### Pipeline run code and environment:
* Command: `/home/mjs5kd/.local/bin/refgenie build rn6_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/d982f0b1888504cccc131d5fa2c11eb3522b9a8e95e0ea89/salmon_index/default/_refgenie_build/
* Pipeline started at: (04-08 16:07:06) 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`: `['rn6_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/d982f0b1888504cccc131d5fa2c11eb3522b9a8e95e0ea89/salmon_index/default/_refgenie_build/d982f0b1888504cccc131d5fa2c11eb3522b9a8e95e0ea89_salmon_index__default.flag`
> `salmon index -t /project/shefflab/deploy/rg.databio.org_full/genomes/data/d982f0b1888504cccc131d5fa2c11eb3522b9a8e95e0ea89/fasta/default/d982f0b1888504cccc131d5fa2c11eb3522b9a8e95e0ea89.fa -i /project/shefflab/deploy/rg.databio.org_full/genomes/data/d982f0b1888504cccc131d5fa2c11eb3522b9a8e95e0ea89/salmon_index/default -k 31 -p 8` (23448)
[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 16:07:06.827] [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 16:07:06.827] [jLog] [info] building index
out : /project/shefflab/deploy/rg.databio.org_full/genomes/data/d982f0b1888504cccc131d5fa2c11eb3522b9a8e95e0ea89/salmon_index/default
[2021-04-08 16:07:06.829] [puff::index::jointLog] [info] Running fixFasta
[Step 1 of 4] : counting k-mers
[2021-04-08 16:07:08.253] [puff::index::jointLog] [warning] Entry with header [ENSRNOT00000085980.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:07:08.416] [puff::index::jointLog] [warning] Entry with header [ENSRNOT00000093397.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:07:08.746] [puff::index::jointLog] [warning] Removed 519 transcripts that were sequence duplicates of indexed transcripts.
[2021-04-08 16:07:08.746] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag
[2021-04-08 16:07:08.754] [puff::index::jointLog] [info] Replaced 2710 non-ATCG nucleotides
[2021-04-08 16:07:08.754] [puff::index::jointLog] [info] Clipped poly-A tails from 57 transcripts
wrote 31194 cleaned references
[2021-04-08 16:07:09.704] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2021-04-08 16:07:10.332] [puff::index::jointLog] [info] ntHll estimated 50011459 distinct k-mers, setting filter size to 2^30
Threads = 8
Vertex length = 31
Hash functions = 5
Filter size = 1073741824
Capacity = 2
Files:
/project/shefflab/deploy/rg.databio.org_full/genomes/data/d982f0b1888504cccc131d5fa2c11eb3522b9a8e95e0ea89/salmon_index/default/ref_k31_fixed.fa
--------------------------------------------------------------------------------
Round 0, 0:1073741824
Pass Filling Filtering
1 22 47
2 14 0
True junctions count = 87436
False junctions count = 234960
Hash table size = 322396
Candidate marks count = 867926
--------------------------------------------------------------------------------
Reallocating bifurcations time: 1
True marks count: 539762
Edges construction time: 478
--------------------------------------------------------------------------------
Distinct junctions = 87436
allowedIn: 20
Max Junction ID: 132470
seen.size():1059769 kmerInfo.size():132471
approximateContigTotalLength: 42278991
counters for complex kmers:
(prec>1 & succ>1)=3403 | (succ>1 & isStart)=46 | (prec>1 & isEnd)=53 | (isStart & isEnd)=0
contig count: 150145 element count: 54419707 complex nodes: 3502
# of ones in rank vector: 150144
[2021-04-08 16:16:38.524] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2021-04-08 16:16:38.524] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory /project/shefflab/deploy/rg.databio.org_full/genomes/data/d982f0b1888504cccc131d5fa2c11eb3522b9a8e95e0ea89/salmon_index/default
size = 54419707
-----------------------------------------
| Loading contigs | Time = 6.586 ms
-----------------------------------------
size = 54419707
-----------------------------------------
| Loading contig boundaries | Time = 4.1364 ms
-----------------------------------------
Number of ones: 150144
Number of ones per inventory item: 512
Inventory entries filled: 294
150144
[2021-04-08 16:16:38.626] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2021-04-08 16:16:38.628] [puff::index::jointLog] [info] contig count for validation: 150144
[2021-04-08 16:16:38.674] [puff::index::jointLog] [info] Total # of Contigs : 150144
[2021-04-08 16:16:38.674] [puff::index::jointLog] [info] Total # of numerical Contigs : 150144
[2021-04-08 16:16:38.677] [puff::index::jointLog] [info] Total # of contig vec entries: 521380
[2021-04-08 16:16:38.677] [puff::index::jointLog] [info] bits per offset entry 19
[2021-04-08 16:16:38.686] [puff::index::jointLog] [info] Done constructing the contig vector. 150145
[2021-04-08 16:16:38.793] [puff::index::jointLog] [info] # segments = 150144
[2021-04-08 16:16:38.793] [puff::index::jointLog] [info] total length = 54419707
[2021-04-08 16:16:38.805] [puff::index::jointLog] [info] Reading the reference files ...
[2021-04-08 16:16:39.201] [puff::index::jointLog] [info] positional integer width = 26
[2021-04-08 16:16:39.201] [puff::index::jointLog] [info] seqSize = 54419707
[2021-04-08 16:16:39.201] [puff::index::jointLog] [info] rankSize = 54419707
[2021-04-08 16:16:39.201] [puff::index::jointLog] [info] edgeVecSize = 0
[2021-04-08 16:16:39.201] [puff::index::jointLog] [info] num keys = 49915387
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[2021-04-08 16:16:46.637] [puff::index::jointLog] [info] mphf size = 31.1787 MB
[2021-04-08 16:16:46.637] [puff::index::jointLog] [info] chunk size = 6802464
[2021-04-08 16:16:46.637] [puff::index::jointLog] [info] chunk 0 = [0, 6802464)
[2021-04-08 16:16:46.637] [puff::index::jointLog] [info] chunk 1 = [6802464, 13604928)
[2021-04-08 16:16:46.637] [puff::index::jointLog] [info] chunk 2 = [13604928, 20407392)
[2021-04-08 16:16:46.637] [puff::index::jointLog] [info] chunk 3 = [20407392, 27209856)
[2021-04-08 16:16:46.637] [puff::index::jointLog] [info] chunk 4 = [27209856, 34012320)
[2021-04-08 16:16:46.637] [puff::index::jointLog] [info] chunk 5 = [34012320, 40814784)
[2021-04-08 16:16:46.637] [puff::index::jointLog] [info] chunk 6 = [40814784, 47617248)
[2021-04-08 16:16:46.637] [puff::index::jointLog] [info] chunk 7 = [47617248, 54419677)
[2021-04-08 16:16:58.249] [puff::index::jointLog] [info] finished populating pos vector
[2021-04-08 16:16:58.249] [puff::index::jointLog] [info] writing index components
[2021-04-08 16:16:59.138] [puff::index::jointLog] [info] finished writing dense pufferfish index
[2021-04-08 16:16:59.159] [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 261546240 bits (100.00 %) (array + ranks )
final hash 0 bits (0.00 %) (nb in final hash 0)
Command completed. Elapsed time: 0:09:53. Running peak memory: 0.266GB.
PID: 23448; Command: salmon; Return code: 0; Memory used: 0.266GB
> `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/d982f0b1888504cccc131d5fa2c11eb3522b9a8e95e0ea89/salmon_index/default/_refgenie_build/d982f0b1888504cccc131d5fa2c11eb3522b9a8e95e0ea89_salmon_index__default.flag` (25791)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.266GB.
PID: 25791; Command: touch; Return code: 0; Memory used: 0.001GB
Asset digest: 9edfd9d0e9fffceb145e2e2eab8d886e
Default tag for 'd982f0b1888504cccc131d5fa2c11eb3522b9a8e95e0ea89/salmon_index' set to: default
### Pipeline completed. Epilogue
* Elapsed time (this run): 0:09:54
* Total elapsed time (all runs): 0:09:53
* Peak memory (this run): 0.2665 GB
* Pipeline completed time: 2021-04-08 16:17:00
Finished building 'salmon_index' asset
Created alias directories:
- /project/shefflab/deploy/rg.databio.org_full/genomes/alias/rn6_cdna/salmon_index/default