Biowulf High Performance Computing at the NIH
Oyster River Protocol (ORP): a multi-assembler and kmer approach for de novo transcriptome assembly

Oyster River Protocol (ORP) implements a standardized and benchmarked set of bioinformatic processes, resulting in a transcriptome assembly with enhanced qualities over other standard assembly methods. Specifically, ORP produced assemblies have higher Detonate and TransRate scores and mapping rates, which is largely a product of the fact that it leverages a multiassembler and kmer assembly process, thereby bypassing the shortcomings i of any one approach.

References:

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=4g
[user@@cn3200 ~]$module load ORP 
[+] Loading hmmer  3.1b2  on cn3098 
[+] Loading gcc  7.2.0  ... 
[+] Loading jellyfish  2.2.7 
[+] Loading Rcorrector 1.0.3.1  ... 
[+] Loading seqtk  1.2-r102 
[+] Loading spades  3.11.0 
[+] Loading salmon  0.11.3 
[-] Unloading jellyfish  2.2.7 
[+] Loading jellyfish  2.2.7 
[+] Loading samtools 1.9  ... 
[+] Loading bowtie  2-2.3.4.1 
[+] Loading python 2.7  ... 
[+] Loading Trinity 2.6.5  ... 
[-] Unloading python 2.7  ... 
[+] Loading python 2.7  ... 
[+] Loading ORP  2.0.0 

[user@biowulf]$ /usr/local/apps/ORP/2.0.0/bin/oyster.mk main MEM=150 CPU=2 READ1=$ORP_DATA/test.1.fq READ2=$ORP_DATA/test.2.fq RUNOUT=test

*****  Welcome to the Oyster River ***** 
*****  This is version 2.0.0 ***** 


     ______  ____   ____  ____   ____  ______  __ __
    |      ||    \ |    ||    \ |    ||      ||  |  |
    |      ||  D  ) |  | |  _  | |  | |      ||  |  |
    |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
      |  |  |    \  |  | |  |  | |  |   |  |  |___, |
      |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
      |__|  |__|\_||____||__|__||____|  |__|  |____/


Left read files: $VAR1 = [
          '/spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/rcorr/test.TRIM_1P.cor.fq'
        ];
Right read files: $VAR1 = [
          '/spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/rcorr/test.TRIM_2P.cor.fq'
        ];
Tuesday, October 23, 2018: 08:06:27	CMD: java -Xmx64m -XX:ParallelGCThreads=2  -jar /usr/local/apps/trinity/trinityrnaseq-2.6.5/util/support_scripts/ExitTester.jar 0
Tuesday, October 23, 2018: 08:06:27	CMD: java -Xmx64m -XX:ParallelGCThreads=2  -jar /usr/local/apps/trinity/trinityrnaseq-2.6.5/util/support_scripts/ExitTester.jar 1
Tuesday, October 23, 2018: 08:06:27	CMD: mkdir -p /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/assemblies/test.trinity
Tuesday, October 23, 2018: 08:06:27	CMD: mkdir -p /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/assemblies/test.trinity/chrysalis


----------------------------------------------------------------------------------
-------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
----------------------------------------------------------------------------------

Converting input files. (in parallel)Tuesday, October 23, 2018: 08:06:27	CMD: cat /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/rcorr/test.TRIM_1P.cor.fq | seqtk-trinity seq -A - >> left.fa
Tuesday, October 23, 2018: 08:06:27	CMD: cat /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/rcorr/test.TRIM_2P.cor.fq | seqtk-trinity seq -A - >> right.fa
Tuesday, October 23, 2018: 08:06:27	CMD: touch left.fa.ok
Tuesday, October 23, 2018: 08:06:27	CMD: touch right.fa.ok
Tuesday, October 23, 2018: 08:06:27	CMD: touch left.fa.ok right.fa.ok
Tuesday, October 23, 2018: 08:06:27	CMD: cat left.fa right.fa > /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/assemblies/test.trinity/both.fa
Tuesday, October 23, 2018: 08:06:27	CMD: touch /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/assemblies/test.trinity/both.fa.ok
-------------------------------------------
----------- Jellyfish  --------------------
-- (building a k-mer catalog from reads) --
-------------------------------------------

* Running CMD: jellyfish count -t 2 -m 25 -s 100000000  --canonical  /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/assemblies/test.trinity/both.fa
* Running CMD: jellyfish dump -L 1 mer_counts.jf > jellyfish.kmers.fa
* Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.fa.histo mer_counts.jf
----------------------------------------------
--------------- Inchworm ---------------------
-- (Linear contig construction from k-mers) --
----------------------------------------------

* Running CMD: /usr/local/apps/trinity/trinityrnaseq-2.6.5/Inchworm/bin//inchworm --kmers jellyfish.kmers.fa --run_inchworm -K 25 -L 25 --monitor 1   --DS  --num_threads 2  --PARALLEL_IWORM  > /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/assemblies/test.trinity/inchworm.K25.L25.DS.fa.tmp
* Running CMD: mv /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/assemblies/test.trinity/inchworm.K25.L25.DS.fa.tmp /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/assemblies/test.trinity/inchworm.K25.L25.DS.fa
Tuesday, October 23, 2018: 08:06:37	CMD: touch /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/assemblies/test.trinity/inchworm.K25.L25.DS.fa.finished
--------------------------------------------------------
-------------------- Chrysalis -------------------------
-- (Contig Clustering & de Bruijn Graph Construction) --
--------------------------------------------------------

inchworm_target: /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/assemblies/test.trinity/both.fa
bowite_reads_fa: /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/assemblies/test.trinity/both.fa
chrysalis_reads_fa: /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/assemblies/test.trinity/both.fa
* Running CMD: /usr/local/apps/trinity/trinityrnaseq-2.6.5/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/assemblies/test.trinity/inchworm.K25.L25.DS.fa 100 10 > /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/assemblies/test.trinity/chrysalis/inchworm.K25.L25.DS.fa.min100
* Running CMD: /usr/local/apps/ORP/2.0.0/bin/bowtie2-build --threads 2 -o 3 /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/assemblies/test.trinity/chrysalis/inchworm.K25.L25.DS.fa.min100 /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/assemblies/test.trinity/chrysalis/inchworm.K25.L25.DS.fa.min100 1>/dev/null
...
--------------------------------------------------------------------------------
------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
--------------------------------------------------------------------------------

...

Number of Commands: 29
succeeded(29)   100% completed.        

All commands completed successfully. :-)
** Harvesting all assembled transcripts into a single multi-fasta file...

...

###################################################################
Butterfly assemblies are written to /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/assemblies/test.trinity.Trinity.fasta
###################################################################

System information:
  SPAdes version: 3.11.0
  Python version: 2.7.15
  OS: Linux-3.10.0-693.21.1.el7.x86_64-x86_64-with-centos-7.4.1708-Core

Output dir: /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/assemblies/test.spades_k75
Mode: ONLY assembling (without read error correction)
Debug mode is turned OFF

Dataset parameters:
  RNA-seq mode
  Reads:
    Library number: 1, library type: paired-end
      orientation: fr
      left reads: ['/spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/rcorr/test.TRIM_1P.cor.fq']
      right reads: ['/spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/rcorr/test.TRIM_2P.cor.fq']
      interlaced reads: not specified
      single reads: not specified
Assembly parameters:
  k: [75]
  Repeat resolution is enabled
  Mismatch careful mode is turned OFF
  MismatchCorrector will be SKIPPED
  Coverage cutoff is turned OFF
Other parameters:
  Dir for temp files: /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/assemblies/test.spades_k75/tmp
  Threads: 2
  Memory limit (in Gb): 150


======= SPAdes pipeline started. Log can be found here: /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/assemblies/test.spades_k75/spades.log


===== Assembling started.


== Running assembler: K75

  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  76)   Loading config from /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/assemblies/test.spades_k75/K75/configs/config.info
  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  76)   Loading config from /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/assemblies/test.spades_k75/K75/configs/mda_mode.info
  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  76)   Loading config from /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/assemblies/test.spades_k75/K75/configs/rna_mode.info
  0:00:00.000     4M / 4M    INFO    General                 (memory_limit.hpp          :  51)   Memory limit set to 150 Gb
  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  89)   Starting SPAdes, built from N/A, git revision N/A
  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  90)   Maximum k-mer length: 128
...

finished
  0:00:07.835     4M / 1G    INFO    General                 (main.cpp                  : 110)   Assembling time: 0 hours 0 minutes 7 seconds

===== Assembling finished. Used k-mer sizes: 75 
...
======= SPAdes pipeline finished.
...
Thank you for using SPAdes!
...
System information:
  SPAdes version: 3.11.0
  Python version: 2.7.15
  OS: Linux-3.10.0-693.21.1.el7.x86_64-x86_64-with-centos-7.4.1708-Core
...
Building the suffix array...
Building the Burrows-Wheeler transform...
Building the character occurrence table...
Removing sequences shorter than 250 ...
CHECKPOINT: Final assembly completed.
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
...
OrthoFinder version 2.2.6 Copyright (C) 2014 David Emms

2 thread(s) for highly parallel tasks (BLAST searches etc.)
2 thread(s) for OrthoFinder algorithm

Checking required programs are installed
----------------------------------------
Test can run "makeblastdb -help" - ok
Test can run "blastn -help" - ok
Test can run "mcl -h" - ok

Dividing up work for BLAST for parallel processing
--------------------------------------------------
2018-10-23 08:09:07 : Creating Blast database 1 of 4
2018-10-23 08:09:07 : Creating Blast database 2 of 4
2018-10-23 08:09:07 : Creating Blast database 3 of 4
2018-10-23 08:09:07 : Creating Blast database 4 of 4

Running BLAST all-versus-all
----------------------------
Using 2 thread(s)
2018-10-23 08:09:07 : This may take some time....
2018-10-23 08:09:07 : Done 0 of 16
2018-10-23 08:09:08 : Done 10 of 16

Running OrthoFinder algorithm
-----------------------------
2018-10-23 08:09:09 : Initial processing of each species
2018-10-23 08:09:09 : Initial processing of species 1 complete
2018-10-23 08:09:09 : Initial processing of species 0 complete
2018-10-23 08:09:09 : Initial processing of species 3 complete
2018-10-23 08:09:09 : Initial processing of species 2 complete
2018-10-23 08:09:13 : Connected putatitive homologs
2018-10-23 08:09:13 : Written final scores for species 1 to graph file
2018-10-23 08:09:13 : Written final scores for species 0 to graph file
2018-10-23 08:09:13 : Written final scores for species 3 to graph file
2018-10-23 08:09:13 : Written final scores for species 2 to graph file
2018-10-23 08:09:13 : Ran MCL

Writing orthogroups to file
---------------------------
...
[ INFO] 2018-10-23 08:09:19 : Calculating contig metrics...
[ INFO] 2018-10-23 08:09:19 : Contig metrics:
[ INFO] 2018-10-23 08:09:19 : -----------------------------------
[ INFO] 2018-10-23 08:09:19 : n seqs                          151
[ INFO] 2018-10-23 08:09:19 : smallest                        220
[ INFO] 2018-10-23 08:09:19 : largest                        2546
[ INFO] 2018-10-23 08:09:19 : n bases                      100800
[ INFO] 2018-10-23 08:09:19 : mean len                     667.55
[ INFO] 2018-10-23 08:09:19 : n under 200                       0
[ INFO] 2018-10-23 08:09:19 : n over 1k                        31
[ INFO] 2018-10-23 08:09:19 : n over 10k                        0
[ INFO] 2018-10-23 08:09:19 : n with orf                       49
[ INFO] 2018-10-23 08:09:19 : mean orf percent              60.51
[ INFO] 2018-10-23 08:09:19 : n90                             312
[ INFO] 2018-10-23 08:09:19 : n70                             538
[ INFO] 2018-10-23 08:09:19 : n50                             969
[ INFO] 2018-10-23 08:09:19 : n30                            1191
[ INFO] 2018-10-23 08:09:19 : n10                            1866
[ INFO] 2018-10-23 08:09:19 : gc                              0.4
[ INFO] 2018-10-23 08:09:19 : bases n                           0
[ INFO] 2018-10-23 08:09:19 : proportion n                    0.0
[ INFO] 2018-10-23 08:09:19 : Contig metrics done in 0 seconds
[ INFO] 2018-10-23 08:09:19 : Calculating read diagnostics...
[ INFO] 2018-10-23 08:09:29 : Read mapping metrics:
[ INFO] 2018-10-23 08:09:29 : -----------------------------------
[ INFO] 2018-10-23 08:09:29 : fragments                     26949
[ INFO] 2018-10-23 08:09:29 : fragments mapped              26701
[ INFO] 2018-10-23 08:09:29 : p fragments mapped             0.99
[ INFO] 2018-10-23 08:09:29 : good mappings                 25060
[ INFO] 2018-10-23 08:09:29 : p good mapping                 0.93
[ INFO] 2018-10-23 08:09:29 : bad mappings                   1641
[ INFO] 2018-10-23 08:09:29 : potential bridges                 4
[ INFO] 2018-10-23 08:09:29 : bases uncovered               32556
[ INFO] 2018-10-23 08:09:29 : p bases uncovered              0.32
[ INFO] 2018-10-23 08:09:29 : contigs uncovbase               120
[ INFO] 2018-10-23 08:09:29 : p contigs uncovbase            0.79
[ INFO] 2018-10-23 08:09:29 : contigs uncovered                67
[ INFO] 2018-10-23 08:09:29 : p contigs uncovered            0.44
[ INFO] 2018-10-23 08:09:29 : contigs lowcovered               95
[ INFO] 2018-10-23 08:09:29 : p contigs lowcovered           0.63
[ INFO] 2018-10-23 08:09:29 : contigs segmented                19
[ INFO] 2018-10-23 08:09:29 : p contigs segmented            0.13
[ INFO] 2018-10-23 08:09:29 : Read metrics done in 10 seconds
[ INFO] 2018-10-23 08:09:29 : No reference provided, skipping comparative diagnostics
[ INFO] 2018-10-23 08:09:29 : TRANSRATE ASSEMBLY SCORE     0.1382
[ INFO] 2018-10-23 08:09:29 : -----------------------------------
[ INFO] 2018-10-23 08:09:29 : TRANSRATE OPTIMAL SCORE      0.4996
[ INFO] 2018-10-23 08:09:29 : TRANSRATE OPTIMAL CUTOFF     0.2723
[ INFO] 2018-10-23 08:09:29 : good contigs                     88
[ INFO] 2018-10-23 08:09:29 : p good contigs                 0.58
...
diamond v0.9.21.122 | by Benjamin Buchfink 
Licensed under the GNU AGPL 
Check http://github.com/bbuchfink/diamond for updates.

#CPU threads: 2
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory: /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/assemblies/diamond
Opening the database...  [0.002627s]
Percentage range of top alignment score to report hits: 0.1
Opening the input file...  [0.000493s]
Opening the output file...  [0.00062s]
Loading query sequences...  [0.000596s]
Masking queries...  [0.017355s]
Building query seed set...  [0.001899s]
Algorithm: Query-indexed
Building query histograms...  [0.000193s]
Allocating buffers...  [1.9e-05s]
Loading reference sequences...  [0.95098s]
Building reference histograms...  [0.756367s]
Allocating buffers...  [2.4e-05s]
Initializing temporary storage...  [0.074555s]
Processing query chunk 0, reference chunk 0, shape 0, index chunk 0.
Building reference index...  [0.851895s]
Building query index...  [0.001861s]
Building seed filter...  [0.006131s]
Searching alignments...  [0.326303s]
Deallocating buffers...  [0.002835s]
Computing alignments...  [0.219154s]
Deallocating reference...  [0.044276s]
Loading reference sequences...  [0.000114s]
Deallocating buffers...  [0.0004s]
Deallocating queries...  [1.9e-05s]
Loading query sequences...  [0.000271s]
Closing the input file...  [4.9e-05s]
Closing the output file...  [0.000495s]
Closing the database file...  [1.6e-05s]
Deallocating taxonomy...  [5e-06s]
Total time = 3.26219s
Reported 49 pairwise alignments, 49 HSPs.
16 queries aligned.
diamond v0.9.21.122 | by Benjamin Buchfink 
Licensed under the GNU AGPL 
Check http://github.com/bbuchfink/diamond for updates.

#CPU threads: 2
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory: /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/assemblies/diamond
Opening the database...  [0.000561s]
Percentage range of top alignment score to report hits: 0.1
Opening the input file...  [0.000713s]
Opening the output file...  [0.000568s]
Loading query sequences...  [0.000648s]
Masking queries...  [0.019813s]
Building query seed set...  [0.002283s]
Algorithm: Query-indexed
Building query histograms...  [0.000218s]
Allocating buffers...  [2.1e-05s]
Loading reference sequences...  [0.513353s]
Building reference histograms...  [0.767316s]
Allocating buffers...  [1.9e-05s]
Initializing temporary storage...  [0.083815s]
Processing query chunk 0, reference chunk 0, shape 0, index chunk 0.
Building reference index...  [0.871658s]
Building query index...  [0.002081s]
Building seed filter...  [0.006396s]
Searching alignments...  [0.31866s]
Deallocating buffers...  [0.003014s]
Computing alignments...  [0.16169s]
Deallocating reference...  [0.046505s]
Loading reference sequences...  [3.7e-05s]
Deallocating buffers...  [0.000362s]
Deallocating queries...  [6.9e-05s]
Loading query sequences...  [3e-05s]
Closing the input file...  [3.5e-05s]
Closing the output file...  [0.000512s]
Closing the database file...  [1.6e-05s]
Deallocating taxonomy...  [4e-06s]
Total time = 2.80332s
Reported 73 pairwise alignments, 73 HSPs.
18 queries aligned.
diamond v0.9.21.122 | by Benjamin Buchfink 
Licensed under the GNU AGPL 
Check http://github.com/bbuchfink/diamond for updates.

#CPU threads: 2
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory: /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/assemblies/diamond
Opening the database...  [0.000272s]
Percentage range of top alignment score to report hits: 0.1
Opening the input file...  [0.000453s]
Opening the output file...  [0.000647s]
Loading query sequences...  [0.000626s]
Masking queries...  [0.016718s]
Building query seed set...  [0.002174s]
Algorithm: Query-indexed
Building query histograms...  [0.000195s]
Allocating buffers...  [2.1e-05s]
Loading reference sequences...  [0.495995s]
Building reference histograms...  [0.76017s]
Allocating buffers...  [2.2e-05s]
Initializing temporary storage...  [0.067678s]
Processing query chunk 0, reference chunk 0, shape 0, index chunk 0.
Building reference index...  [0.868439s]
Building query index...  [0.001728s]
Building seed filter...  [0.006554s]
Searching alignments...  [0.307871s]
Deallocating buffers...  [0.003335s]
Computing alignments...  [0.158572s]
Deallocating reference...  [0.04449s]
Loading reference sequences...  [0.000114s]
Deallocating buffers...  [0.000371s]
Deallocating queries...  [2.8e-05s]
Loading query sequences...  [3.1e-05s]
Closing the input file...  [2.8e-05s]
Closing the output file...  [0.000491s]
Closing the database file...  [1.6e-05s]
Deallocating taxonomy...  [6e-06s]
Total time = 2.74026s
Reported 49 pairwise alignments, 49 HSPs.
13 queries aligned.
diamond v0.9.21.122 | by Benjamin Buchfink 
Licensed under the GNU AGPL 
Check http://github.com/bbuchfink/diamond for updates.
...
================================================================
Program: CD-HIT, V4.7 (+OpenMP), Jul 13 2018, 17:17:44
Command: cd-hit-est -M 5000 -T 2 -c .98 -i
         /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/assemblies/test.orthomerged.fasta
         -o
         /spin1/scratch/denisovga/ORP_Rcorrector_detonate_shmlast/assemblies/test.ORP.fasta

Started: Tue Oct 23 08:09:46 2018
================================================================
                            Output                              
----------------------------------------------------------------
total seq: 44
longest and shortest : 2546 and 164
Total letters: 29542
Sequences have been sorted

Approximated minimal memory consumption:
Sequence        : 0M
Buffer          : 2 X 12M = 25M
Table           : 2 X 16M = 33M
Miscellaneous   : 4M
Total           : 62M

Table limit with the given memory limit:
Max number of representatives: 4000000
Max number of word counting entries: 617130647

# comparing sequences from          0  to         44
---------- new table with       39 representatives

       44  finished         39  clusters

Apprixmated maximum memory consumption: 63M
writing new database
writing clustering information
program completed !
...
INFO	****************** Start a BUSCO 3.0.2 analysis, current time: 10/23/2018 08:09:50 ******************
INFO	Configuration loaded from /usr/local/apps/busco/3.0.2/../config/config.ini
INFO	Init tools...
INFO	Check dependencies...
INFO	Check input file...
...
INFO	Mode is: transcriptome
INFO	The lineage dataset is: sample dataset BUSCO 2.0 (eukaryota)
INFO	Temp directory is ./tmp/
INFO	****** Step 1/2, current time: 10/23/2018 08:09:50 ******
INFO	Create blast database...
INFO	[makeblastdb]	Building a new DB, current time: 10/23/2018 08:09:50
...
[ INFO] 2018-10-23 08:09:52 : Calculating contig metrics...
[ INFO] 2018-10-23 08:09:52 : Contig metrics:
[ INFO] 2018-10-23 08:09:52 : -----------------------------------
[ INFO] 2018-10-23 08:09:52 : n seqs                           39
[ INFO] 2018-10-23 08:09:52 : smallest                        164
[ INFO] 2018-10-23 08:09:52 : largest                        2546
[ INFO] 2018-10-23 08:09:52 : n bases                       25781
[ INFO] 2018-10-23 08:09:52 : mean len                     652.64
[ INFO] 2018-10-23 08:09:52 : n under 200                       2
[ INFO] 2018-10-23 08:09:52 : n over 1k                         8
[ INFO] 2018-10-23 08:09:52 : n over 10k                        0
[ INFO] 2018-10-23 08:09:52 : n with orf                       14
[ INFO] 2018-10-23 08:09:52 : mean orf percent              62.67
[ INFO] 2018-10-23 08:09:52 : n90                             301
[ INFO] 2018-10-23 08:09:52 : n70                             543
[ INFO] 2018-10-23 08:09:52 : n50                             969
[ INFO] 2018-10-23 08:09:52 : n30                            1243
[ INFO] 2018-10-23 08:09:52 : n10                            2546
[ INFO] 2018-10-23 08:09:52 : gc                             0.41
[ INFO] 2018-10-23 08:09:52 : bases n                           0
[ INFO] 2018-10-23 08:09:52 : proportion n                    0.0
[ INFO] 2018-10-23 08:09:52 : Contig metrics done in 0 seconds
[ INFO] 2018-10-23 08:09:52 : Calculating read diagnostics...
[ INFO] 2018-10-23 08:09:59 : Read mapping metrics:
[ INFO] 2018-10-23 08:09:59 : -----------------------------------
[ INFO] 2018-10-23 08:09:59 : fragments                     26208
[ INFO] 2018-10-23 08:09:59 : fragments mapped              26149
[ INFO] 2018-10-23 08:09:59 : p fragments mapped              1.0
[ INFO] 2018-10-23 08:09:59 : good mappings                 25025
[ INFO] 2018-10-23 08:09:59 : p good mapping                 0.95
[ INFO] 2018-10-23 08:09:59 : bad mappings                   1124
[ INFO] 2018-10-23 08:09:59 : potential bridges                 3
[ INFO] 2018-10-23 08:09:59 : bases uncovered                 542
[ INFO] 2018-10-23 08:09:59 : p bases uncovered              0.02
[ INFO] 2018-10-23 08:09:59 : contigs uncovbase                 8
[ INFO] 2018-10-23 08:09:59 : p contigs uncovbase            0.21
[ INFO] 2018-10-23 08:09:59 : contigs uncovered                 1
[ INFO] 2018-10-23 08:09:59 : p contigs uncovered            0.03
[ INFO] 2018-10-23 08:09:59 : contigs lowcovered                8
[ INFO] 2018-10-23 08:09:59 : p contigs lowcovered           0.21
[ INFO] 2018-10-23 08:09:59 : contigs segmented                 8
[ INFO] 2018-10-23 08:09:59 : p contigs segmented            0.21
[ INFO] 2018-10-23 08:09:59 : Read metrics done in 7 seconds
[ INFO] 2018-10-23 08:09:59 : No reference provided, skipping comparative diagnostics
[ INFO] 2018-10-23 08:09:59 : TRANSRATE ASSEMBLY SCORE     0.4345
[ INFO] 2018-10-23 08:09:59 : -----------------------------------
[ INFO] 2018-10-23 08:09:59 : TRANSRATE OPTIMAL SCORE      0.5741
[ INFO] 2018-10-23 08:09:59 : TRANSRATE OPTIMAL CUTOFF     0.2313
[ INFO] 2018-10-23 08:09:59 : good contigs                     34
[ INFO] 2018-10-23 08:09:59 : p good contigs                 0.87
...
*****  BUSCO SCORE ~~~~~>           	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:10
*****  TRANSRATE SCORE ~~~~~>           0.43449
*****  TRANSRATE OPTIMAL SCORE ~~~~~>   0.57414
*****  UNIQUE GENES ORP ~~~~~>          34
*****  UNIQUE GENES TRINITY ~~~~~>      32
*****  UNIQUE GENES SPADES55 ~~~~~>     30
*****  UNIQUE GENES SPADES75 ~~~~~>     31
*****  UNIQUE GENES TRANSABYSS ~~~~~>   32
...

End the interactive session:
[user@cn3200 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$