Workshop on Genomics (Notes, Day 5) – Assembly

Bridge will be under construction tomorrow, so we must find a cut-through:
http://www.flickr.com/photos/lpcohen/11995110086/

Trying different assembly methods with bacterial sequences: http://evomics.org/learning/assembly-and-alignment/2014-assembly-lab/

Using Velvet:
http://www.ebi.ac.uk/~zerbino/velvet/
Manual: http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf

Here’s another tutorial on Velvet:
https://wiki.hpcc.msu.edu/display/Bioinfo/Velvet+Short+Read+Assembly

Article: http://www.ncbi.nlm.nih.gov/pubmed/20836074

There are two main commands: velveth and velvetg

First use trimmed and split data set (about half of the reads), then try whole dataset and see the difference.

ubuntu@domU-12-31-39-0C-6C-E1:~$ velveth
velveth - simple hashing program
Version 1.2.10

Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Compilation settings:
CATEGORIES = 9
MAXKMERLENGTH = 101

Usage:
./velveth directory hash_length {[-file_format][-read_type][-separate|-interleaved] filename1 [filename2 ...]} {...} [options]

	directory	: directory name for output files
	hash_length	: EITHER an odd integer (if even, it will be decremented) <= 101 (if above, will be reduced)
			: OR: m,M,s where m and M are odd integers (if not, they will be decremented) with m < M <= 101 (if above, will be reduced)
				and s is a step (even number). Velvet will then hash from k=m to k=M with a step of s
	filename	: path to sequence file or - for standard input

File format options:
	-fasta	-fastq	-raw	-fasta.gz	-fastq.gz	-raw.gz	-sam	-bam	-fmtAuto
	(Note: -fmtAuto will detect fasta or fastq, and will try the following programs for decompression : gunzip, pbunzip2, bunzip2

File layout options for paired reads (only for fasta and fastq formats):
	-interleaved	: File contains paired reads interleaved in the one file (default)
	-separate	: Read 2 separate files for paired reads

Read type options:
	-short	-shortPaired
	...
	-short8	-shortPaired8
	-short9	-shortPaired9
	-long	-longPaired
	-reference

Options:
	-strand_specific	: for strand specific transcriptome sequencing data (default: off)
	-reuse_Sequences	: reuse Sequences file (or link) already in directory (no need to provide original filenames in this case (default: off)
	-reuse_binary	: reuse binary sequences file (or link) already in directory (no need to provide original filenames in this case (default: off)
	-noHash			: simply prepare Sequences file, do not hash reads or prepare Roadmaps file (default: off)
	-create_binary  	: create binary CnyUnifiedSeq file (default: off)

Synopsis:

- Short single end reads:
	velveth Assem 29 -short -fastq s_1_sequence.txt

- Paired-end short reads (remember to interleave paired reads):
	velveth Assem 31 -shortPaired -fasta interleaved.fna

- Paired-end short reads (using separate files for the paired reads)
	velveth Assem 31 -shortPaired -fasta -separate left.fa right.fa

- Two channels and some long reads:
	velveth Assem 43 -short -fastq unmapped.fna -longPaired -fasta SangerReads.fasta

- Three channels:
	velveth Assem 35 -shortPaired -fasta pe_lib1.fasta -shortPaired2 pe_lib2.fasta -short3 se_lib1.fa

Output:
	directory/Roadmaps
	directory/Sequences
		[Both files are picked up by graph, so please leave them there]
ubuntu@domU-12-31-39-0C-6C-E1:~$ ls
assembly             include   shell
bin                  install   shotgun_metagenomics
build                lib       software
conf                 libexec   stacks
configure_freenx.sh  logs      Templates
Desktop              Music     tmp
Documents            nxsetup   transcriptomics
Downloads            Pictures  tutorial_materials
etc                  Public    UTI189.genome
genomics_tutorial    qc        var
html                 sbin      Videos
igv                  share
ubuntu@domU-12-31-39-0C-6C-E1:~$ cd assembly
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly$ ls
vcholerae_reads_1.trimmed.fastq.gz
vcholerae_reads_1.trimmed.subsampled.250k.fastq.gz
vcholerae_reads_2.trimmed.fastq.gz
vcholerae_reads_2.trimmed.subsampled.250k.fastq.gz
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly$ gunzip vcholerae_reads_1.trimmed.subsampled.250k.fastq.gz 
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly$ gunzip vcholerae_reads_2.trimmed.subsampled.250k.fastq.gz 
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly$ gzip --help
Usage: gzip [OPTION]... [FILE]...
Compress or uncompress FILEs (by default, compress FILES in-place).

Mandatory arguments to long options are mandatory for short options too.

  -c, --stdout      write on standard output, keep original files unchanged
  -d, --decompress  decompress
  -f, --force       force overwrite of output file and compress links
  -h, --help        give this help
  -l, --list        list compressed file contents
  -L, --license     display software license
  -n, --no-name     do not save or restore the original name and time stamp
  -N, --name        save or restore the original name and time stamp
  -q, --quiet       suppress all warnings
  -r, --recursive   operate recursively on directories
  -S, --suffix=SUF  use suffix SUF on compressed files
  -t, --test        test compressed file integrity
  -v, --verbose     verbose mode
  -V, --version     display version number
  -1, --fast        compress faster
  -9, --best        compress better
  --rsyncable       Make rsync-friendly archive

With no FILE, or when FILE is -, read standard input.

Report bugs to .
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly$ ls
vcholerae_reads_1.trimmed.fastq.gz               vcholerae_reads_2.trimmed.fastq.gz
vcholerae_reads_1.trimmed.subsampled.250k.fastq  vcholerae_reads_2.trimmed.subsampled.250k.fastq
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly$ velveth
velveth - simple hashing program
Version 1.2.10

Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Compilation settings:
CATEGORIES = 9
MAXKMERLENGTH = 101

Usage:
./velveth directory hash_length {[-file_format][-read_type][-separate|-interleaved] filename1 [filename2 ...]} {...} [options]

	directory	: directory name for output files
	hash_length	: EITHER an odd integer (if even, it will be decremented) <= 101 (if above, will be reduced)
			: OR: m,M,s where m and M are odd integers (if not, they will be decremented) with m < M <= 101 (if above, will be reduced)
				and s is a step (even number). Velvet will then hash from k=m to k=M with a step of s
	filename	: path to sequence file or - for standard input

File format options:
	-fasta	-fastq	-raw	-fasta.gz	-fastq.gz	-raw.gz	-sam	-bam	-fmtAuto
	(Note: -fmtAuto will detect fasta or fastq, and will try the following programs for decompression : gunzip, pbunzip2, bunzip2

File layout options for paired reads (only for fasta and fastq formats):
	-interleaved	: File contains paired reads interleaved in the one file (default)
	-separate	: Read 2 separate files for paired reads

Read type options:
	-short	-shortPaired
	...
	-short8	-shortPaired8
	-short9	-shortPaired9
	-long	-longPaired
	-reference

Options:
	-strand_specific	: for strand specific transcriptome sequencing data (default: off)
	-reuse_Sequences	: reuse Sequences file (or link) already in directory (no need to provide original filenames in this case (default: off)
	-reuse_binary	: reuse binary sequences file (or link) already in directory (no need to provide original filenames in this case (default: off)
	-noHash			: simply prepare Sequences file, do not hash reads or prepare Roadmaps file (default: off)
	-create_binary  	: create binary CnyUnifiedSeq file (default: off)

Synopsis:

- Short single end reads:
	velveth Assem 29 -short -fastq s_1_sequence.txt

- Paired-end short reads (remember to interleave paired reads):
	velveth Assem 31 -shortPaired -fasta interleaved.fna

- Paired-end short reads (using separate files for the paired reads)
	velveth Assem 31 -shortPaired -fasta -separate left.fa right.fa

- Two channels and some long reads:
	velveth Assem 43 -short -fastq unmapped.fna -longPaired -fasta SangerReads.fasta

- Three channels:
	velveth Assem 35 -shortPaired -fasta pe_lib1.fasta -shortPaired2 pe_lib2.fasta -short3 se_lib1.fa

Output:
	directory/Roadmaps
	directory/Sequences
		[Both files are picked up by graph, so please leave them there]
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly$ velveth Assem 30 -shortPaired -fastq -separate vcholerae_reads_1.trimmed.subsampled.250k.fastq vcholerae_reads_2.trimmed.subsampled.250k.fastq 
[0.000001] Velvet can't work with even length k-mers, such as 30. We'll use 29 instead, if you don't mind.
[0.000494] Reading FastQ file vcholerae_reads_1.trimmed.subsampled.250k.fastq;
[0.000564] Reading FastQ file vcholerae_reads_2.trimmed.subsampled.250k.fastq;
[4.058952] 500000 sequences found in total in the paired sequence files
[4.058994] Done
[4.059122] Reading read set file Assem/Sequences;
[4.345354] 500000 sequences found
[5.657970] Done
[5.658036] 500000 sequences in total.
[5.658136] Writing into roadmap file Assem/Roadmaps...
[6.622388] Inputting sequences...
[6.622457] Inputting sequence 0 / 500000
[26.905454]  === Sequences loaded in 20.283071 s
[26.905572] Done inputting sequences
[26.905587] Destroying splay table
[27.013449] Splay table destroyed
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly$ ls
Assem                               vcholerae_reads_1.trimmed.subsampled.250k.fastq  vcholerae_reads_2.trimmed.subsampled.250k.fastq
vcholerae_reads_1.trimmed.fastq.gz  vcholerae_reads_2.trimmed.fastq.gz
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly$ cd Assem
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly/Assem$ ls
Log  Roadmaps  Sequences
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly/Assem$ cd ..
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly$ #velveth Assem2 43 -shortPaired -fastq -separate vcholerae_reads_1.trimmed.
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly$ ls
Assem                                            vcholerae_reads_2.trimmed.fastq.gz
vcholerae_reads_1.trimmed.fastq.gz               vcholerae_reads_2.trimmed.subsampled.250k.fastq
vcholerae_reads_1.trimmed.subsampled.250k.fastq
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly$ velveth Assem2 43 -shortPaired -fastq -separate vcholerae_reads_1.trimmed.subsampled.250k.fastq vcholerae_reads_2.trimmed.subsampled.250k.fastq 
[0.000001] Reading FastQ file vcholerae_reads_1.trimmed.subsampled.250k.fastq;
[0.000083] Reading FastQ file vcholerae_reads_2.trimmed.subsampled.250k.fastq;
[4.437596] 500000 sequences found in total in the paired sequence files
[4.437774] Done
[4.437949] Reading read set file Assem2/Sequences;
[4.727121] 500000 sequences found
[6.080263] Done
[6.080430] 500000 sequences in total.
[6.080525] Writing into roadmap file Assem2/Roadmaps...
[6.962806] Inputting sequences...
[6.962869] Inputting sequence 0 / 500000
[26.192815]  === Sequences loaded in 19.230015 s
[26.192937] Done inputting sequences
[26.192952] Destroying splay table
[26.374562] Splay table destroyed
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly$ ls
Assem   vcholerae_reads_1.trimmed.fastq.gz               vcholerae_reads_2.trimmed.fastq.gz
Assem2  vcholerae_reads_1.trimmed.subsampled.250k.fastq  vcholerae_reads_2.trimmed.subsampled.250k.fastq
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly$ cd Assem2
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly/Assem2$ ls
Log  Roadmaps  Sequences
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly/Assem2$ less Road^C
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly/Assem2$ ls -l
total 146616
-rw-rw-r-- 1 ubuntu ubuntu       450 Jan 17 14:00 Log
-rw-rw-r-- 1 ubuntu ubuntu  28038956 Jan 17 14:00 Roadmaps
-rw-rw-r-- 1 ubuntu ubuntu 122086683 Jan 17 14:00 Sequences
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly/Assem2$ velvetg
velvetg - de Bruijn graph construction, error removal and repeat resolution
Version 1.2.10
Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Compilation settings:
CATEGORIES = 9
MAXKMERLENGTH = 101

Usage:
./velvetg directory [options]

	directory			: working directory name

Standard options:
	-cov_cutoff 	: removal of low coverage nodes AFTER tour bus or allow the system to infer it
		(default: no removal)
	-ins_length 		: expected distance between two paired end reads (default: no read pairing)
	-read_trkg 		: tracking of short read positions in assembly (default: no tracking)
	-min_contig_lgth 	: minimum contig length exported to contigs.fa file (default: hash length * 2)
	-amos_file 		: export assembly to AMOS file (default: no export)
	-exp_cov 	: expected coverage of unique regions or allow the system to infer it
		(default: no long or paired-end read resolution)
	-long_cov_cutoff : removal of nodes with low long-read coverage AFTER tour bus
		(default: no removal)

Advanced options:
	-ins_length* 		: expected distance between two paired-end reads in the respective short-read dataset (default: no read pairing)
	-ins_length_long 	: expected distance between two long paired-end reads (default: no read pairing)
	-ins_length*_sd 	: est. standard deviation of respective dataset (default: 10% of corresponding length)
		[replace '*' by nothing, '2' or '_long' as necessary]
	-scaffolding 		: scaffolding of contigs used paired end information (default: on)
	-max_branch_length 	: maximum length in base pair of bubble (default: 100)
	-max_divergence : maximum divergence rate between two branches in a bubble (default: 0.2)
	-max_gap_count 	: maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)
	-min_pair_count 	: minimum number of paired end connections to justify the scaffolding of two long contigs (default: 5)
	-max_coverage 	: removal of high coverage nodes AFTER tour bus (default: no removal)
	-coverage_mask 	: minimum coverage required for confident regions of contigs (default: 1)
	-long_mult_cutoff 		: minimum number of long reads required to merge contigs (default: 2)
	-unused_reads 		: export unused reads in UnusedReads.fa file (default: no)
	-alignments 		: export a summary of contig alignment to the reference sequences (default: no)
	-exportFiltered 	: export the long nodes which were eliminated by the coverage filters (default: no)
	-clean 			: remove all the intermediary files which are useless for recalculation (default : no)
	-very_clean 		: remove all the intermediary files (no recalculation possible) (default: no)
	-paired_exp_fraction 	: remove all the paired end connections which less than the specified fraction of the expected count (default: 0.1)
	-shortMatePaired* 	: for mate-pair libraries, indicate that the library might be contaminated with paired-end reads (default no)
	-conserveLong 		: preserve sequences with long reads in them (default no)

Output:
	directory/contigs.fa		: fasta file of contigs longer than twice hash length
	directory/stats.txt		: stats file (tab-spaced) useful for determining appropriate coverage cutoff
	directory/LastGraph		: special formatted file with all the information on the final graph
	directory/velvet_asm.afg	: (if requested) AMOS compatible assembly file
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly/Assem2$ velvetg Assem2^C
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly/Assem2$ cd ..
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly$ velvetg Assem2
[0.000000] Reading roadmap file Assem2/Roadmaps
[1.484147] 500000 roadmaps read
[1.486378] Creating insertion markers
[1.768271] Ordering insertion markers
[2.364767] Counting preNodes
[2.530988] 676517 preNodes counted, creating them now
[6.879732] Adjusting marker info...
[7.060320] Connecting preNodes
[7.934708] Cleaning up memory
[7.944252] Done creating preGraph
[7.944308] Concatenation...
[8.343361] Renumbering preNodes
[8.343439] Initial preNode count 676517
[8.374341] Destroyed 520721 preNodes
[8.374397] Concatenation over!
[8.374408] Clipping short tips off preGraph
[8.401486] Concatenation...
[8.570460] Renumbering preNodes
[8.570541] Initial preNode count 155796
[8.586582] Destroyed 65542 preNodes
[8.586655] Concatenation over!
[8.586666] 33212 tips cut off
[8.586677] 90254 nodes left
[8.586770] Writing into pregraph file Assem2/PreGraph...
[9.378458] Reading read set file Assem2/Sequences;
[9.655885] 500000 sequences found
[10.973079] Done
[11.869294] Reading pre-graph file Assem2/PreGraph
[11.869671] Graph has 90254 nodes and 500000 sequences
[12.343412] Scanning pre-graph file Assem2/PreGraph for k-mers
[12.453898] 5377080 kmers found
[13.302362] Sorting kmer occurence table ... 
[20.429577] Sorting done.
[20.429730] Computing acceleration table... 
[20.626156] Computing offsets... 
[20.717901] Ghost Threading through reads 0 / 500000
[44.404327]  === Ghost-Threaded in 23.686426 s
[44.404418] Threading through reads 0 / 500000
[69.452870]  === Threaded in 25.048452 s
[69.521949] Correcting graph with cutoff 0.200000
[69.594345] Determining eligible starting points
[69.737418] Done listing starting nodes
[69.737495] Initializing todo lists
[69.842537] Done with initilization
[69.842618] Activating arc lookup table
[69.899442] Done activating arc lookup table
[70.120761] 10000 / 90254 nodes visited
[70.377353] 20000 / 90254 nodes visited
[70.649430] 30000 / 90254 nodes visited
[70.937784] 40000 / 90254 nodes visited
[71.235976] 50000 / 90254 nodes visited
[71.592198] 60000 / 90254 nodes visited
[71.855646] 70000 / 90254 nodes visited
[72.106759] 80000 / 90254 nodes visited
[72.238511] 90000 / 90254 nodes visited
[72.239477] Concatenation...
[72.244643] Renumbering nodes
[72.244712] Initial node count 90254
[72.247962] Removed 74445 null nodes
[72.248024] Concatenation over!
[72.248035] Clipping short tips off graph, drastic
[72.329202] Concatenation...
[72.384609] Renumbering nodes
[72.384682] Initial node count 15809
[72.385532] Removed 8109 null nodes
[72.385549] Concatenation over!
[72.385600] 7700 nodes left
[72.385699] Writing into graph file Assem2/Graph...
[73.095382] WARNING: NO COVERAGE CUTOFF PROVIDED
[73.095433] Velvet will probably leave behind many detectable errors
[73.095445] See manual for instructions on how to set the coverage cutoff parameter
[73.095470] Removing contigs with coverage < -1.000000...
[73.096428] Concatenation...
[73.097377] Renumbering nodes
[73.097396] Initial node count 7700
[73.097438] Removed 0 null nodes
[73.097450] Concatenation over!
[73.097847] Concatenation...
[73.098374] Renumbering nodes
[73.098388] Initial node count 7700
[73.098421] Removed 0 null nodes
[73.098432] Concatenation over!
[73.098464] Clipping short tips off graph, drastic
[73.098682] Concatenation...
[73.099134] Renumbering nodes
[73.099153] Initial node count 7700
[73.099178] Removed 0 null nodes
[73.099188] Concatenation over!
[73.099201] 7700 nodes left
[73.099214] WARNING: NO EXPECTED COVERAGE PROVIDED
[73.099228] Velvet will be unable to resolve any repeats
[73.099241] See manual for instructions on how to set the expected coverage parameter
[73.099257] Concatenation...
[73.099672] Renumbering nodes
[73.099687] Initial node count 7700
[73.099711] Removed 0 null nodes
[73.099722] Concatenation over!
[73.099734] Removing reference contigs with coverage  contigs

2014-01-17 14:06:37
Running Basic statistics processor...
  Contig files: 
    contigs
  Calculating N50 and L50...
    contigs, N50 = 3768, L50 = 286, Total length = 3722836, GC % = 47.70, # N's per 100 kbp =  0.00
  Drawing cumulative plot...
    saved to /home/ubuntu/assembly/Assem2/output1/basic_stats/cumulative_plot.pdf
  Drawing GC content plot...
    saved to /home/ubuntu/assembly/Assem2/output1/basic_stats/GC_content_plot.pdf
  Drawing Nx plot...
    saved to /home/ubuntu/assembly/Assem2/output1/basic_stats/Nx_plot.pdf
Done.

NOTICE: Genes are not predicted by default. Use --gene-finding option to enable it.

2014-01-17 14:06:39
Summarizing...
  Creating total report...
    saved to /home/ubuntu/assembly/Assem2/output1/report.txt, report.tsv, and report.tex
  Transposed version of total report...
    saved to /home/ubuntu/assembly/Assem2/output1/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version saved to /home/ubuntu/assembly/Assem2/output1/report.html
  All pdf files are merged to /home/ubuntu/assembly/Assem2/output1/plots.pdf
Log saved to /home/ubuntu/assembly/Assem2/output1/quast.log

Finished: 2014-01-17 14:06:39
Elapsed time: 0:00:03.139799
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly/Assem2$ ls
contigs.fa  Graph  LastGraph  Log  output1  PreGraph  Roadmaps  Sequences  stats.txt
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly/Assem2$ cd output1
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly/Assem2/output1$ ls
basic_stats  plots.pdf  report.html      report.tex  report.txt             transposed_report.tsv
json         quast.log  report_html_aux  report.tsv  transposed_report.tex  transposed_report.txt
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly/Assem2/output1$ firefox report.html
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly/Assem2/output1$ cd ..
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly/Assem2$ cd ..
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly$ velvetg Assem
[0.000000] Reading roadmap file Assem/Roadmaps
[1.612518] 500000 roadmaps read
[1.614553] Creating insertion markers
[1.888414] Ordering insertion markers
[2.566517] Counting preNodes
[2.675889] 717318 preNodes counted, creating them now
[6.942157] Adjusting marker info...
[7.124399] Connecting preNodes
[8.191134] Cleaning up memory
[8.199661] Done creating preGraph
[8.199697] Concatenation...
[8.626041] Renumbering preNodes
[8.626299] Initial preNode count 717318
[8.666926] Destroyed 516170 preNodes
[8.666986] Concatenation over!
[8.666998] Clipping short tips off preGraph
[8.695092] Concatenation...
[8.871705] Renumbering preNodes
[8.871780] Initial preNode count 201148
[8.894360] Destroyed 56619 preNodes
[8.894433] Concatenation over!
[8.894444] 28813 tips cut off
[8.894477] 144529 nodes left
[8.894578] Writing into pregraph file Assem/PreGraph...
[9.745634] Reading read set file Assem/Sequences;
[10.079567] 500000 sequences found
[11.316718] Done
[12.211954] Reading pre-graph file Assem/PreGraph
[12.212491] Graph has 144529 nodes and 500000 sequences
[12.668231] Scanning pre-graph file Assem/PreGraph for k-mers
[12.846345] 5526378 kmers found
[13.653035] Sorting kmer occurence table ... 
[21.506031] Sorting done.
[21.506102] Computing acceleration table... 
[21.637177] Computing offsets... 
[21.791207] Ghost Threading through reads 0 / 500000
[47.672287]  === Ghost-Threaded in 25.881080 s
[47.672357] Threading through reads 0 / 500000
[75.090878]  === Threaded in 27.418520 s
[75.216504] Correcting graph with cutoff 0.200000
[75.236141] Determining eligible starting points
[75.518660] Done listing starting nodes
[75.518713] Initializing todo lists
[75.589577] Done with initilization
[75.589649] Activating arc lookup table
[75.739150] Done activating arc lookup table
[75.919068] 10000 / 144529 nodes visited
[76.042347] 20000 / 144529 nodes visited
[76.239176] 30000 / 144529 nodes visited
[76.441351] 40000 / 144529 nodes visited
[76.648717] 50000 / 144529 nodes visited
[76.818537] 60000 / 144529 nodes visited
[77.046706] 70000 / 144529 nodes visited
[77.264235] 80000 / 144529 nodes visited
[77.489694] 90000 / 144529 nodes visited
[77.727152] 100000 / 144529 nodes visited
[77.939256] 110000 / 144529 nodes visited
[78.063556] 120000 / 144529 nodes visited
[78.248555] 130000 / 144529 nodes visited
[78.428864] 140000 / 144529 nodes visited
[78.456981] Concatenation...
[78.464772] Renumbering nodes
[78.464847] Initial node count 144529
[78.469508] Removed 123321 null nodes
[78.469594] Concatenation over!
[78.469645] Clipping short tips off graph, drastic
[78.478382] Concatenation...
[78.485871] Renumbering nodes
[78.485917] Initial node count 21208
[78.489142] Removed 747 null nodes
[78.489196] Concatenation over!
[78.489213] 20461 nodes left
[78.489319] Writing into graph file Assem/Graph...
[79.259328] WARNING: NO COVERAGE CUTOFF PROVIDED
[79.259424] Velvet will probably leave behind many detectable errors
[79.259437] See manual for instructions on how to set the coverage cutoff parameter
[79.259463] Removing contigs with coverage < -1.000000...
[79.262157] Concatenation...
[79.267144] Renumbering nodes
[79.267224] Initial node count 20461
[79.267328] Removed 0 null nodes
[79.267353] Concatenation over!
[79.269908] Concatenation...
[79.275061] Renumbering nodes
[79.275150] Initial node count 20461
[79.275213] Removed 0 null nodes
[79.275239] Concatenation over!
[79.275275] Clipping short tips off graph, drastic
[79.277257] Concatenation...
[79.282549] Renumbering nodes
[79.282653] Initial node count 20461
[79.282762] Removed 0 null nodes
[79.282786] Concatenation over!
[79.282797] 20461 nodes left
[79.282822] WARNING: NO EXPECTED COVERAGE PROVIDED
[79.282847] Velvet will be unable to resolve any repeats
[79.282872] See manual for instructions on how to set the expected coverage parameter
[79.282904] Concatenation...
[79.287785] Renumbering nodes
[79.287850] Initial node count 20461
[79.287917] Removed 0 null nodes
[79.287932] Concatenation over!
[79.287949] Removing reference contigs with coverage  contigs

2014-01-17 14:10:01
Running Basic statistics processor...
  Contig files: 
    contigs
  Calculating N50 and L50...
    contigs, N50 = 1344, L50 = 772, Total length = 3195658, GC % = 47.64, # N's per 100 kbp =  0.00
  Drawing cumulative plot...
    saved to /home/ubuntu/assembly/Assem/quastoutput/basic_stats/cumulative_plot.pdf
  Drawing GC content plot...
    saved to /home/ubuntu/assembly/Assem/quastoutput/basic_stats/GC_content_plot.pdf
  Drawing Nx plot...
    saved to /home/ubuntu/assembly/Assem/quastoutput/basic_stats/Nx_plot.pdf
Done.

NOTICE: Genes are not predicted by default. Use --gene-finding option to enable it.

2014-01-17 14:10:02
Summarizing...
  Creating total report...
    saved to /home/ubuntu/assembly/Assem/quastoutput/report.txt, report.tsv, and report.tex
  Transposed version of total report...
    saved to /home/ubuntu/assembly/Assem/quastoutput/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version saved to /home/ubuntu/assembly/Assem/quastoutput/report.html
  All pdf files are merged to /home/ubuntu/assembly/Assem/quastoutput/plots.pdf
Log saved to /home/ubuntu/assembly/Assem/quastoutput/quast.log

Finished: 2014-01-17 14:10:02
Elapsed time: 0:00:01.954170
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly/Assem$ cd output
bash: cd: output: No such file or directory
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly/Assem$ cd quastoutput
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly/Assem/quastoutput$ ls
basic_stats  plots.pdf  report.html      report.tex  report.txt             transposed_report.tsv
json         quast.log  report_html_aux  report.tsv  transposed_report.tex  transposed_report.txt
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly/Assem/quastoutput$ firefox report.html
^C
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly/Assem/quastoutput$ ls
basic_stats  plots.pdf  report.html      report.tex  report.txt             transposed_report.tsv
json         quast.log  report_html_aux  report.tsv  transposed_report.tex  transposed_report.txt
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly/Assem/quastoutput$ cd ..
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly/Assem$ 
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly/Assem$ cd ..
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly$ ls
Assem   vcholerae_reads_1.trimmed.fastq.gz               vcholerae_reads_2.trimmed.fastq.gz
Assem2  vcholerae_reads_1.trimmed.subsampled.250k.fastq  vcholerae_reads_2.trimmed.subsampled.250k.fastq
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly$ cd Assem2
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly/Assem2$ ls
contigs.fa  Graph  LastGraph  Log  output1  PreGraph  Roadmaps  Sequences  stats.txt
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly/Assem2$ cd output1
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly/Assem2/output1$ firefox report.html
^C
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly/Assem2/output1$ cd ..
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly/Assem2$ ls
contigs.fa  Graph  LastGraph  Log  output1  PreGraph  Roadmaps  Sequences  stats.txt

Prokaryotic genome annotation program, prokka (very cool): http://www.vicbioinformatics.com/software.prokka.shtml

ubuntu@domU-12-31-39-0C-6C-E1:~/assembly/Assem2$ prokka contigs.fa
[14:55:05] This is prokka 1.8
[14:55:05] Written by Torsten Seemann 
[14:55:05] Victorian Bioinformatics Consortium - http://www.vicbioinformatics.com
[14:55:05] Local time is Fri Jan 17 14:55:05 2014
[14:55:05] You are ubuntu
[14:55:05] Operating system is linux
[14:55:05] You have BioPerl 1.006923
[14:55:05] System has 4 cores.
[14:55:05] Option --cpu asked for 8 cores, but system only has 4
[14:55:05] Will use maximum of 4 cores.
[14:55:05] Annotating as >>> Bacteria <<<
[14:55:05] Folder 'PROKKA_01172014' already exists! Please change --outdir or use --force
ubuntu@domU-12-31-39-0C-6C-E1:~/assembly/Assem2$ prokka contigs.fa --force
[14:55:15] This is prokka 1.8
[14:55:15] Written by Torsten Seemann 
[14:55:15] Victorian Bioinformatics Consortium - http://www.vicbioinformatics.com
[14:55:15] Local time is Fri Jan 17 14:55:15 2014
[14:55:15] You are ubuntu
[14:55:15] Operating system is linux
[14:55:15] You have BioPerl 1.006923
[14:55:15] System has 4 cores.
[14:55:15] Option --cpu asked for 8 cores, but system only has 4
[14:55:15] Will use maximum of 4 cores.
[14:55:15] Annotating as >>> Bacteria << end (21) - skipping.
[14:55:19] 1 tRNA-Gln [65,139] 33 (ttg)
[14:55:19] 1 tRNA-Arg [5147,5223] 35 (tct)
[14:55:19] 1 tRNA-Asp [16,92] 35 (gtc)
[14:55:19] 1 tRNA-Trp c[3832,3908] 35 (cca)
[14:55:19] 1 tRNA-Cys c[66,38] 30 (gca)
[14:55:19] tRNA c[66,38] has start(66) > end (38) - skipping.
[14:55:19] 1 tRNA-Leu c[3,89] 35 (taa)
[14:55:20] 1 tRNA-Gln [148,69] 33 (ttg)
[14:55:20] tRNA [148,69] has start(148) > end (69) - skipping.
[14:55:20] 1 tRNA-Thr [50,125] 34 (ggt)
[14:55:20] 1 tRNA-Asp c[77,36] 35 (atc)
[14:55:20] tRNA c[77,36] has start(77) > end (36) - skipping.
[14:55:20] 1 tRNA-Cys [116,73] 33 (gca)
[14:55:20] tRNA [116,73] has start(116) > end (73) - skipping.
[14:55:20] 1 tRNA-Ser c[2,92] 35 (tga)
[14:55:20] 1 tRNA-Ser [642,729] 35 (gga)
[14:55:20] 1 tRNA-Ile [48,124] 35 (gat)
[14:55:20] 1 tRNA-Leu c[33,10] 37 (tag)
[14:55:20] tRNA c[33,10] has start(33) > end (10) - skipping.
[14:55:20] 1 tRNA-Lys [25,99] 33 (ttt)
[14:55:20] 2 tRNA-Val [130,205] 34 (tac)
[14:55:20] 1 tRNA-Ala [49,42] 33 (tgc)
[14:55:20] tRNA [49,42] has start(49) > end (42) - skipping.
[14:55:20] 1 tRNA-Ala c[35,110] 34 (ggc)
[14:55:20] 1 tRNA-Gly [65,30] 34 (gcc)
[14:55:20] tRNA [65,30] has start(65) > end (30) - skipping.
[14:55:20] 1 tRNA-Ala c[35,110] 34 (tgc)
[14:55:20] 1 tRNA-Thr c[167,12] 39 (ggt)
[14:55:20] tRNA c[167,12] has start(167) > end (12) - skipping.
[14:55:20] 1 tRNA-Thr c[63,49] 34 (ggt)
[14:55:20] tRNA c[63,49] has start(63) > end (49) - skipping.
[14:55:20] 1 tRNA-Leu c[92,2] 35 (gag)
[14:55:20] tRNA c[92,2] has start(92) > end (2) - skipping.
[14:55:20] 1 tRNA-Arg c[84,72] 35 (acg)
[14:55:20] tRNA c[84,72] has start(84) > end (72) - skipping.
[14:55:20] 1 tRNA-Arg [81,72] 35 (acg)
[14:55:20] tRNA [81,72] has start(81) > end (72) - skipping.
[14:55:20] 1 tRNA-Ala [9,84] 34 (ggc)
[14:55:20] 1 tRNA-Val c[47,122] 34 (gac)
[14:55:21] 1 tRNA-Met [11,82] 34 (cat)
[14:55:21] 1 tRNA-Gln c[11,85] 33 (ttg)
[14:55:21] Found 19 tRNAs
[14:55:21] Predicting Ribosomal RNAs
[14:55:21] You need either Barrnap or RNAmmer installed to predict rRNAs!
[14:55:21] Skipping ncRNA search, enable with --rfam if desired.
[14:55:21] Total of 18 tRNA + rRNA features
[14:55:21] Predicting coding sequences
[14:55:21] Contigs total 4290423 bp, so using single mode
[14:55:21] Running: prodigal -i PROKKA_01172014/PROKKA_01172014.fna -c -m -g 11 -p single -f sco -q
[14:55:31] Excluding CDS which overlaps existing RNA (tRNA) at NODE_528_length_150_cov_25.833334:17..127 on - strand
[14:55:33] Found 3342 CDS
[14:55:33] Connecting features back to sequences
[14:55:33] Option --gram not specified, will NOT check for signal peptides.
[14:55:33] Not using genus-specific database. Try --usegenus to enable it.
[14:55:33] Annotating CDS, please be patient.
[14:55:33] Will use 4 CPUs for similarity searching.
[14:55:35] There are still 3342 unannotated CDS left (started with 3342)
[14:55:35] Will use blast to search against /home/ubuntu/software/prokka-1.7/bin/../db/kingdom/Bacteria/sprot with 4 CPUs
[14:55:35] Running: cat PROKKA_01172014/proteins.faa | parallel --gnu -j 4 --block 110869 --recstart '>' --pipe blastp -query - -db /home/ubuntu/software/prokka-1.7/bin/../db/kingdom/Bacteria/sprot -evalue 1e-06 -num_threads 1 -num_descriptions 1 -num_alignments 1 > PROKKA_01172014/proteins.bls 2> /dev/null
[14:57:03] Modify product: Probable TonB-dependent receptor HI_1217 precursor => putative TonB-dependent receptor precursor
[14:57:03] Modify product: Probable cysteine desulfurase => putative cysteine desulfurase
[14:57:03] Modify product: Probable GTP-binding protein EngB => putative GTP-binding protein EngB
[14:57:03] Modify product: Stress response UPF0229 protein YhbH => hypothetical protein
[14:57:03] Modify product: Probable diguanylate cyclase YdaM => putative diguanylate cyclase YdaM
[14:57:03] Modify product: Probable glutamine ABC transporter permease protein GlnM => putative glutamine ABC transporter permease protein GlnM
[14:57:03] Modify product: Probable diguanylate cyclase AdrA => putative diguanylate cyclase AdrA
[14:57:03] Modify product: Cytochrome b561 homolog 2 => hypothetical protein
[14:57:03] Modify product: Probable L-ascorbate-6-phosphate lactonase UlaG => putative L-ascorbate-6-phosphate lactonase UlaG
[14:57:03] Modify product: Probable phospholipid-binding protein MlaC precursor => putative phospholipid-binding protein MlaC precursor
[14:57:03] Modify product: Probable phospholipid ABC transporter-binding protein MlaD => putative phospholipid ABC transporter-binding protein MlaD
[14:57:03] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE
[14:57:03] Modify product: Probable phospholipid import ATP-binding protein MlaF => putative phospholipid import ATP-binding protein MlaF
[14:57:03] Modify product: Probable sulfate transporter Rv1739c/MT1781 => putative sulfate transporterc/MT1781
[14:57:03] Modify product: Phosphorylated carbohydrates phosphatase TM_1254 => Phosphorylated carbohydrates phosphatase
[14:57:03] Modify product: Uncharacterized membrane protein YjcC => putative membrane protein YjcC
[14:57:03] Modify product: Uncharacterized oxidoreductase YdgJ => putative oxidoreductase YdgJ
[14:57:03] Modify product: Probable phospholipid-binding lipoprotein MlaA precursor => putative phospholipid-binding lipoprotein MlaA precursor
[14:57:03] Modify product: Probable diguanylate cyclase YeaP => putative diguanylate cyclase YeaP
[14:57:03] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv0986/MT1014 => putative ABC transporter ATP-binding protein/MT1014
[14:57:03] Modify product: Putative reductase CA_C0462 => Putative reductase
[14:57:03] Modify product: Probable amino-acid permease protein YxeN => putative amino-acid permease protein YxeN
[14:57:03] Modify product: Probable amino-acid import ATP-binding protein YxeO => putative amino-acid import ATP-binding protein YxeO
[14:57:04] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase
[14:57:04] Modify product: 21K => hypothetical protein
[14:57:04] Modify product: Uncharacterized acyl-CoA thioester hydrolase HI_0827 => putative acyl-CoA thioester hydrolase
[14:57:04] Modify product: Probable diguanylate cyclase YdaM => putative diguanylate cyclase YdaM
[14:57:04] Modify product: Probable diguanylate cyclase YegE => putative diguanylate cyclase YegE
[14:57:04] Modify product: Probable diguanylate cyclase AdrA => putative diguanylate cyclase AdrA
[14:57:04] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase
[14:57:04] Modify product: P20 => hypothetical protein
[14:57:04] Modify product: Cyclic di-GMP binding protein VCA0042 => Cyclic di-GMP binding protein
[14:57:04] Modify product: Probable enoyl-CoA hydratase 1 => putative enoyl-CoA hydratase 1
[14:57:04] Modify product: Uncharacterized ABC transporter ATP-binding protein YheS => putative ABC transporter ATP-binding protein YheS
[14:57:04] Modify product: Uncharacterized inner membrane transporter yiJE => putative inner membrane transporter yiJE
[14:57:04] Modify product: Probable diguanylate cyclase AdrA => putative diguanylate cyclase AdrA
[14:57:04] Modify product: Probable aromatic acid decarboxylase => putative aromatic acid decarboxylase
[14:57:04] Modify product: Uncharacterized HTH-type transcriptional regulator YdfH => putative HTH-type transcriptional regulator YdfH
[14:57:04] Modify product: Probable peroxiredoxin => putative peroxiredoxin
[14:57:04] Modify product: Probable ATP-dependent helicase DinG homolog => hypothetical protein
[14:57:04] Modify product: Probable diguanylate cyclase YdaM => putative diguanylate cyclase YdaM
[14:57:05] Modify product: Transcription termination/antitermination L factor => hypothetical protein
[14:57:05] Modify product: Probable acyltransferase YihG => putative acyltransferase YihG
[14:57:05] Modify product: Putative multidrug export ATP-binding/permease protein SAV1866 => Putative multidrug export ATP-binding/permease protein
[14:57:05] Modify product: Probable transcriptional regulatory protein YeeN => putative transcriptional regulatory protein YeeN
[14:57:05] Modify product: Probable diguanylate cyclase YcdT => putative diguanylate cyclase YcdT
[14:57:05] Modify product: Cytochrome c oxidase subunit 1 homolog, bacteroid => hypothetical protein
[14:57:05] Modify product: Cytochrome b561 homolog 2 => hypothetical protein
[14:57:05] Modify product: Tricorn protease homolog 1 => hypothetical protein
[14:57:05] Modify product: Uncharacterized ABC transporter ATP-binding protein YbhF => putative ABC transporter ATP-binding protein YbhF
[14:57:05] Modify product: Probable phosphatase YcdX => putative phosphatase YcdX
[14:57:05] Modify product: Uncharacterized ferredoxin-like protein YfhL => putative ferredoxin-like protein YfhL
[14:57:05] Modify product: Uncharacterized protease YhbU precursor => putative protease YhbU precursor
[14:57:05] Modify product: Probable peptidoglycan biosynthesis protein MurJ => putative peptidoglycan biosynthesis protein MurJ
[14:57:05] Modify product: Uncharacterized protease YhbU precursor => putative protease YhbU precursor
[14:57:05] Modify product: G20.3 => hypothetical protein
[14:57:05] Modify product: Probable L,D-transpeptidase YcfS precursor => putative L,D-transpeptidase YcfS precursor
[14:57:05] Modify product: Probable inorganic polyphosphate/ATP-NAD kinase => putative inorganic polyphosphate/ATP-NAD kinase
[14:57:06] Modify product: Probable diguanylate cyclase YdaM => putative diguanylate cyclase YdaM
[14:57:06] Modify product: Probable DNA endonuclease SmrA => putative DNA endonuclease SmrA
[14:57:06] Modify product: Probable galacturonate locus repressor => putative galacturonate locus repressor
[14:57:06] Modify product: Probable siderophore transport system ATP-binding protein YusV => putative siderophore transport system ATP-binding protein YusV
[14:57:06] Modify product: Probable siderophore transport system permease protein YfiZ precursor => putative siderophore transport system permease protein YfiZ precursor
[14:57:06] Modify product: Probable DNA endonuclease SmrA => putative DNA endonuclease SmrA
[14:57:06] Modify product: Putative 2-hydroxyacid dehydrogenase HI_1556 => Putative 2-hydroxyacid dehydrogenase
[14:57:06] Modify product: Uncharacterized sugar transferase EpsL => putative sugar transferase EpsL
[14:57:06] Modify product: Uncharacterized HTH-type transcriptional regulator YbbH => putative HTH-type transcriptional regulator YbbH
[14:57:06] Modify product: Uncharacterized oxidoreductase SAV2478 => putative oxidoreductase
[14:57:06] Modify product: Probable transcriptional regulatory protein NarL => putative transcriptional regulatory protein NarL
[14:57:06] Modify product: H1 => hypothetical protein
[14:57:06] Modify product: Uncharacterized ABC transporter solute-binding protein YclQ precursor => putative ABC transporter solute-binding protein YclQ precursor
[14:57:06] Modify product: H3 => hypothetical protein
[14:57:06] Modify product: Uncharacterized acyl-CoA thioester hydrolase HI_0827 => putative acyl-CoA thioester hydrolase
[14:57:06] Modify product: Probable intracellular septation protein A => putative intracellular septation protein A
[14:57:06] Modify product: Probable polyketide biosynthesis zinc-dependent hydrolase PksB => putative polyketide biosynthesis zinc-dependent hydrolase PksB
[14:57:06] Modify product: Uncharacterized HTH-type transcriptional regulator YbbH => putative HTH-type transcriptional regulator YbbH
[14:57:06] Modify product: Putative reductase XOO0026 => Putative reductase
[14:57:06] Modify product: Probable 6-phospho-beta-glucosidase => putative 6-phospho-beta-glucosidase
[14:57:07] Modify product: Uncharacterized HTH-type transcriptional regulator HI_0893 => putative HTH-type transcriptional regulator
[14:57:07] Modify product: Uncharacterized SufE-like protein YgdK => putative SufE-like protein YgdK
[14:57:07] Modify product: Probable chromosome-partitioning protein ParB => putative chromosome-partitioning protein ParB
[14:57:07] Modify product: Putative acetyltransferase SACOL2570 => Putative acetyltransferase
[14:57:07] Modify product: Chemotaxis protein CheY homolog => hypothetical protein
[14:57:07] Modify product: P-43 => hypothetical protein
[14:57:07] Modify product: Probable diguanylate cyclase YcdT => putative diguanylate cyclase YcdT
[14:57:07] Modify product: Uncharacterized ABC transporter ATP-binding protein YbhF => putative ABC transporter ATP-binding protein YbhF
[14:57:07] Modify product: Uncharacterized ABC transporter ATP-binding protein YheS => putative ABC transporter ATP-binding protein YheS
[14:57:07] Modify product: Putative monooxygenase Rv0793 => Putative monooxygenase
[14:57:07] Modify product: Probable amino-acid-binding protein YxeM precursor => putative amino-acid-binding protein YxeM precursor
[14:57:07] Modify product: Probable Fe(2+)-trafficking protein => putative Fe(2+)-trafficking protein
[14:57:07] Modify product: L8 => hypothetical protein
[14:57:07] Modify product: Transcription termination/antitermination protein NusG => hypothetical protein
[14:57:07] Modify product: H1 => hypothetical protein
[14:57:07] Modify product: Transcription termination factor Rho => hypothetical protein
[14:57:07] Modify product: H1 => hypothetical protein
[14:57:07] Modify product: Symbiotic regulator homolog 1 => hypothetical protein
[14:57:07] Modify product: Probable diguanylate cyclase YcdT => putative diguanylate cyclase YcdT
[14:57:07] Modify product: Probable endopeptidase Spr precursor => putative endopeptidase Spr precursor
[14:57:07] Modify product: H3 => hypothetical protein
[14:57:08] Modify product: Uncharacterized membrane protein YjcC => putative membrane protein YjcC
[14:57:08] Modify product: Ribonuclease TTHA0252 => Ribonuclease
[14:57:08] Modify product: Uncharacterized deoxyribonuclease YcfH => putative deoxyribonuclease YcfH
[14:57:08] Modify product: Zinc-type alcohol dehydrogenase-like protein SA1988 => Zinc-type alcohol dehydrogenase-like protein
[14:57:08] Modify product: Uncharacterized EAL-domain containing protein YkuI => putative EAL-domain containing protein YkuI
[14:57:08] Modify product: Probable ferritin-1 => putative ferritin-1
[14:57:08] Modify product: Probable acrylyl-CoA reductase AcuI => putative acrylyl-CoA reductase AcuI
[14:57:08] Modify product: Co-chaperone protein HscB homolog => hypothetical protein
[14:57:08] Modify product: NS1 => hypothetical protein
[14:57:08] Modify product: HIT-like protein HI_0961 => HIT-like protein
[14:57:08] Modify product: Probable diguanylate cyclase YcdT => putative diguanylate cyclase YcdT
[14:57:08] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase
[14:57:08] Modify product: NS2 => hypothetical protein
[14:57:08] Modify product: Probable cadaverine/lysine antiporter => putative cadaverine/lysine antiporter
[14:57:09] Modify product: Epimerase family protein SA0724 => Epimerase family protein
[14:57:09] Modify product: Probable deferrochelatase/peroxidase YfeX => putative deferrochelatase/peroxidase YfeX
[14:57:09] Modify product: Probable diguanylate cyclase AdrA => putative diguanylate cyclase AdrA
[14:57:09] Modify product: Probable diguanylate cyclase YcdT => putative diguanylate cyclase YcdT
[14:57:09] Modify product: Uncharacterized HTH-type transcriptional regulator BA_1941/GBAA_1941/BAS1801 => putative HTH-type transcriptional regulator/GBAA_1941/BAS1801
[14:57:09] Modify product: Probable diguanylate cyclase YdaM => putative diguanylate cyclase YdaM
[14:57:09] Modify product: DPS protein homolog => hypothetical protein
[14:57:09] Modify product: Probable ubiquinone biosynthesis protein UbiB => putative ubiquinone biosynthesis protein UbiB
[14:57:09] Modify product: Probable protease SohB => putative protease SohB
[14:57:09] Modify product: Uncharacterized oxidoreductase YciK => putative oxidoreductase YciK
[14:57:09] Modify product: Uncharacterized MFS-type transporter YcaD => putative MFS-type transporter YcaD
[14:57:09] Modify product: Putative multidrug export ATP-binding/permease protein SAV1866 => Putative multidrug export ATP-binding/permease protein
[14:57:09] Modify product: PPDC => hypothetical protein
[14:57:09] Modify product: Probable chromate transport protein => putative chromate transport protein
[14:57:09] Modify product: Probable diguanylate cyclase YfiN => putative diguanylate cyclase YfiN
[14:57:09] Modify product: Uncharacterized deoxyribonuclease YcfH => putative deoxyribonuclease YcfH
[14:57:09] Modify product: Probable diguanylate cyclase AdrA => putative diguanylate cyclase AdrA
[14:57:09] Modify product: Uncharacterized PIN and TRAM-domain containing protein TTHA0540 precursor => putative PIN and TRAM-domain containing protein precursor
[14:57:09] Cleaned 131 /product names
[14:57:09] Deleting temporary file: PROKKA_01172014/proteins.faa
[14:57:09] Deleting temporary file: PROKKA_01172014/proteins.bls
[14:57:10] There are still 1252 unannotated CDS left (started with 3342)
[14:57:10] Will use hmmer3 to search against /home/ubuntu/software/prokka-1.7/bin/../db/hmm/CLUSTERS.hmm with 4 CPUs
[14:57:10] Running: cat PROKKA_01172014/proteins.faa | parallel --gnu -j 4 --block 28927 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-06 --cpu 1 /home/ubuntu/software/prokka-1.7/bin/../db/hmm/CLUSTERS.hmm /dev/stdin > PROKKA_01172014/proteins.bls 2> /dev/null
[15:03:43] Deleting temporary file: PROKKA_01172014/proteins.faa
[15:03:43] Deleting temporary file: PROKKA_01172014/proteins.bls
[15:03:43] There are still 1058 unannotated CDS left (started with 3342)
[15:03:43] Will use hmmer3 to search against /home/ubuntu/software/prokka-1.7/bin/../db/hmm/TIGRFAMs.hmm with 4 CPUs
[15:03:43] Running: cat PROKKA_01172014/proteins.faa | parallel --gnu -j 4 --block 23637 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-06 --cpu 1 /home/ubuntu/software/prokka-1.7/bin/../db/hmm/TIGRFAMs.hmm /dev/stdin > PROKKA_01172014/proteins.bls 2> /dev/null
[15:06:59] Modify product: type VI secretion protein, VC_A0114 family => type VI secretion protein, family
[15:06:59] Modify product: type VI secretion lipoprotein, VC_A0113 family => type VI secretion lipoprotein, family
[15:06:59] Modify product: type VI secretion protein, VC_A0111 family => type VI secretion protein, family
[15:06:59] Modify product: type VI secretion protein, VC_A0110 family => type VI secretion protein, family
[15:06:59] Modify product: type VI secretion protein, VC_A0107 family => type VI secretion protein, family
[15:06:59] Modify product: type VI secretion protein, EvpB/VC_A0108 family => type VI secretion protein, EvpB/ family
[15:06:59] Modify product: putative thioesterase domain => putative thioesterase domain protein
[15:06:59] Modify product: 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal subunit => hypothetical protein
[15:06:59] Modify product: flavoprotein, HI0933 family => flavoprotein, family
[15:07:00] Modify product: peroxiredoxin, SACOL1771 subfamily => peroxiredoxin, subfamily
[15:07:00] Modify product: VWFA-related Acidobacterial domain => VWFA-related Acidobacterial domain protein
[15:07:00] Modify product: FimV C-terminal domain => hypothetical protein
[15:07:00] Modify product: selT/selW/selH selenoprotein domain => selT/selW/selH selenoprotein domain protein
[15:07:00] Modify product: type VI secretion-associated protein, VC_A0118 family => type VI secretion-associated protein, family
[15:07:00] Modify product: probable O-glycosylation ligase, exosortase A-associated => putative O-glycosylation ligase, exosortase A-associated
[15:07:00] Modify product: 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal subunit => hypothetical protein
[15:07:00] Cleaned 16 /product names
[15:07:00] Deleting temporary file: PROKKA_01172014/proteins.faa
[15:07:00] Deleting temporary file: PROKKA_01172014/proteins.bls
[15:07:00] There are still 943 unannotated CDS left (started with 3342)
[15:07:00] Will use hmmer3 to search against /home/ubuntu/software/prokka-1.7/bin/../db/hmm/Cdd.hmm with 4 CPUs
[15:07:00] Running: cat PROKKA_01172014/proteins.faa | parallel --gnu -j 4 --block 20095 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-06 --cpu 1 /home/ubuntu/software/prokka-1.7/bin/../db/hmm/Cdd.hmm /dev/stdin > PROKKA_01172014/proteins.bls 2> /dev/null
[15:09:25] Modify product: putative conserved protein => hypothetical protein
[15:09:25] Modify product: Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily => Phosphoglycerol transferase, alkaline phosphatase superfamily
[15:09:25] Modify product: Transposase and inactivated derivatives => Transposase
[15:09:25] Modify product: putative conserved protein => hypothetical protein
[15:09:25] Modify product: putative esterase of the alpha/beta hydrolase fold => putative esterase of the alpha/beta hydrolase fold protein
[15:09:25] Modify product: Arsenate reductase and related proteins, glutaredoxin family => Arsenate reductase, glutaredoxin family
[15:09:25] Modify product: putative conserved protein => hypothetical protein
[15:09:25] Modify product: Na+-dependent transporters of the SNF family => Na+-dependent transporters of the SNF family protein
[15:09:25] Modify product: Response regulator containing a CheY-like receiver domain and an HD-GYP domain => Response regulator containing a CheY-like receiver domain and an HD-GYP domain protein
[15:09:25] Modify product: putative conserved protein => hypothetical protein
[15:09:25] Modify product: putative conserved protein => hypothetical protein
[15:09:25] Modify product: putative conserved protein => hypothetical protein
[15:09:25] Modify product: Arsenate reductase and related proteins, glutaredoxin family => Arsenate reductase, glutaredoxin family
[15:09:25] Modify product: putative conserved protein => hypothetical protein
[15:09:25] Modify product: putative conserved protein, contains double-stranded beta-helix domain => hypothetical protein
[15:09:25] Modify product: Na+-dependent transporters of the SNF family => Na+-dependent transporters of the SNF family protein
[15:09:25] Modify product: putative conserved protein (some members contain a von Willebrand factor type A (vWA) domain) => hypothetical protein
[15:09:25] Modify product: putative conserved protein => hypothetical protein
[15:09:25] Modify product: Transposase and inactivated derivatives => Transposase
[15:09:25] Modify product: Penicillin V acylase and related amidases => Penicillin V acylase
[15:09:25] Modify product: putative conserved protein => hypothetical protein
[15:09:25] Modify product: putative conserved protein => hypothetical protein
[15:09:25] Modify product: putative conserved protein => hypothetical protein
[15:09:25] Modify product: putative conserved protein => hypothetical protein
[15:09:25] Modify product: putative protein containing caspase domain => putative protein containing caspase domain protein
[15:09:25] Modify product: putative conserved protein => hypothetical protein
[15:09:25] Modify product: putative conserved protein => hypothetical protein
[15:09:25] Modify product: putative conserved protein => hypothetical protein
[15:09:25] Modify product: putative conserved protein => hypothetical protein
[15:09:25] Modify product: putative conserved protein => hypothetical protein
[15:09:25] Modify product: putative conserved protein => hypothetical protein
[15:09:25] Modify product: putative conserved protein => hypothetical protein
[15:09:25] Modify product: putative conserved protein => hypothetical protein
[15:09:25] Modify product: putative protein, similar to the N-terminal domain of Lon protease => hypothetical protein
[15:09:25] Modify product: putative conserved protein => hypothetical protein
[15:09:25] Modify product: putative conserved protein => hypothetical protein
[15:09:25] Modify product: Na+-dependent transporters of the SNF family => Na+-dependent transporters of the SNF family protein
[15:09:25] Modify product: Lipid A core - O-antigen ligase and related enzymes => Lipid A core - O-antigen ligase
[15:09:25] Modify product: Mannosyltransferase OCH1 and related enzymes => Mannosyltransferase OCH1
[15:09:25] Modify product: putative conserved protein => hypothetical protein
[15:09:25] Modify product: Phosphate transport regulator (distant homolog of PhoU) => hypothetical protein
[15:09:25] Cleaned 41 /product names
[15:09:25] Deleting temporary file: PROKKA_01172014/proteins.faa
[15:09:25] Deleting temporary file: PROKKA_01172014/proteins.bls
[15:09:26] There are still 808 unannotated CDS left (started with 3342)
[15:09:26] Will use hmmer3 to search against /home/ubuntu/software/prokka-1.7/bin/../db/hmm/Pfam.hmm with 4 CPUs
[15:09:26] Running: cat PROKKA_01172014/proteins.faa | parallel --gnu -j 4 --block 15836 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-06 --cpu 1 /home/ubuntu/software/prokka-1.7/bin/../db/hmm/Pfam.hmm /dev/stdin > PROKKA_01172014/proteins.bls 2> /dev/null
[15:13:12] Modify product: YHS domain => YHS domain protein
[15:13:12] Modify product: PAS fold => PAS fold protein
[15:13:12] Modify product: Na+/H+ antiporter family => Na+/H+ antiporter family protein
[15:13:12] Modify product: Phage antirepressor protein KilAC domain => Phage antirepressor protein KilAC domain protein
[15:13:12] Modify product: Hpt domain => Hpt domain protein
[15:13:12] Modify product: IclR helix-turn-helix domain => IclR helix-turn-helix domain protein
[15:13:12] Modify product: Phosphorylase superfamily => Phosphorylase superfamily protein
[15:13:12] Modify product: TraB family => TraB family protein
[15:13:12] Modify product: Cyclic nucleotide-binding domain => Cyclic nucleotide-binding domain protein
[15:13:12] Modify product: Modulator of Rho-dependent transcription termination (ROF) => hypothetical protein
[15:13:12] Modify product: Endonuclease/Exonuclease/phosphatase family => Endonuclease/Exonuclease/phosphatase family protein
[15:13:12] Modify product: PilZ domain => PilZ domain protein
[15:13:12] Modify product: Methyltransferase domain => Methyltransferase domain protein
[15:13:12] Modify product: ASCH domain => ASCH domain protein
[15:13:12] Modify product: Peptidase M16 inactive domain => Peptidase M16 inactive domain protein
[15:13:12] Modify product: DSBA-like thioredoxin domain => DSBA-like thioredoxin domain protein
[15:13:12] Modify product: YheO-like PAS domain => YheO-like PAS domain protein
[15:13:12] Modify product: Peptidase M16 inactive domain => Peptidase M16 inactive domain protein
[15:13:12] Modify product: Methyl-accepting chemotaxis protein (MCP) signaling domain => Methyl-accepting chemotaxis protein (MCP) signaling domain protein
[15:13:12] Modify product: YGGT family => YGGT family protein
[15:13:12] Modify product: Protein of unknown function (Duf2374) => hypothetical protein
[15:13:12] Modify product: CheW-like domain => CheW-like domain protein
[15:13:12] Modify product: Na+/H+ antiporter family => Na+/H+ antiporter family protein
[15:13:12] Modify product: RDD family => RDD family protein
[15:13:12] Modify product: Metallo-beta-lactamase superfamily => Metallo-beta-lactamase superfamily protein
[15:13:12] Modify product: PEGA domain => PEGA domain protein
[15:13:12] Modify product: Sporulation related domain => Sporulation related domain protein
[15:13:12] Modify product: HDOD domain => HDOD domain protein
[15:13:12] Modify product: Metallo-beta-lactamase superfamily => Metallo-beta-lactamase superfamily protein
[15:13:12] Modify product: OmpA-like transmembrane domain => OmpA-like transmembrane domain protein
[15:13:12] Modify product: Helix-turn-helix domain => Helix-turn-helix domain protein
[15:13:12] Modify product: Methyl-accepting chemotaxis protein (MCP) signaling domain => Methyl-accepting chemotaxis protein (MCP) signaling domain protein
[15:13:12] Modify product: Fatty acid hydroxylase superfamily => Fatty acid hydroxylase superfamily protein
[15:13:12] Modify product: Uracil DNA glycosylase superfamily => Uracil DNA glycosylase superfamily protein
[15:13:12] Modify product: Heme NO binding => Heme NO binding protein
[15:13:12] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:13:12] Modify product: HDOD domain => HDOD domain protein
[15:13:12] Modify product: FtsX-like permease family => FtsX-like permease family protein
[15:13:12] Modify product: SCP-2 sterol transfer family => SCP-2 sterol transfer family protein
[15:13:12] Modify product: Tim44-like domain => Tim44-like domain protein
[15:13:12] Modify product: Methyl-accepting chemotaxis protein (MCP) signaling domain => Methyl-accepting chemotaxis protein (MCP) signaling domain protein
[15:13:12] Modify product: Methyl-accepting chemotaxis protein (MCP) signaling domain => Methyl-accepting chemotaxis protein (MCP) signaling domain protein
[15:13:12] Modify product: Phage Conserved Open Reading Frame 51 => hypothetical protein
[15:13:12] Modify product: Oxidoreductase molybdopterin binding domain => Oxidoreductase molybdopterin binding domain protein
[15:13:12] Modify product: Acetyltransferase (GNAT) family => Acetyltransferase (GNAT) family protein
[15:13:12] Modify product: OmpA-like transmembrane domain => OmpA-like transmembrane domain protein
[15:13:12] Modify product: PBP superfamily domain => PBP superfamily domain protein
[15:13:12] Modify product: Methyl-accepting chemotaxis protein (MCP) signaling domain => Methyl-accepting chemotaxis protein (MCP) signaling domain protein
[15:13:12] Modify product: Methyl-accepting chemotaxis protein (MCP) signaling domain => Methyl-accepting chemotaxis protein (MCP) signaling domain protein
[15:13:12] Modify product: NYN domain => NYN domain protein
[15:13:12] Modify product: Beta-lactamase superfamily domain => Beta-lactamase superfamily domain protein
[15:13:12] Modify product: Methyl-accepting chemotaxis protein (MCP) signaling domain => Methyl-accepting chemotaxis protein (MCP) signaling domain protein
[15:13:12] Modify product: Methyl-accepting chemotaxis protein (MCP) signaling domain => Methyl-accepting chemotaxis protein (MCP) signaling domain protein
[15:13:12] Modify product: SprT-like family => SprT-like family protein
[15:13:12] Modify product: TrkA-N domain => TrkA-N domain protein
[15:13:12] Modify product: Virulence activator alpha C-term => hypothetical protein
[15:13:12] Modify product: Glyoxalase-like domain => Glyoxalase-like domain protein
[15:13:12] Modify product: YcgL domain => YcgL domain protein
[15:13:12] Modify product: Tripartite tricarboxylate transporter TctB family => Tripartite tricarboxylate transporter TctB family protein
[15:13:12] Cleaned 59 /product names
[15:13:12] Deleting temporary file: PROKKA_01172014/proteins.faa
[15:13:12] Deleting temporary file: PROKKA_01172014/proteins.bls
[15:13:12] Labelling remaining 676 proteins as 'hypothetical protein'
[15:13:12] Possible /pseudo 'Putative proximal rod protein' at NODE_1314_length_3223_cov_16.290724 position 2430
[15:13:12] Possible /pseudo 'Spermidine/putrescine-binding periplasmic protein precursor' at NODE_144_length_5930_cov_20.574535 position 5531
[15:13:12] Possible /pseudo 'Cytochrome c-type biogenesis protein CcmH precursor' at NODE_1480_length_8526_cov_16.777269 position 5312
[15:13:12] Possible /pseudo 'type VI secretion protein, family' at NODE_16_length_8293_cov_17.180031 position 6886
[15:13:12] Possible /pseudo 'Putative arginine/ornithine antiporter' at NODE_2133_length_3831_cov_17.600887 position 658
[15:13:12] Possible /pseudo 'Macrolide export ATP-binding/permease protein MacB' at NODE_2683_length_3894_cov_16.632769 position 3387
[15:13:12] Possible /pseudo 'GTP-binding protein HflX' at NODE_287_length_6749_cov_20.247740 position 5379
[15:13:12] Possible /pseudo 'Chemotaxis protein CheW' at NODE_297_length_8309_cov_17.877724 position 5598
[15:13:12] Possible /pseudo 'Twitching mobility protein' at NODE_36_length_6252_cov_21.742002 position 5964
[15:13:12] Possible /pseudo 'WavE lipopolysaccharide synthesis' at NODE_4043_length_3732_cov_16.747589 position 2930
[15:13:12] Possible /pseudo 'Alpha-galactosidase' at NODE_40_length_8322_cov_15.877434 position 5568
[15:13:12] Possible /pseudo 'Macrolide export ATP-binding/permease protein MacB' at NODE_548_length_2766_cov_22.198843 position 1406
[15:13:12] Possible /pseudo 'Molecular chaperone Hsp31 and glyoxalase 3' at NODE_622_length_3974_cov_16.775038 position 2827
[15:13:12] Possible /pseudo 'Alpha-acetolactate decarboxylase' at NODE_911_length_17073_cov_13.548586 position 11937
[15:13:12] Possible /pseudo 'RNA polymerase sigma factor RpoS' at NODE_979_length_7686_cov_22.014442 position 3041
[15:13:12] Found 1738 unique /gene codes.
[15:13:12] Fixed 200 colliding /gene names.
[15:13:12] Adding /locus_tag identifiers
[15:13:13] Assigned 3361 locus_tags to CDS and RNA features.
[15:13:13] Writing outputs to PROKKA_01172014/
[15:13:17] Generating annotation statistics file
[15:13:17] Generating Genbank and Sequin files
[15:13:17] Running: tbl2asn -V b -a s -N 1 -y 'Annotated using prokka 1.8 from http://www.vicbioinformatics.com' -Z PROKKA_01172014/PROKKA_01172014.err -i PROKKA_01172014/PROKKA_01172014.fsa 2> /dev/null
[15:13:50] Deleting temporary file: PROKKA_01172014/errorsummary.val
[15:13:50] Deleting temporary file: PROKKA_01172014/PROKKA_01172014.dr
[15:13:50] Deleting temporary file: PROKKA_01172014/PROKKA_01172014.fixedproducts
[15:13:50] Deleting temporary file: PROKKA_01172014/PROKKA_01172014.ecn
[15:13:50] Deleting temporary file: PROKKA_01172014/PROKKA_01172014.val
[15:13:50] Output files:
[15:13:50] PROKKA_01172014/PROKKA_01172014.txt
[15:13:50] PROKKA_01172014/PROKKA_01172014.ffn
[15:13:50] PROKKA_01172014/PROKKA_01172014.gff
[15:13:50] PROKKA_01172014/PROKKA_01172014.fna
[15:13:50] PROKKA_01172014/PROKKA_01172014.err
[15:13:50] PROKKA_01172014/PROKKA_01172014.sqn
[15:13:50] PROKKA_01172014/PROKKA_01172014.gbk
[15:13:50] PROKKA_01172014/PROKKA_01172014.faa
[15:13:50] PROKKA_01172014/PROKKA_01172014.tbl
[15:13:50] PROKKA_01172014/PROKKA_01172014.log
[15:13:50] PROKKA_01172014/PROKKA_01172014.fsa
[15:13:50] Walltime used: 18.58 minutes
[15:13:50] Share and enjoy!
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About Lisa Johnson

PhD candidate at UC Davis.
This entry was posted in Bioinformatics, Genomics Workshop. Bookmark the permalink.

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