 0; Memory used: 0.324GB
> `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/9a02d64909100f146272f8e16563178e9e93c218b1126ff9/salmon_index/default/_refgenie_build/9a02d64909100f146272f8e16563178e9e93c218b1126ff9_salmon_index__default.flag` (2135)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.324GB.
PID: 2135; Command: touch; Return code: 0; Memory used: 0.001GB
Asset digest: 9ede2cc5de22cb075e3df6d80d404f11
Default tag for '9a02d64909100f146272f8e16563178e9e93c218b1126ff9/salmon_index' set to: default
### Pipeline completed. Epilogue
* Elapsed time (this run): 0:52:41
* Total elapsed time (all runs): 0:52:39
* Peak memory (this run): 0.3244 GB
* Pipeline completed time: 2021-04-08 16:58:16
Finished building 'salmon_index' asset
Created alias directories:
- /project/shefflab/deploy/rg.databio.org_full/genomes/alias/hg38_cdna/salmon_index/default