to trim or not to trim for de novo assembly?

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sjki...@gmail.com

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Apr 28, 2018, 10:07:55 PM4/28/18
to dDocent User Help Forum
Hi, Group:
I suspect I am missing something obvious, but this is my first attempt at dDocent so I need to ask anyway. I am trying to get SNPs from a nonmodel organism with no genome available for my species, or for any close species, so I need to do a de novo assembly. Walking through the User Guide, I see "If performing de novo assembly, it’s essential that no read trimming or adapter removal has taken place before the dDocent pipeline." Assembly works okay, but when I try to map the reads, I get ""dDocent cannot locate trimmed reads files" and "Please rerun dDocent with quality trimming". Attempts to trim the assemblies do not appear to work, as I get "unable to look up public/pickup: No such file or directory".
Any suggestions? Is there something fundamental that I am not understanding?
Thanks,
Steve

sjki...@gmail.com

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Apr 29, 2018, 2:46:16 PM4/29/18
to dDocent User Help Forum
here are my outputs:
dDocent.runs:
Variables used in dDocent Run at Sat Apr 28 18:48:30 PDT 2018
Number of Processors
24
Maximum Memory
120g
Trimming
yes
Assembly?
no
Type_of_Assembly
SE
Clustering_Similarity%
0.8
Mapping_Reads?
no
Mapping_Match_Value
1
Mapping_MisMatch_Value
4
Mapping_GapOpen_Penalty
6
Calling_SNPs?
no
Email
sjki...@gmail.com

dDocent_main.LOG:
dDocent run started Sat Apr 28 18:48:30 PDT 2018

At this point, all configuration information has been entered and dDocent may take several hours to run.
It is recommended that you move this script to a background operation and disable terminal input and output.
All data and logfiles will still be recorded.
To do this:
Press control and Z simultaneously
Type 'bg' without the quotes and press enter
Type 'disown -h' again without the quotes and press enter
Now sit back, relax, and wait for your analysis to finish.
Trimming reads
mawk: cannot open ./logfiles/VCFtools.log (No such file or directory)
postdrop: warning: unable to look up public/pickup: No such file or directory

and the contents of my directory:
[skimble5@comet-ln2 crawfish_frogs_SNPs_ND]$ ls -l
total 691
drwxr-xr-x 2 skimble5 sds154 33280 Apr 26 13:17 assembled
drwxr-xr-x 2 skimble5 sds154 57856 Apr 24 12:47 demultiplexed_samples_no_RAD_check
drwxr-xr-x 4 skimble5 sds154 90624 Apr 26 19:16 demultiplexed_samples_no_RAD_check_gzipped_assembled_no_trim
drwxr-xr-x 4 skimble5 sds154 107008 Apr 28 18:50 demultiplexed_samples_no_RAD_check_gzipped_assembled_trim
-rw-r--r-- 1 skimble5 sds154 617 Apr 23 18:23 process_radtags_fastq_10_min_1_node_1_processor.o15704302.comet-20-61
-rw-r--r-- 1 skimble5 sds154 892 Apr 23 18:22 process_radtags_fastq_10_min_1_node_24_processors.o15704277.comet-04-59
-rw-r--r-- 1 skimble5 sds154 856 Apr 23 18:41 process_radtags_fastq_10_min_4_node_1_processor.o15704434.comet-04-09
-rw-r--r-- 1 skimble5 sds154 602 Apr 23 18:41 process_radtags_fastq_10_min_4_node_24_processors.o15704436.comet-28-17
-rw-r--r-- 1 skimble5 sds154 5615 Apr 24 07:17 process_radtags_fastq_1_node_24_processors.o15714720.comet-07-48
-rw-r--r-- 1 skimble5 sds154 209 Jan 18 10:45 process_radtags_fastq.o13873042.comet-10-31
-rw-r--r-- 1 skimble5 sds154 1779 Jan 18 11:01 process_radtags_fastq.o13873046.comet-10-31
-rw-r--r-- 1 skimble5 sds154 1953 Jan 18 12:21 process_radtags_fastq.o13873835.comet-19-11
-rw-r--r-- 1 skimble5 sds154 245 Jan 18 12:31 process_radtags_fastq.o13874470.comet-12-58
-rw-r--r-- 1 skimble5 sds154 245 Jan 18 12:38 process_radtags_fastq.o13874735.comet-16-66
-rw-r--r-- 1 skimble5 sds154 4411 Jan 18 13:38 process_radtags_fastq.o13874785.comet-16-55
-rw-r--r-- 1 skimble5 sds154 5456 Jan 18 14:54 process_radtags_fastq.o13875310.comet-16-55
-rw-r--r-- 1 skimble5 sds154 5350 Jan 19 10:51 process_radtags_fastq.o13889665.comet-03-16
-rw-r--r-- 1 skimble5 sds154 5434 Jan 19 13:52 process_radtags_fastq.o13890637.comet-16-20
-rw-r--r-- 1 skimble5 sds154 5456 Jan 22 10:14 process_radtags_fastq.o13915999.comet-05-02
-rw-r--r-- 1 skimble5 sds154 5456 Jan 31 14:30 process_radtags_fastq.o14047419.comet-02-61
-rw-r--r-- 1 skimble5 sds154 5456 Feb 1 06:46 process_radtags_fastq.o14061630.comet-07-43
-rw-r--r-- 1 skimble5 sds154 5456 Feb 1 11:30 process_radtags_fastq.o14065161.comet-07-35
-rw-r--r-- 1 skimble5 sds154 103 Apr 23 13:24 process_radtags_fastq.o15701229.comet-10-72
-rw-r--r-- 1 skimble5 sds154 216 Apr 23 13:25 process_radtags_fastq.o15701235.comet-10-72
-rw-r--r-- 1 skimble5 sds154 784 Apr 23 13:34 process_radtags_fastq.o15701254.comet-07-19
drwxr-xr-x 2 skimble5 sds154 90624 Apr 26 18:50 QC_trimmed_samples_DO_NOT_USE
drwxr-xr-x 2 skimble5 sds154 33280 Apr 23 13:28 raw_reads_fastq_format
drwxrwxrwx 2 skimble5 sds154 41472 Jan 22 09:05 raw_reads_fastq.gz_format
-rwxrwxrwx 1 skimble5 sds154 390 Apr 23 13:22 stacksscript_process_radtags
-rwxrwxrwx 1 skimble5 sds154 408 Jan 4 08:36 stacksscript_process_radtags_ND
-rwxrwxrwx 1 skimble5 sds154 349 Jan 22 09:06 stacksscript_process_radtags_ND_fastq
-rwxrwxrwx 1 skimble5 sds154 311 Jan 3 12:17 submittercomet_process_radtags_ND.sh
-rwxrwxrwx 1 skimble5 sds154 342 Apr 24 07:26 submittercomet_process_radtags.sh

Jon Puritz

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Apr 30, 2018, 12:11:43 PM4/30/18
to ddo...@googlegroups.com

Hi Steve,

In your ls -l output, I don’t actually see any sequence files.

You should have demultipled, raw files in your directory. The files for each individuals need to be named in this connection:

PopA_001.F.fq.gz        PopA_001.R.fq.gz
PopA_002.F.fq.gz        PopA_002.R.fq.gz
PopB_001.F.fq.gz        PopB_001.R.fq.gz
PopB_002.F.fq.gz        PopB_002.R.fq.gz

In the example above, we have two individuals from two different localities/populations. Each individual has two sequence files in this example, assuming you are using paired-end sequencing. If not, it should look like this:

PopA_001.F.fq.gz
PopA_002.F.fq.gz
PopB_001.F.fq.gz
PopB_002.F.fq.gz

This is critical for all aspects of dDocent working properly. I also saw in your settings, that you had mapping set to no which would also prevent reads from mapping.

Hope that helps,

Jon


-- 
Jon Puritz, PhD

Assistant Professor
Department of Biological Sciences
University of Rhode Island
120 Flagg Road, Kingston, RI 02881

Webpage: MarineEvoEco.com

Email: 
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Steve Kimble

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May 5, 2018, 9:46:15 PM5/5/18
to ddo...@googlegroups.com
Jon:

Thanks for the email and I apologize: I sent the contents of the wrong directory. It should be:

$ll -l
-rw-r--r-- 1 skimble5 sds154         247 May  2 06:12 config.file
-rw-r--r-- 1 skimble5 sds154         250 May  2 06:38 config.file2
-rw-r--r-- 1 skimble5 sds154         818 Apr 26 19:21 dDocent.15763490.comet-15-46.1node1core.out
-rw-r--r-- 1 skimble5 sds154         818 Apr 26 19:27 dDocent.15763555.comet-05-30.1node24cores.out
-rw-r--r-- 1 skimble5 sds154         818 Apr 26 19:43 dDocent.15763715.comet-18-10.4nodes1core.out
-rw-r--r-- 1 skimble5 sds154         818 Apr 26 19:54 dDocent.15763835.comet-10-22.4nodes24cores.out
-rw-r--r-- 1 skimble5 sds154         748 Apr 28 18:08 dDocent.15813371.comet-02-20.4nodes24cores.out
-rw-r--r-- 1 skimble5 sds154         748 Apr 28 18:28 dDocent.15813575.comet-02-55.4nodes24cores.out
-rw-r--r-- 1 skimble5 sds154         748 Apr 28 18:34 dDocent.15813649.comet-06-54.1node24cores.out
-rw-r--r-- 1 skimble5 sds154         818 Apr 28 18:50 dDocent.15813864.comet-10-56.1node24cores.out
-rw-r--r-- 1 skimble5 sds154         818 Apr 30 10:34 dDocent.15841836.comet-03-70.1node24cores.out
-rw-r--r-- 1 skimble5 sds154         748 Apr 30 10:55 dDocent.15842106.comet-07-27.1node24cores.out
-rw-r--r-- 1 skimble5 sds154         747 May  1 13:40 dDocent.15861423.comet-07-08.1node24cores.out
-rw-r--r-- 1 skimble5 sds154         747 May  2 06:14 dDocent.15876534.comet-28-25.1node24cores.out
-rw-r--r-- 1 skimble5 sds154        4476 May  2 06:32 dDocent.15876876.comet-20-10.1node24cores.out
-rw-r--r-- 1 skimble5 sds154        1169 May  2 06:35 dDocent.15877056.comet-05-56.1node24cores.out
-rw-r--r-- 1 skimble5 sds154        4272 May  2 06:39 dDocent.15877058.comet-05-56.1node24cores.out
-rw-r--r-- 1 skimble5 sds154       17136 May  2 06:39 dDocent_main.LOG
-rw-r--r-- 1 skimble5 sds154        4672 May  2 06:36 dDocent.runs
-rw-r--r-- 1 skimble5 sds154         349 May  2 06:20 dDocent.sb
-rw-r--r-- 1 skimble5 sds154       41010 May  2 06:35 hs_err_pid28475.log
-rw-r--r-- 1 skimble5 sds154       40419 May  2 06:20 hs_err_pid2934.log
-rw-r--r-- 1 skimble5 sds154       16650 May  2 06:36 lengths.txt
-rw-r--r-- 1 skimble5 sds154    63562472 Apr 24 07:17 LIAR1_10560.F.fq.gz
-rw-r--r-- 1 skimble5 sds154       50891 May  2 06:36 LIAR1_10560.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154       55655 May  2 06:36 LIAR1_10560.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154    52878830 Apr 24 07:17 LIAR1_10560.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2040 May  2 06:36 LIAR1_10560.trim.log
-rw-r--r-- 1 skimble5 sds154    34469715 May  2 06:21 LIAR1_10560.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   181968436 Apr 24 07:17 LIAR1_10561.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      128900 May  2 06:36 LIAR1_10561.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      143597 May  2 06:36 LIAR1_10561.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   200280493 Apr 24 07:17 LIAR1_10561.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2044 May  2 06:36 LIAR1_10561.trim.log
-rw-r--r-- 1 skimble5 sds154   108865301 May  2 06:21 LIAR1_10561.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   216080228 Apr 24 07:17 LIAR1_10562.F.fq.gz
-rw-r--r-- 1 skimble5 sds154       24501 May  2 06:36 LIAR1_10562.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154       29022 May  2 06:36 LIAR1_10562.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   234684340 Apr 24 07:17 LIAR1_10562.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2004 May  2 06:36 LIAR1_10562.trim.log
-rw-r--r-- 1 skimble5 sds154   301273349 May  2 06:21 LIAR1_10562.uniq.seqs
-rw-r--r-- 1 skimble5 sds154    47277733 Apr 24 07:17 LIAR1_10563.F.fq.gz
-rw-r--r-- 1 skimble5 sds154    29294461 May  2 06:36 LIAR1_10563.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154    31264129 May  2 06:36 LIAR1_10563.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154    45174830 Apr 24 07:17 LIAR1_10563.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        1265 May  2 06:36 LIAR1_10563.trim.log
-rw-r--r-- 1 skimble5 sds154    23410625 May  2 06:21 LIAR1_10563.uniq.seqs
-rw-r--r-- 1 skimble5 sds154    79731205 Apr 24 07:17 LIAR1_10564.F.fq.gz
-rw-r--r-- 1 skimble5 sds154       94984 May  2 06:36 LIAR1_10564.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      114606 May  2 06:36 LIAR1_10564.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154    78327056 Apr 24 07:17 LIAR1_10564.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2030 May  2 06:36 LIAR1_10564.trim.log
-rw-r--r-- 1 skimble5 sds154   146131456 May  2 06:21 LIAR1_10564.uniq.seqs
-rw-r--r-- 1 skimble5 sds154    36822225 Apr 24 07:17 LIAR1_111.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      499012 May  2 06:36 LIAR1_111.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      616802 May  2 06:36 LIAR1_111.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154    34510959 Apr 24 07:17 LIAR1_111.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2026 May  2 06:36 LIAR1_111.trim.log
-rw-r--r-- 1 skimble5 sds154    25723793 May  2 06:21 LIAR1_111.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   226381561 Apr 24 07:17 LIAR1_11GLA1120.F.fq.gz
-rw-r--r-- 1 skimble5 sds154          20 May  2 06:36 LIAR1_11GLA1120.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154          20 May  2 06:36 LIAR1_11GLA1120.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   244371436 Apr 24 07:17 LIAR1_11GLA1120.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2136 May  2 06:36 LIAR1_11GLA1120.trim.log
-rw-r--r-- 1 skimble5 sds154   127789334 May  2 06:21 LIAR1_11GLA1120.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   177759035 Apr 24 07:17 LIAR1_13GLA039.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      136393 May  2 06:36 LIAR1_13GLA039.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      174838 May  2 06:36 LIAR1_13GLA039.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   197928650 Apr 24 07:17 LIAR1_13GLA039.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2024 May  2 06:36 LIAR1_13GLA039.trim.log
-rw-r--r-- 1 skimble5 sds154   117332032 May  2 06:21 LIAR1_13GLA039.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   240299116 Apr 24 07:17 LIAR1_14GLA745.F.fq.gz
-rw-r--r-- 1 skimble5 sds154       95157 May  2 06:36 LIAR1_14GLA745.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      118619 May  2 06:36 LIAR1_14GLA745.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   262321305 Apr 24 07:17 LIAR1_14GLA745.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2031 May  2 06:36 LIAR1_14GLA745.trim.log
-rw-r--r-- 1 skimble5 sds154   136325063 May  2 06:21 LIAR1_14GLA745.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   182764770 Apr 24 07:17 LIAR1_15GLA1172.F.fq.gz
-rw-r--r-- 1 skimble5 sds154       90432 May  2 06:36 LIAR1_15GLA1172.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      116427 May  2 06:36 LIAR1_15GLA1172.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   199157933 Apr 24 07:17 LIAR1_15GLA1172.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2007 May  2 06:36 LIAR1_15GLA1172.trim.log
-rw-r--r-- 1 skimble5 sds154   249541659 May  2 06:21 LIAR1_15GLA1172.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   227929571 Apr 24 07:17 LIAR1_17GLA748.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      117416 May  2 06:36 LIAR1_17GLA748.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      143963 May  2 06:36 LIAR1_17GLA748.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   237998507 Apr 24 07:17 LIAR1_17GLA748.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2032 May  2 06:36 LIAR1_17GLA748.trim.log
-rw-r--r-- 1 skimble5 sds154   137507407 May  2 06:21 LIAR1_17GLA748.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   239370601 Apr 24 07:17 LIAR1_18GLA053.F.fq.gz
-rw-r--r-- 1 skimble5 sds154       61624 May  2 06:36 LIAR1_18GLA053.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154       53860 May  2 06:36 LIAR1_18GLA053.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   252702339 Apr 24 07:17 LIAR1_18GLA053.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2024 May  2 06:36 LIAR1_18GLA053.trim.log
-rw-r--r-- 1 skimble5 sds154   146385507 May  2 06:21 LIAR1_18GLA053.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   241659763 Apr 24 07:17 LIAR1_19GLA058.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      695338 May  2 06:36 LIAR1_19GLA058.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      913871 May  2 06:36 LIAR1_19GLA058.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   269734744 Apr 24 07:17 LIAR1_19GLA058.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2041 May  2 06:36 LIAR1_19GLA058.trim.log
-rw-r--r-- 1 skimble5 sds154   317966714 May  2 06:21 LIAR1_19GLA058.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   263590425 Apr 24 07:17 LIAR1_1GLA743.F.fq.gz
-rw-r--r-- 1 skimble5 sds154       28300 May  2 06:36 LIAR1_1GLA743.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154       33665 May  2 06:36 LIAR1_1GLA743.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   284133935 Apr 24 07:17 LIAR1_1GLA743.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2043 May  2 06:36 LIAR1_1GLA743.trim.log
-rw-r--r-- 1 skimble5 sds154   370942530 May  2 06:21 LIAR1_1GLA743.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   257363506 Apr 24 07:17 LIAR1_20GLA1190.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      482947 May  2 06:36 LIAR1_20GLA1190.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      618437 May  2 06:36 LIAR1_20GLA1190.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   276102003 Apr 24 07:17 LIAR1_20GLA1190.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2064 May  2 06:36 LIAR1_20GLA1190.trim.log
-rw-r--r-- 1 skimble5 sds154   144029563 May  2 06:21 LIAR1_20GLA1190.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   223934293 Apr 24 07:17 LIAR1_21GLA1100.F.fq.gz
-rw-r--r-- 1 skimble5 sds154       32888 May  2 06:36 LIAR1_21GLA1100.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154       31370 May  2 06:36 LIAR1_21GLA1100.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   236064376 Apr 24 07:17 LIAR1_21GLA1100.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2062 May  2 06:36 LIAR1_21GLA1100.trim.log
-rw-r--r-- 1 skimble5 sds154   141829363 May  2 06:21 LIAR1_21GLA1100.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   258113583 Apr 24 07:17 LIAR1_22GLA752.F.fq.gz
-rw-r--r-- 1 skimble5 sds154       47328 May  2 06:36 LIAR1_22GLA752.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154       61018 May  2 06:36 LIAR1_22GLA752.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   262969104 Apr 24 07:17 LIAR1_22GLA752.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2055 May  2 06:36 LIAR1_22GLA752.trim.log
-rw-r--r-- 1 skimble5 sds154   138405884 May  2 06:21 LIAR1_22GLA752.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   239074151 Apr 24 07:17 LIAR1_23GLA020.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      384632 May  2 06:36 LIAR1_23GLA020.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      460878 May  2 06:36 LIAR1_23GLA020.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   260802577 Apr 24 07:17 LIAR1_23GLA020.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2018 May  2 06:36 LIAR1_23GLA020.trim.log
-rw-r--r-- 1 skimble5 sds154   136377979 May  2 06:21 LIAR1_23GLA020.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   230980106 Apr 24 07:17 LIAR1_24GLA1187.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      234858 May  2 06:36 LIAR1_24GLA1187.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      300701 May  2 06:36 LIAR1_24GLA1187.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   251278041 Apr 24 07:17 LIAR1_24GLA1187.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2068 May  2 06:36 LIAR1_24GLA1187.trim.log
-rw-r--r-- 1 skimble5 sds154   131300250 May  2 06:21 LIAR1_24GLA1187.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   154647793 Apr 24 07:17 LIAR1_28GLA933.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      155486 May  2 06:36 LIAR1_28GLA933.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      176978 May  2 06:36 LIAR1_28GLA933.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   153518286 Apr 24 07:17 LIAR1_28GLA933.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2036 May  2 06:36 LIAR1_28GLA933.trim.log
-rw-r--r-- 1 skimble5 sds154   101791117 May  2 06:21 LIAR1_28GLA933.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   257032668 Apr 24 07:17 LIAR1_2GLA740.F.fq.gz
-rw-r--r-- 1 skimble5 sds154       22854 May  2 06:36 LIAR1_2GLA740.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154       29817 May  2 06:36 LIAR1_2GLA740.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   277568703 Apr 24 07:17 LIAR1_2GLA740.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2125 May  2 06:36 LIAR1_2GLA740.trim.log
-rw-r--r-- 1 skimble5 sds154   347842711 May  2 06:21 LIAR1_2GLA740.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   121715156 Apr 24 07:17 LIAR1_30GLA1122.F.fq.gz
-rw-r--r-- 1 skimble5 sds154       47055 May  2 06:36 LIAR1_30GLA1122.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154       56111 May  2 06:36 LIAR1_30GLA1122.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   132785124 Apr 24 07:17 LIAR1_30GLA1122.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2054 May  2 06:36 LIAR1_30GLA1122.trim.log
-rw-r--r-- 1 skimble5 sds154    93899321 May  2 06:21 LIAR1_30GLA1122.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   229181102 Apr 24 07:17 LIAR1_31GLA1117.F.fq.gz
-rw-r--r-- 1 skimble5 sds154          20 May  2 06:36 LIAR1_31GLA1117.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154          20 May  2 06:36 LIAR1_31GLA1117.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   246118309 Apr 24 07:17 LIAR1_31GLA1117.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2020 May  2 06:36 LIAR1_31GLA1117.trim.log
-rw-r--r-- 1 skimble5 sds154   131908166 May  2 06:21 LIAR1_31GLA1117.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   196743038 Apr 24 07:17 LIAR1_37GLA004.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      244237 May  2 06:36 LIAR1_37GLA004.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      239252 May  2 06:36 LIAR1_37GLA004.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   215709480 Apr 24 07:17 LIAR1_37GLA004.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2076 May  2 06:36 LIAR1_37GLA004.trim.log
-rw-r--r-- 1 skimble5 sds154   260746886 May  2 06:21 LIAR1_37GLA004.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   179292593 Apr 24 07:17 LIAR1_39GLA1125.F.fq.gz
-rw-r--r-- 1 skimble5 sds154          20 May  2 06:36 LIAR1_39GLA1125.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154          20 May  2 06:36 LIAR1_39GLA1125.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   184519333 Apr 24 07:17 LIAR1_39GLA1125.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        1988 May  2 06:36 LIAR1_39GLA1125.trim.log
-rw-r--r-- 1 skimble5 sds154   112492377 May  2 06:21 LIAR1_39GLA1125.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   277188143 Apr 24 07:17 LIAR1_3GLA040.F.fq.gz
-rw-r--r-- 1 skimble5 sds154       54447 May  2 06:36 LIAR1_3GLA040.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154       54344 May  2 06:36 LIAR1_3GLA040.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   298753555 Apr 24 07:17 LIAR1_3GLA040.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2072 May  2 06:36 LIAR1_3GLA040.trim.log
-rw-r--r-- 1 skimble5 sds154   150536333 May  2 06:21 LIAR1_3GLA040.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   255123385 Apr 24 07:17 LIAR1_4GLA088.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      608633 May  2 06:36 LIAR1_4GLA088.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      703606 May  2 06:36 LIAR1_4GLA088.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   274698644 Apr 24 07:17 LIAR1_4GLA088.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2092 May  2 06:36 LIAR1_4GLA088.trim.log
-rw-r--r-- 1 skimble5 sds154   344287044 May  2 06:21 LIAR1_4GLA088.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   230370093 Apr 24 07:17 LIAR1_6GLA167.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      302686 May  2 06:36 LIAR1_6GLA167.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      336090 May  2 06:36 LIAR1_6GLA167.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   247267462 Apr 24 07:17 LIAR1_6GLA167.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2042 May  2 06:36 LIAR1_6GLA167.trim.log
-rw-r--r-- 1 skimble5 sds154   134726923 May  2 06:21 LIAR1_6GLA167.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   199234047 Apr 24 07:17 LIAR1_7GLA729.F.fq.gz
-rw-r--r-- 1 skimble5 sds154          20 May  2 06:36 LIAR1_7GLA729.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154          20 May  2 06:36 LIAR1_7GLA729.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   206332023 Apr 24 07:17 LIAR1_7GLA729.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2060 May  2 06:36 LIAR1_7GLA729.trim.log
-rw-r--r-- 1 skimble5 sds154   305137173 May  2 06:21 LIAR1_7GLA729.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   234717877 Apr 24 07:17 LIAR1_8GLA746.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      644790 May  2 06:36 LIAR1_8GLA746.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      815640 May  2 06:36 LIAR1_8GLA746.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   245556818 Apr 24 07:17 LIAR1_8GLA746.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2059 May  2 06:36 LIAR1_8GLA746.trim.log
-rw-r--r-- 1 skimble5 sds154   131643647 May  2 06:21 LIAR1_8GLA746.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   202282203 Apr 24 07:17 LIAR1_9GLA043.F.fq.gz
-rw-r--r-- 1 skimble5 sds154       52112 May  2 06:36 LIAR1_9GLA043.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154       56836 May  2 06:36 LIAR1_9GLA043.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   222479041 Apr 24 07:17 LIAR1_9GLA043.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2026 May  2 06:36 LIAR1_9GLA043.trim.log
-rw-r--r-- 1 skimble5 sds154   272603023 May  2 06:21 LIAR1_9GLA043.uniq.seqs
-rw-r--r-- 1 skimble5 sds154    57419783 Apr 24 07:17 LIAR1_A1.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      178512 May  2 06:36 LIAR1_A1.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      204686 May  2 06:36 LIAR1_A1.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154    44866296 Apr 24 07:17 LIAR1_A1.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        1986 May  2 06:36 LIAR1_A1.trim.log
-rw-r--r-- 1 skimble5 sds154    32811643 May  2 06:21 LIAR1_A1.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   226779110 Apr 24 07:17 LIAR1_BO1204.R.fq.gz
-rw-r--r-- 1 skimble5 sds154   154132113 Apr 24 07:17 LIAR1_BO12-06.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      319717 May  2 06:36 LIAR1_BO12-06.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154   159143828 Apr 24 07:17 LIAR1_BO1206.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        1445 May  2 06:36 LIAR1_BO12-06.trim.log
-rw-r--r-- 1 skimble5 sds154    70970633 May  2 06:21 LIAR1_BO12-06.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   300623753 Apr 24 07:17 LIAR1_BO12-08.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      341879 May  2 06:36 LIAR1_BO12-08.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      402833 May  2 06:36 LIAR1_BO12-08.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   327885145 Apr 24 07:17 LIAR1_BO12-08.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2026 May  2 06:36 LIAR1_BO12-08.trim.log
-rw-r--r-- 1 skimble5 sds154   153027136 May  2 06:21 LIAR1_BO12-08.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   239173981 Apr 24 07:17 LIAR1_BO12-09.F.fq.gz
-rw-r--r-- 1 skimble5 sds154       70721 May  2 06:36 LIAR1_BO12-09.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154   248064395 Apr 24 07:17 LIAR1_BO1209.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        1488 May  2 06:36 LIAR1_BO12-09.trim.log
-rw-r--r-- 1 skimble5 sds154   372615427 May  2 06:21 LIAR1_BO12-09.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   263311167 Apr 24 07:17 LIAR1_BO12-11.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      168303 May  2 06:36 LIAR1_BO12-11.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154   277970973 Apr 24 07:17 LIAR1_BO1211.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        1478 May  2 06:36 LIAR1_BO12-11.trim.log
-rw-r--r-- 1 skimble5 sds154   147941621 May  2 06:21 LIAR1_BO12-11.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   269899039 Apr 24 07:17 LIAR1_BO12-40.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      362797 May  2 06:36 LIAR1_BO12-40.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154   291308663 Apr 24 07:17 LIAR1_BO1240.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        1444 May  2 06:36 LIAR1_BO12-40.trim.log
-rw-r--r-- 1 skimble5 sds154   148115607 May  2 06:21 LIAR1_BO12-40.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   279966498 Apr 24 07:17 LIAR1_BO12-42.F.fq.gz
-rw-r--r-- 1 skimble5 sds154       91982 May  2 06:36 LIAR1_BO12-42.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154   302417959 Apr 24 07:17 LIAR1_BO1242.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        1504 May  2 06:36 LIAR1_BO12-42.trim.log
-rw-r--r-- 1 skimble5 sds154   393750938 May  2 06:21 LIAR1_BO12-42.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   289685081 Apr 24 07:17 LIAR1_BO12-44.F.fq.gz
-rw-r--r-- 1 skimble5 sds154       23595 May  2 06:36 LIAR1_BO12-44.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154   313048284 Apr 24 07:17 LIAR1_BO1244.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        1453 May  2 06:36 LIAR1_BO12-44.trim.log
-rw-r--r-- 1 skimble5 sds154   390581500 May  2 06:21 LIAR1_BO12-44.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   255173083 Apr 24 07:17 LIAR1_BO12-46.F.fq.gz
-rw-r--r-- 1 skimble5 sds154          20 May  2 06:36 LIAR1_BO12-46.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154   275176473 Apr 24 07:17 LIAR1_BO1246.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        1503 May  2 06:36 LIAR1_BO12-46.trim.log
-rw-r--r-- 1 skimble5 sds154   133211993 May  2 06:21 LIAR1_BO12-46.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   232139192 Apr 24 07:17 LIAR1_BO12-47.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      381736 May  2 06:36 LIAR1_BO12-47.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      481375 May  2 06:36 LIAR1_BO12-47.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   256171461 Apr 24 07:17 LIAR1_BO12-47.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2121 May  2 06:36 LIAR1_BO12-47.trim.log
-rw-r--r-- 1 skimble5 sds154   307179936 May  2 06:21 LIAR1_BO12-47.uniq.seqs
-rw-r--r-- 1 skimble5 sds154    33084998 Apr 24 07:17 LIAR1_BO12-48.F.fq.gz
-rw-r--r-- 1 skimble5 sds154       29229 May  2 06:36 LIAR1_BO12-48.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154    33959387 Apr 24 07:17 LIAR1_BO1248.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        1498 May  2 06:36 LIAR1_BO12-48.trim.log
-rw-r--r-- 1 skimble5 sds154    87941287 May  2 06:21 LIAR1_BO12-48.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   170599008 Apr 24 07:17 LIAR1_BO12-49.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      623895 May  2 06:36 LIAR1_BO12-49.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154   176890410 Apr 24 07:17 LIAR1_BO1249.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        1500 May  2 06:36 LIAR1_BO12-49.trim.log
-rw-r--r-- 1 skimble5 sds154   108567119 May  2 06:21 LIAR1_BO12-49.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   171417806 Apr 24 07:17 LIAR1_BO12-50.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      120853 May  2 06:36 LIAR1_BO12-50.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      133880 May  2 06:36 LIAR1_BO12-50.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   177162340 Apr 24 07:17 LIAR1_BO12-50.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2056 May  2 06:36 LIAR1_BO12-50.trim.log
-rw-r--r-- 1 skimble5 sds154   111645671 May  2 06:21 LIAR1_BO12-50.uniq.seqs
-rw-r--r-- 1 skimble5 sds154    30250054 Apr 24 07:17 LIAR1_BO12-52.F.fq.gz
-rw-r--r-- 1 skimble5 sds154          20 May  2 06:36 LIAR1_BO12-52.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154          20 May  2 06:36 LIAR1_BO12-52.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154    22037392 Apr 24 07:17 LIAR1_BO12-52.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2008 May  2 06:36 LIAR1_BO12-52.trim.log
-rw-r--r-- 1 skimble5 sds154    10635717 May  2 06:21 LIAR1_BO12-52.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   261658664 Apr 24 07:17 LIAR1_BO12-54.F.fq.gz
-rw-r--r-- 1 skimble5 sds154   250315587 May  2 06:38 LIAR1_BO12-54.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154   250315587 Apr 28 18:08 LIAR1_BO1254.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154   286841461 Apr 24 07:17 LIAR1_BO1254.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        1091 May  2 06:38 LIAR1_BO12-54.trim.log
-rw-r--r-- 1 skimble5 sds154   140396609 May  2 06:21 LIAR1_BO12-54.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   283441980 Apr 24 07:17 LIAR1_BO12-58.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      438090 May  2 06:36 LIAR1_BO12-58.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      568205 May  2 06:36 LIAR1_BO12-58.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   301494888 Apr 24 07:17 LIAR1_BO12-58.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2109 May  2 06:36 LIAR1_BO12-58.trim.log
-rw-r--r-- 1 skimble5 sds154   178123449 May  2 06:21 LIAR1_BO12-58.uniq.seqs
-rw-r--r-- 1 skimble5 sds154    54695250 Apr 24 07:17 LIAR1_BO1260.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      527653 May  2 06:36 LIAR1_BO1260.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      635703 May  2 06:36 LIAR1_BO1260.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154    48760332 Apr 24 07:17 LIAR1_BO1260.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        1999 May  2 06:36 LIAR1_BO1260.trim.log
-rw-r--r-- 1 skimble5 sds154   113062536 May  2 06:21 LIAR1_BO1260.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   230200777 Apr 24 07:17 LIAR1_BO1262.F.fq.gz
-rw-r--r-- 1 skimble5 sds154          20 May  2 06:36 LIAR1_BO1262.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154          20 May  2 06:36 LIAR1_BO1262.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   245649426 Apr 24 07:17 LIAR1_BO1262.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        1998 May  2 06:36 LIAR1_BO1262.trim.log
-rw-r--r-- 1 skimble5 sds154   129094999 May  2 06:21 LIAR1_BO1262.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   153706014 Apr 24 07:17 LIAR1_BO1263.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      632704 May  2 06:36 LIAR1_BO1263.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      731415 May  2 06:36 LIAR1_BO1263.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   160431099 Apr 24 07:17 LIAR1_BO1263.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2009 May  2 06:36 LIAR1_BO1263.trim.log
-rw-r--r-- 1 skimble5 sds154   108946710 May  2 06:21 LIAR1_BO1263.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   161163729 Apr 24 07:17 LIAR1_BO1264.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      244939 May  2 06:36 LIAR1_BO1264.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      304644 May  2 06:36 LIAR1_BO1264.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   175404548 Apr 24 07:17 LIAR1_BO1264.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2004 May  2 06:36 LIAR1_BO1264.trim.log
-rw-r--r-- 1 skimble5 sds154   116374119 May  2 06:21 LIAR1_BO1264.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   268941118 Apr 24 07:17 LIAR1_BO1265.F.fq.gz
-rw-r--r-- 1 skimble5 sds154       48205 May  2 06:36 LIAR1_BO1265.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154       60504 May  2 06:36 LIAR1_BO1265.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   289436717 Apr 24 07:17 LIAR1_BO1265.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2023 May  2 06:36 LIAR1_BO1265.trim.log
-rw-r--r-- 1 skimble5 sds154   367699493 May  2 06:21 LIAR1_BO1265.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   269148894 Apr 24 07:17 LIAR1_BO1266.F.fq.gz
-rw-r--r-- 1 skimble5 sds154       98159 May  2 06:36 LIAR1_BO1266.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      116144 May  2 06:36 LIAR1_BO1266.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   295149692 Apr 24 07:17 LIAR1_BO1266.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2036 May  2 06:36 LIAR1_BO1266.trim.log
-rw-r--r-- 1 skimble5 sds154   350129623 May  2 06:21 LIAR1_BO1266.uniq.seqs
-rw-r--r-- 1 skimble5 sds154    83502516 Apr 24 07:17 LIAR1_BO1267.F.fq.gz
-rw-r--r-- 1 skimble5 sds154          20 May  2 06:36 LIAR1_BO1267.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154          20 May  2 06:36 LIAR1_BO1267.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154    78754514 Apr 24 07:17 LIAR1_BO1267.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        1982 May  2 06:36 LIAR1_BO1267.trim.log
-rw-r--r-- 1 skimble5 sds154    56320613 May  2 06:21 LIAR1_BO1267.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   241554420 Apr 24 07:17 LIAR1_BO1277.F.fq.gz
-rw-r--r-- 1 skimble5 sds154          20 May  2 06:36 LIAR1_BO1277.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154          20 May  2 06:36 LIAR1_BO1277.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   256832545 Apr 24 07:17 LIAR1_BO1277.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2048 May  2 06:36 LIAR1_BO1277.trim.log
-rw-r--r-- 1 skimble5 sds154   345197716 May  2 06:21 LIAR1_BO1277.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   194741708 Apr 24 07:17 LIAR1_BO1279.F.fq.gz
-rw-r--r-- 1 skimble5 sds154       23616 May  2 06:36 LIAR1_BO1279.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154       28939 May  2 06:36 LIAR1_BO1279.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   203760600 Apr 24 07:17 LIAR1_BO1279.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2012 May  2 06:36 LIAR1_BO1279.trim.log
-rw-r--r-- 1 skimble5 sds154   286718296 May  2 06:21 LIAR1_BO1279.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   136642457 Apr 24 07:17 LIAR1_G1.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      175818 May  2 06:36 LIAR1_G1.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      181250 May  2 06:36 LIAR1_G1.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   145942381 Apr 24 07:17 LIAR1_G1.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2024 May  2 06:36 LIAR1_G1.trim.log
-rw-r--r-- 1 skimble5 sds154   201245595 May  2 06:21 LIAR1_G1.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   183250809 Apr 24 07:17 LIAR1_G2.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      183922 May  2 06:36 LIAR1_G2.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      227053 May  2 06:36 LIAR1_G2.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   190758452 Apr 24 07:17 LIAR1_G2.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        1987 May  2 06:36 LIAR1_G2.trim.log
-rw-r--r-- 1 skimble5 sds154   110031933 May  2 06:21 LIAR1_G2.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   130997913 Apr 24 07:17 LIAR1_G3.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      610302 May  2 06:36 LIAR1_G3.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      768056 May  2 06:36 LIAR1_G3.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   133070486 Apr 24 07:17 LIAR1_G3.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2008 May  2 06:36 LIAR1_G3.trim.log
-rw-r--r-- 1 skimble5 sds154   205354748 May  2 06:21 LIAR1_G3.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   184706196 Apr 24 07:17 LIAR1_G4.F.fq.gz
-rw-r--r-- 1 skimble5 sds154       23184 May  2 06:36 LIAR1_G4.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154       31055 May  2 06:36 LIAR1_G4.R2.fq.gz
-rw------- 1 skimble5 sds154     9682944 Apr 24 10:37 LIAR1_G4.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        1981 May  2 06:36 LIAR1_G4.trim.log
-rw-r--r-- 1 skimble5 sds154   114440048 May  2 06:21 LIAR1_G4.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   218371798 Apr 24 07:17 LIAR1_G5.F.fq.gz
-rw-r--r-- 1 skimble5 sds154          20 May  2 06:36 LIAR1_G5.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154          20 May  2 06:36 LIAR1_G5.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   238699247 Apr 24 07:17 LIAR1_G5.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2028 May  2 06:36 LIAR1_G5.trim.log
-rw-r--r-- 1 skimble5 sds154   307600993 May  2 06:21 LIAR1_G5.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   258272528 Apr 24 07:17 LIAR1_MO21.F.fq.gz
-rw-r--r-- 1 skimble5 sds154          20 May  2 06:36 LIAR1_MO21.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154          20 May  2 06:36 LIAR1_MO21.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   279035235 Apr 24 07:17 LIAR1_MO21.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2004 May  2 06:36 LIAR1_MO21.trim.log
-rw-r--r-- 1 skimble5 sds154   377660316 May  2 06:21 LIAR1_MO21.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   175428262 Apr 24 07:17 LIAR1_MO2-2.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      506282 May  2 06:36 LIAR1_MO2-2.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154   186355153 Apr 24 07:17 LIAR1_MO22.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        1506 May  2 06:36 LIAR1_MO2-2.trim.log
-rw-r--r-- 1 skimble5 sds154   267516695 May  2 06:21 LIAR1_MO2-2.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   202219994 Apr 24 07:17 LIAR1_MO2-3.F.fq.gz
-rw-r--r-- 1 skimble5 sds154       24429 May  2 06:36 LIAR1_MO2-3.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154       31109 May  2 06:36 LIAR1_MO2-3.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   220221985 Apr 24 07:17 LIAR1_MO2-3.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2118 May  2 06:36 LIAR1_MO2-3.trim.log
-rw-r--r-- 1 skimble5 sds154   118754000 May  2 06:21 LIAR1_MO2-3.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   225912007 Apr 24 07:17 LIAR1_MO2-4.F.fq.gz
-rw-r--r-- 1 skimble5 sds154          20 May  2 06:36 LIAR1_MO2-4.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154          20 May  2 06:36 LIAR1_MO2-4.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   233976129 Apr 24 07:17 LIAR1_MO2-4.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        1982 May  2 06:36 LIAR1_MO2-4.trim.log
-rw-r--r-- 1 skimble5 sds154   124067504 May  2 06:21 LIAR1_MO2-4.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   139708188 Apr 24 07:17 LIAR1_P1.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      190306 May  2 06:36 LIAR1_P1.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      232795 May  2 06:36 LIAR1_P1.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   146422910 Apr 24 07:17 LIAR1_P1.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2073 May  2 06:36 LIAR1_P1.trim.log
-rw-r--r-- 1 skimble5 sds154   207795561 May  2 06:21 LIAR1_P1.uniq.seqs
-rw-r--r-- 1 skimble5 sds154    91477073 Apr 24 07:17 LIAR1_P2.F.fq.gz
-rw-r--r-- 1 skimble5 sds154          20 May  2 06:36 LIAR1_P2.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154          20 May  2 06:36 LIAR1_P2.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154    93856715 Apr 24 07:17 LIAR1_P2.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        1996 May  2 06:36 LIAR1_P2.trim.log
-rw-r--r-- 1 skimble5 sds154    62260725 May  2 06:21 LIAR1_P2.uniq.seqs
-rw-r--r-- 1 skimble5 sds154    12796952 Apr 24 07:17 LIAR1_P3.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      571039 May  2 06:36 LIAR1_P3.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      694721 May  2 06:36 LIAR1_P3.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154    13248201 Apr 24 07:17 LIAR1_P3.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2060 May  2 06:36 LIAR1_P3.trim.log
-rw-r--r-- 1 skimble5 sds154    13616421 May  2 06:20 LIAR1_P3.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   147499779 Apr 24 07:17 LIAR1_P4.F.fq.gz
-rw-r--r-- 1 skimble5 sds154          20 May  2 06:36 LIAR1_P4.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154          20 May  2 06:36 LIAR1_P4.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   146456077 Apr 24 07:17 LIAR1_P4.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2070 May  2 06:36 LIAR1_P4.trim.log
-rw-r--r-- 1 skimble5 sds154   105900613 May  2 06:21 LIAR1_P4.uniq.seqs
-rw-r--r-- 1 skimble5 sds154    86107133 Apr 24 07:17 LIAR1_P5.F.fq.gz
-rw-r--r-- 1 skimble5 sds154       46338 May  2 06:36 LIAR1_P5.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154       55000 May  2 06:36 LIAR1_P5.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154    73013038 Apr 24 07:17 LIAR1_P5.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        1960 May  2 06:36 LIAR1_P5.trim.log
-rw-r--r-- 1 skimble5 sds154    57925828 May  2 06:21 LIAR1_P5.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   207510648 Apr 24 07:17 LIAR1_Ra1.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      407415 May  2 06:36 LIAR1_Ra1.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      476046 May  2 06:36 LIAR1_Ra1.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   225538096 Apr 24 07:17 LIAR1_Ra1.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        1993 May  2 06:36 LIAR1_Ra1.trim.log
-rw-r--r-- 1 skimble5 sds154   127312471 May  2 06:21 LIAR1_Ra1.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   239346602 Apr 24 07:17 LIAR1_Ra2.F.fq.gz
-rw-r--r-- 1 skimble5 sds154          20 May  2 06:36 LIAR1_Ra2.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154          20 May  2 06:36 LIAR1_Ra2.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   257965309 Apr 24 07:17 LIAR1_Ra2.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        1952 May  2 06:36 LIAR1_Ra2.trim.log
-rw-r--r-- 1 skimble5 sds154   137034622 May  2 06:21 LIAR1_Ra2.uniq.seqs
-rw-r--r-- 1 skimble5 sds154    87278840 Apr 24 07:17 LIAR1_Ra3.F.fq.gz
-rw-r--r-- 1 skimble5 sds154       23940 May  2 06:36 LIAR1_Ra3.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154       29315 May  2 06:36 LIAR1_Ra3.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154    76952015 Apr 24 07:17 LIAR1_Ra3.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2051 May  2 06:36 LIAR1_Ra3.trim.log
-rw-r--r-- 1 skimble5 sds154    60562672 May  2 06:21 LIAR1_Ra3.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   260338537 Apr 24 07:17 LIAR1_Ra4.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      287772 May  2 06:36 LIAR1_Ra4.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      364103 May  2 06:36 LIAR1_Ra4.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   281885623 Apr 24 07:17 LIAR1_Ra4.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2051 May  2 06:36 LIAR1_Ra4.trim.log
-rw-r--r-- 1 skimble5 sds154   360308529 May  2 06:21 LIAR1_Ra4.uniq.seqs
-rw-r--r-- 1 skimble5 sds154   137961774 Apr 24 07:17 LIAR1_Ra5.F.fq.gz
-rw-r--r-- 1 skimble5 sds154      137947 May  2 06:36 LIAR1_Ra5.R1.fq.gz
-rw-r--r-- 1 skimble5 sds154      126545 May  2 06:36 LIAR1_Ra5.R2.fq.gz
-rw-r--r-- 1 skimble5 sds154   139774074 Apr 24 07:17 LIAR1_Ra5.R.fq.gz
-rw-r--r-- 1 skimble5 sds154        2037 May  2 06:36 LIAR1_Ra5.trim.log
-rw-r--r-- 1 skimble5 sds154    97969427 May  2 06:21 LIAR1_Ra5.uniq.seqs
drwxr-xr-x 2 skimble5 sds154       41472 May  2 06:14 logfiles
-rw-r--r-- 1 skimble5 sds154         968 May  2 06:36 namelist
-rw-r--r-- 1 skimble5 sds154           0 May  2 06:36 trim.log
-rw-r--r-- 1 skimble5 sds154           0 May  2 06:39 uniqCperindv
-rw-r--r-- 1 skimble5 sds154         199 May  2 06:39 uniqseq.data
-rw-r--r-- 1 skimble5 sds154 13041641337 May  2 06:22 uniq.seqs
drwxr-xr-x 2 skimble5 sds154       57856 May  2 06:38 unpaired

I also sent the wrong config.file; correct config.file:
Number of Processors
24
Maximum Memory
0
Trimming
yes
Assembly?
yes
Type_of_Assembly
SE
Clustering_Similarity%
0.8
Mapping_Reads?
yes
Mapping_Match_Value
1
Mapping_MisMatch_Value
4
Mapping_GapOpen_Penalty
6
Calling_SNPs?

 ***

Anyway, I took a step back to assembly, to make sure that wasn't the problem, and realized that I had been passing SE instead of PE for the assembly. Now it takes much longer and has not been completing before the 48hr walltime. I have a small allocation I am unwilling to let it run longer until I can tell if it's working. I am unsure how to gauge this, however.


dDocent.runs:
Variables used in dDocent Run at Thu May 3 11:32:45 PDT 2018
Number of Processors
24
Maximum Memory
0
Trimming
no
Assembly?
yes
Type_of_Assembly
PE
Clustering_Similarity%
0.8
Mapping_Reads?
yes
Mapping_Match_Value
1
Mapping_MisMatch_Value
4
Mapping_GapOpen_Penalty
6
Calling_SNPs?
no
Email
ski...@towson.eduFor



 ll -tr

total 90595400

-rw-r--r-- 1 skimble5 sds154   260338537 Apr 24 07:17 LIAR1_Ra4.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   207510648 Apr 24 07:17 LIAR1_Ra1.F.fq.gz

-rw-r--r-- 1 skimble5 sds154    86107133 Apr 24 07:17 LIAR1_P5.F.fq.gz

-rw-r--r-- 1 skimble5 sds154    12796952 Apr 24 07:17 LIAR1_P3.F.fq.gz

-rw-r--r-- 1 skimble5 sds154    91477073 Apr 24 07:17 LIAR1_P2.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   139708188 Apr 24 07:17 LIAR1_P1.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   225912007 Apr 24 07:17 LIAR1_MO2-4.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   202219994 Apr 24 07:17 LIAR1_MO2-3.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   175428262 Apr 24 07:17 LIAR1_MO2-2.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   218371798 Apr 24 07:17 LIAR1_G5.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   184706196 Apr 24 07:17 LIAR1_G4.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   130997913 Apr 24 07:17 LIAR1_G3.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   183250809 Apr 24 07:17 LIAR1_G2.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   136642457 Apr 24 07:17 LIAR1_G1.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   194741708 Apr 24 07:17 LIAR1_BO1279.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   269148894 Apr 24 07:17 LIAR1_BO1266.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   268941118 Apr 24 07:17 LIAR1_BO1265.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   161163729 Apr 24 07:17 LIAR1_BO1264.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   153706014 Apr 24 07:17 LIAR1_BO1263.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   283441980 Apr 24 07:17 LIAR1_BO12-58.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   171417806 Apr 24 07:17 LIAR1_BO12-50.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   300623753 Apr 24 07:17 LIAR1_BO12-08.F.fq.gz

-rw-r--r-- 1 skimble5 sds154    57419783 Apr 24 07:17 LIAR1_A1.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   202282203 Apr 24 07:17 LIAR1_9GLA043.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   234717877 Apr 24 07:17 LIAR1_8GLA746.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   255123385 Apr 24 07:17 LIAR1_4GLA088.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   196743038 Apr 24 07:17 LIAR1_37GLA004.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   229181102 Apr 24 07:17 LIAR1_31GLA1117.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   121715156 Apr 24 07:17 LIAR1_30GLA1122.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   154647793 Apr 24 07:17 LIAR1_28GLA933.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   230980106 Apr 24 07:17 LIAR1_24GLA1187.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   239074151 Apr 24 07:17 LIAR1_23GLA020.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   258113583 Apr 24 07:17 LIAR1_22GLA752.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   263590425 Apr 24 07:17 LIAR1_1GLA743.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   241659763 Apr 24 07:17 LIAR1_19GLA058.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   240299116 Apr 24 07:17 LIAR1_14GLA745.F.fq.gz

-rw-r--r-- 1 skimble5 sds154   177759035 Apr 24 07:17 LIAR1_13GLA039.F.fq.gz

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-rw-r--r-- 1 skimble5 sds154         818 Apr 28 18:50 dDocent.15813864.comet-10-56.1node24cores.out

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-rw-r--r-- 1 skimble5 sds154         747 May  1 13:40 dDocent.15861423.comet-07-08.1node24cores.out

-rw-r--r-- 1 skimble5 sds154         747 May  2 06:14 dDocent.15876534.comet-28-25.1node24cores.out

-rw-r--r-- 1 skimble5 sds154    13616421 May  2 06:20 LIAR1_P3.uniq.seqs

-rw-r--r-- 1 skimble5 sds154    10635717 May  2 06:21 LIAR1_BO12-52.uniq.seqs

-rw-r--r-- 1 skimble5 sds154    25723793 May  2 06:21 LIAR1_111.uniq.seqs

-rw-r--r-- 1 skimble5 sds154    23410625 May  2 06:21 LIAR1_10563.uniq.seqs

-rw-r--r-- 1 skimble5 sds154    87941287 May  2 06:21 LIAR1_BO12-48.uniq.seqs

-rw-r--r-- 1 skimble5 sds154    32811643 May  2 06:21 LIAR1_A1.uniq.seqs

-rw-r--r-- 1 skimble5 sds154    34469715 May  2 06:21 LIAR1_10560.uniq.seqs

-rw-r--r-- 1 skimble5 sds154    56320613 May  2 06:21 LIAR1_BO1267.uniq.seqs

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-rw-r--r-- 1 skimble5 sds154   113062536 May  2 06:21 LIAR1_BO1260.uniq.seqs

-rw-r--r-- 1 skimble5 sds154    60562672 May  2 06:21 LIAR1_Ra3.uniq.seqs

-rw-r--r-- 1 skimble5 sds154    62260725 May  2 06:21 LIAR1_P2.uniq.seqs

-rw-r--r-- 1 skimble5 sds154    97969427 May  2 06:21 LIAR1_Ra5.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   146131456 May  2 06:21 LIAR1_10564.uniq.seqs

-rw-r--r-- 1 skimble5 sds154    93899321 May  2 06:21 LIAR1_30GLA1122.uniq.seqs

-rw-r--r-- 1 skimble5 sds154    70970633 May  2 06:21 LIAR1_BO12-06.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   105900613 May  2 06:21 LIAR1_P4.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   101791117 May  2 06:21 LIAR1_28GLA933.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   205354748 May  2 06:21 LIAR1_G3.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   201245595 May  2 06:21 LIAR1_G1.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   108946710 May  2 06:21 LIAR1_BO1263.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   111645671 May  2 06:21 LIAR1_BO12-50.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   207795561 May  2 06:21 LIAR1_P1.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   110031933 May  2 06:21 LIAR1_G2.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   116374119 May  2 06:21 LIAR1_BO1264.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   117332032 May  2 06:21 LIAR1_13GLA039.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   108567119 May  2 06:21 LIAR1_BO12-49.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   108865301 May  2 06:21 LIAR1_10561.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   112492377 May  2 06:21 LIAR1_39GLA1125.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   118754000 May  2 06:21 LIAR1_MO2-3.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   114440048 May  2 06:21 LIAR1_G4.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   136377979 May  2 06:21 LIAR1_23GLA020.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   129094999 May  2 06:21 LIAR1_BO1262.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   131643647 May  2 06:21 LIAR1_8GLA746.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   141829363 May  2 06:21 LIAR1_21GLA1100.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   127312471 May  2 06:21 LIAR1_Ra1.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   124067504 May  2 06:21 LIAR1_MO2-4.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   134726923 May  2 06:21 LIAR1_6GLA167.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   249541659 May  2 06:21 LIAR1_15GLA1172.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   127789334 May  2 06:21 LIAR1_11GLA1120.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   140396609 May  2 06:21 LIAR1_BO12-54.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   133211993 May  2 06:21 LIAR1_BO12-46.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   260746886 May  2 06:21 LIAR1_37GLA004.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   146385507 May  2 06:21 LIAR1_18GLA053.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   137507407 May  2 06:21 LIAR1_17GLA748.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   136325063 May  2 06:21 LIAR1_14GLA745.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   267516695 May  2 06:21 LIAR1_MO2-2.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   148115607 May  2 06:21 LIAR1_BO12-40.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   305137173 May  2 06:21 LIAR1_7GLA729.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   131300250 May  2 06:21 LIAR1_24GLA1187.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   137034622 May  2 06:21 LIAR1_Ra2.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   272603023 May  2 06:21 LIAR1_9GLA043.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   138405884 May  2 06:21 LIAR1_22GLA752.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   317966714 May  2 06:21 LIAR1_19GLA058.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   301273349 May  2 06:21 LIAR1_10562.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   307600993 May  2 06:21 LIAR1_G5.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   286718296 May  2 06:21 LIAR1_BO1279.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   307179936 May  2 06:21 LIAR1_BO12-47.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   153027136 May  2 06:21 LIAR1_BO12-08.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   377660316 May  2 06:21 LIAR1_MO21.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   345197716 May  2 06:21 LIAR1_BO1277.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   350129623 May  2 06:21 LIAR1_BO1266.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   178123449 May  2 06:21 LIAR1_BO12-58.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   393750938 May  2 06:21 LIAR1_BO12-42.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   147941621 May  2 06:21 LIAR1_BO12-11.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   150536333 May  2 06:21 LIAR1_3GLA040.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   144029563 May  2 06:21 LIAR1_20GLA1190.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   370942530 May  2 06:21 LIAR1_1GLA743.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   372615427 May  2 06:21 LIAR1_BO12-09.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   131908166 May  2 06:21 LIAR1_31GLA1117.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   360308529 May  2 06:21 LIAR1_Ra4.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   367699493 May  2 06:21 LIAR1_BO1265.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   344287044 May  2 06:21 LIAR1_4GLA088.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   347842711 May  2 06:21 LIAR1_2GLA740.uniq.seqs

-rw-r--r-- 1 skimble5 sds154   390581500 May  2 06:21 LIAR1_BO12-44.uniq.seqs

-rw-r--r-- 1 skimble5 sds154 13041641337 May  2 06:22 uniq.seqs

-rw-r--r-- 1 skimble5 sds154        4476 May  2 06:32 dDocent.15876876.comet-20-10.1node24cores.out

-rw-r--r-- 1 skimble5 sds154        1169 May  2 06:35 dDocent.15877056.comet-05-56.1node24cores.out

-rw-r--r-- 1 skimble5 sds154         250 May  2 06:38 config.file2

-rw-r--r-- 1 skimble5 sds154        4371 May  2 06:47 dDocent.15877058.comet-05-56.1node24cores.out

-rw-r--r-- 1 skimble5 sds154         747 May  2 07:00 dDocent.15877158.comet-11-64.1node24cores.out

-rw-r--r-- 1 skimble5 sds154        4371 May  2 10:12 dDocent.15880462.comet-11-06.1node24cores.out

-rw-r--r-- 1 skimble5 sds154       53860 May  2 10:14 LIAR1_18GLA053.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154       61624 May  2 10:14 LIAR1_18GLA053.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      118619 May  2 10:14 LIAR1_14GLA745.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154       95157 May  2 10:14 LIAR1_14GLA745.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154          20 May  2 10:14 LIAR1_11GLA1120.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154          20 May  2 10:14 LIAR1_11GLA1120.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154       29022 May  2 10:14 LIAR1_10562.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154       24501 May  2 10:14 LIAR1_10562.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154       55655 May  2 10:14 LIAR1_10560.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154       50891 May  2 10:14 LIAR1_10560.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154          20 May  2 10:14 LIAR1_39GLA1125.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154          20 May  2 10:14 LIAR1_39GLA1125.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154          20 May  2 10:14 LIAR1_31GLA1117.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154          20 May  2 10:14 LIAR1_31GLA1117.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154       56111 May  2 10:14 LIAR1_30GLA1122.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154       47055 May  2 10:14 LIAR1_30GLA1122.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154       29817 May  2 10:14 LIAR1_2GLA740.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154       22854 May  2 10:14 LIAR1_2GLA740.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      176978 May  2 10:14 LIAR1_28GLA933.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154      155486 May  2 10:14 LIAR1_28GLA933.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      300701 May  2 10:14 LIAR1_24GLA1187.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154      234858 May  2 10:14 LIAR1_24GLA1187.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      460878 May  2 10:14 LIAR1_23GLA020.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154      384632 May  2 10:14 LIAR1_23GLA020.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154       61018 May  2 10:14 LIAR1_22GLA752.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154       47328 May  2 10:14 LIAR1_22GLA752.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154       31370 May  2 10:14 LIAR1_21GLA1100.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154       32888 May  2 10:14 LIAR1_21GLA1100.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      618437 May  2 10:14 LIAR1_20GLA1190.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154      482947 May  2 10:14 LIAR1_20GLA1190.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154       33665 May  2 10:14 LIAR1_1GLA743.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154       28300 May  2 10:14 LIAR1_1GLA743.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      143963 May  2 10:14 LIAR1_17GLA748.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154      117416 May  2 10:14 LIAR1_17GLA748.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      116427 May  2 10:14 LIAR1_15GLA1172.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154       90432 May  2 10:14 LIAR1_15GLA1172.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      174838 May  2 10:14 LIAR1_13GLA039.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154      136393 May  2 10:14 LIAR1_13GLA039.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      616802 May  2 10:14 LIAR1_111.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154      499012 May  2 10:14 LIAR1_111.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      114606 May  2 10:14 LIAR1_10564.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154       94984 May  2 10:14 LIAR1_10564.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      143597 May  2 10:14 LIAR1_10561.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154      128900 May  2 10:14 LIAR1_10561.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154       91982 May  2 10:14 LIAR1_BO12-42.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      168303 May  2 10:14 LIAR1_BO12-11.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154       70721 May  2 10:14 LIAR1_BO12-09.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      402833 May  2 10:14 LIAR1_BO12-08.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154      341879 May  2 10:14 LIAR1_BO12-08.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      319717 May  2 10:14 LIAR1_BO12-06.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      204686 May  2 10:14 LIAR1_A1.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154      178512 May  2 10:14 LIAR1_A1.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154       56836 May  2 10:14 LIAR1_9GLA043.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154       52112 May  2 10:14 LIAR1_9GLA043.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154          20 May  2 10:14 LIAR1_7GLA729.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154          20 May  2 10:14 LIAR1_7GLA729.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      336090 May  2 10:14 LIAR1_6GLA167.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154      302686 May  2 10:14 LIAR1_6GLA167.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      703606 May  2 10:14 LIAR1_4GLA088.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154      608633 May  2 10:14 LIAR1_4GLA088.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154       54344 May  2 10:14 LIAR1_3GLA040.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154       54447 May  2 10:14 LIAR1_3GLA040.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      239252 May  2 10:14 LIAR1_37GLA004.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154      244237 May  2 10:14 LIAR1_37GLA004.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      913871 May  2 10:14 LIAR1_19GLA058.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154      695338 May  2 10:14 LIAR1_19GLA058.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      304644 May  2 10:14 LIAR1_BO1264.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154      244939 May  2 10:14 LIAR1_BO1264.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154          20 May  2 10:14 LIAR1_BO1262.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154          20 May  2 10:14 LIAR1_BO1262.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      568205 May  2 10:14 LIAR1_BO12-58.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154      438090 May  2 10:14 LIAR1_BO12-58.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154          20 May  2 10:14 LIAR1_BO12-52.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154          20 May  2 10:14 LIAR1_BO12-52.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      133880 May  2 10:14 LIAR1_BO12-50.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154      120853 May  2 10:14 LIAR1_BO12-50.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      623895 May  2 10:14 LIAR1_BO12-49.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154       29229 May  2 10:14 LIAR1_BO12-48.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      481375 May  2 10:14 LIAR1_BO12-47.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154      381736 May  2 10:14 LIAR1_BO12-47.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154          20 May  2 10:14 LIAR1_BO12-46.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154       23595 May  2 10:14 LIAR1_BO12-44.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      362797 May  2 10:14 LIAR1_BO12-40.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      815640 May  2 10:14 LIAR1_8GLA746.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154      644790 May  2 10:14 LIAR1_8GLA746.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154          20 May  2 10:14 LIAR1_P4.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154          20 May  2 10:14 LIAR1_P4.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154          20 May  2 10:14 LIAR1_P2.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154          20 May  2 10:14 LIAR1_P2.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154          20 May  2 10:14 LIAR1_MO2-4.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154          20 May  2 10:14 LIAR1_MO2-4.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154       31109 May  2 10:14 LIAR1_MO2-3.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154       24429 May  2 10:14 LIAR1_MO2-3.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      506282 May  2 10:14 LIAR1_MO2-2.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154          20 May  2 10:14 LIAR1_MO21.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154          20 May  2 10:14 LIAR1_MO21.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154          20 May  2 10:14 LIAR1_G5.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154          20 May  2 10:14 LIAR1_G5.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154       31055 May  2 10:14 LIAR1_G4.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154       23184 May  2 10:14 LIAR1_G4.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      227053 May  2 10:14 LIAR1_G2.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154      183922 May  2 10:14 LIAR1_G2.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      181250 May  2 10:14 LIAR1_G1.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154      175818 May  2 10:14 LIAR1_G1.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154       28939 May  2 10:14 LIAR1_BO1279.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154       23616 May  2 10:14 LIAR1_BO1279.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154          20 May  2 10:14 LIAR1_BO1277.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154          20 May  2 10:14 LIAR1_BO1277.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154          20 May  2 10:14 LIAR1_BO1267.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154          20 May  2 10:14 LIAR1_BO1267.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      116144 May  2 10:14 LIAR1_BO1266.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154       98159 May  2 10:14 LIAR1_BO1266.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154       60504 May  2 10:14 LIAR1_BO1265.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154       48205 May  2 10:14 LIAR1_BO1265.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      731415 May  2 10:14 LIAR1_BO1263.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154      632704 May  2 10:14 LIAR1_BO1263.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      635703 May  2 10:14 LIAR1_BO1260.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154      527653 May  2 10:14 LIAR1_BO1260.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      126545 May  2 10:14 LIAR1_Ra5.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154      137947 May  2 10:14 LIAR1_Ra5.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      364103 May  2 10:14 LIAR1_Ra4.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154      287772 May  2 10:14 LIAR1_Ra4.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154       29315 May  2 10:14 LIAR1_Ra3.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154       23940 May  2 10:14 LIAR1_Ra3.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154          20 May  2 10:14 LIAR1_Ra2.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154          20 May  2 10:14 LIAR1_Ra2.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      476046 May  2 10:14 LIAR1_Ra1.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154      407415 May  2 10:14 LIAR1_Ra1.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154       55000 May  2 10:14 LIAR1_P5.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154       46338 May  2 10:14 LIAR1_P5.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      694721 May  2 10:14 LIAR1_P3.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154      571039 May  2 10:14 LIAR1_P3.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      232795 May  2 10:14 LIAR1_P1.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154      190306 May  2 10:14 LIAR1_P1.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154      768056 May  2 10:14 LIAR1_G3.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154      610302 May  2 10:14 LIAR1_G3.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154    31264129 May  2 10:14 LIAR1_10563.R2.fq.gz

-rw-r--r-- 1 skimble5 sds154    29294461 May  2 10:14 LIAR1_10563.R1.fq.gz

-rw-r--r-- 1 skimble5 sds154   250315587 May  2 10:16 LIAR1_BO12-54.R1.fq.gz

drwxr-xr-x 2 skimble5 sds154       57856 May  2 10:16 unpaired

-rw-r--r-- 1 skimble5 sds154        1200 May  2 10:17 dDocent.15880683.comet-11-06.1node24cores.out

-rw-r--r-- 1 skimble5 sds154         396 May  2 10:20 dDocent.15880717.comet-07-67.1node24cores.out

-rw-r--r-- 1 skimble5 sds154        3703 May  2 10:31 dDocent.15880741.comet-07-67.1node24cores.out

-rw-r--r-- 1 skimble5 sds154        7438 May  2 12:33 dDocent.15882254.comet-28-27.1node24cores.out

-rw-r--r-- 1 skimble5 sds154 11984519841 May  2 14:08 totalover.fasta

-rw-r--r-- 1 skimble5 sds154   469167013 May  3 07:15 reference.fasta.original

-rw-r--r-- 1 skimble5 sds154  1337409003 May  3 07:16 reference.fasta.original.clstr

-rw-r--r-- 1 skimble5 sds154   474146148 May  3 07:16 reference.fasta

-rw-r--r-- 1 skimble5 sds154   202507264 May  3 07:16 reference.fasta.fai

-rw-r--r-- 1 skimble5 sds154   351132844 May  3 07:21 reference.fasta.bwt

-rw-r--r-- 1 skimble5 sds154    87783187 May  3 07:22 reference.fasta.pac

-rw-r--r-- 1 skimble5 sds154   225870805 May  3 07:22 reference.fasta.ann

-rw-r--r-- 1 skimble5 sds154   265688542 May  3 07:23 reference.fasta.amb

-rw-r--r-- 1 skimble5 sds154   175566424 May  3 07:24 reference.fasta.sa

drwxr-xr-x 2 skimble5 sds154       41472 May  3 07:25 logfiles

-rw-r--r-- 1 skimble5 sds154 19371036237 May  3 07:25 dDocent.15882830.comet-28-27.1node24cores.out

-rw-r--r-- 1 skimble5 sds154           0 May  3 10:33 LIAR1_10560.bam.log

-rw-r--r-- 1 skimble5 sds154        5376 May  3 10:33 lengths.txt

-rw-r--r-- 1 skimble5 sds154         508 May  3 10:34 bwa.LIAR1_10560.log

-rw-r--r-- 1 skimble5 sds154    33778185 May  3 10:34 LIAR1_10560-RG.bam

-rw-r--r-- 1 skimble5 sds154           0 May  3 10:34 LIAR1_10561.bam.log

-rw-r--r-- 1 skimble5 sds154    37936648 May  3 10:34 LIAR1_10560-RG.bam.bai

-rw-r--r-- 1 skimble5 sds154         509 May  3 10:34 bwa.LIAR1_10561.log

-rw-r--r-- 1 skimble5 sds154    33909431 May  3 10:34 LIAR1_10561-RG.bam

-rw-r--r-- 1 skimble5 sds154           0 May  3 10:34 LIAR1_10562.bam.log

-rw-r--r-- 1 skimble5 sds154    38015560 May  3 10:34 LIAR1_10561-RG.bam.bai

-rw-r--r-- 1 skimble5 sds154         508 May  3 10:35 bwa.LIAR1_10562.log

-rw-r--r-- 1 skimble5 sds154    33705037 May  3 10:35 LIAR1_10562-RG.bam

-rw-r--r-- 1 skimble5 sds154           0 May  3 10:35 LIAR1_10563.bam.log

-rw-r--r-- 1 skimble5 sds154    37936792 May  3 10:35 LIAR1_10562-RG.bam.bai

-rw-r--r-- 1 skimble5 sds154         525 May  3 10:37 bwa.LIAR1_10563.log

-rw-r--r-- 1 skimble5 sds154    62267059 May  3 10:37 LIAR1_10563-RG.bam

-rw-r--r-- 1 skimble5 sds154    44883136 May  3 10:37 LIAR1_10563-RG.bam.bai

-rw-r--r-- 1 skimble5 sds154           0 May  3 10:37 LIAR1_10564.bam.log

-rw-r--r-- 1 skimble5 sds154         508 May  3 10:37 bwa.LIAR1_10564.log

-rw-r--r-- 1 skimble5 sds154    33903239 May  3 10:38 LIAR1_10564-RG.bam

-rw-r--r-- 1 skimble5 sds154           0 May  3 10:38 LIAR1_111.bam.log

-rw-r--r-- 1 skimble5 sds154    37942624 May  3 10:38 LIAR1_10564-RG.bam.bai

-rw-r--r-- 1 skimble5 sds154         504 May  3 10:38 bwa.LIAR1_111.log

-rw-r--r-- 1 skimble5 sds154    34856470 May  3 10:38 LIAR1_111-RG.bam

-rw-r--r-- 1 skimble5 sds154           0 May  3 10:39 LIAR1_11GLA1120.bam.log

-rw-r--r-- 1 skimble5 sds154    37992736 May  3 10:39 LIAR1_111-RG.bam.bai

-rw-r--r-- 1 skimble5 sds154         399 May  3 10:39 bwa.LIAR1_11GLA1120.log

-rw-r--r-- 1 skimble5 sds154    33644322 May  3 10:39 LIAR1_11GLA1120-RG.bam

-rw-r--r-- 1 skimble5 sds154           0 May  3 10:39 LIAR1_13GLA039.bam.log

-rw-r--r-- 1 skimble5 sds154    37934704 May  3 10:39 LIAR1_11GLA1120-RG.bam.bai

-rw-r--r-- 1 skimble5 sds154         523 May  3 10:39 bwa.LIAR1_13GLA039.log

-rw-r--r-- 1 skimble5 sds154    34043085 May  3 10:40 LIAR1_13GLA039-RG.bam

-rw-r--r-- 1 skimble5 sds154           0 May  3 10:40 LIAR1_14GLA745.bam.log

-rw-r--r-- 1 skimble5 sds154    37943128 May  3 10:40 LIAR1_13GLA039-RG.bam.bai

-rw-r--r-- 1 skimble5 sds154         520 May  3 10:40 bwa.LIAR1_14GLA745.log

-rw-r--r-- 1 skimble5 sds154    33916271 May  3 10:40 LIAR1_14GLA745-RG.bam

-rw-r--r-- 1 skimble5 sds154           0 May  3 10:40 LIAR1_15GLA1172.bam.log

-rw-r--r-- 1 skimble5 sds154    37941760 May  3 10:40 LIAR1_14GLA745-RG.bam.bai

-rw-r--r-- 1 skimble5 sds154         524 May  3 10:41 bwa.LIAR1_15GLA1172.log

-rw-r--r-- 1 skimble5 sds154    33910101 May  3 10:41 LIAR1_15GLA1172-RG.bam

-rw-r--r-- 1 skimble5 sds154           0 May  3 10:41 LIAR1_17GLA748.bam.log

-rw-r--r-- 1 skimble5 sds154    37937800 May  3 10:41 LIAR1_15GLA1172-RG.bam.bai

-rw-r--r-- 1 skimble5 sds154         520 May  3 10:41 bwa.LIAR1_17GLA748.log

-rw-r--r-- 1 skimble5 sds154    33980589 May  3 10:41 LIAR1_17GLA748-RG.bam

-rw-r--r-- 1 skimble5 sds154           0 May  3 10:42 LIAR1_18GLA053.bam.log

-rw-r--r-- 1 skimble5 sds154    37940320 May  3 10:42 LIAR1_17GLA748-RG.bam.bai

-rw-r--r-- 1 skimble5 sds154         520 May  3 10:42 bwa.LIAR1_18GLA053.log

-rw-r--r-- 1 skimble5 sds154    33792832 May  3 10:42 LIAR1_18GLA053-RG.bam

-rw-r--r-- 1 skimble5 sds154           0 May  3 10:42 LIAR1_19GLA058.bam.log

-rw-r--r-- 1 skimble5 sds154    37938232 May  3 10:42 LIAR1_18GLA053-RG.bam.bai

-rw-r--r-- 1 skimble5 sds154         525 May  3 10:42 bwa.LIAR1_19GLA058.log

-rw-r--r-- 1 skimble5 sds154    35523943 May  3 10:43 LIAR1_19GLA058-RG.bam

-rw-r--r-- 1 skimble5 sds154           0 May  3 10:43 LIAR1_1GLA743.bam.log

-rw-r--r-- 1 skimble5 sds154    37954864 May  3 10:43 LIAR1_19GLA058-RG.bam.bai

-rw-r--r-- 1 skimble5 sds154         516 May  3 10:43 bwa.LIAR1_1GLA743.log

-rw-r--r-- 1 skimble5 sds154    33715292 May  3 10:43 LIAR1_1GLA743.bam

-rw-r--r-- 1 skimble5 sds154         777 May  3 10:43 dDocent.15907814.comet-13-21.1node24cores.out

-rw-r--r-- 1 skimble5 sds154         248 May  3 11:06 config.file

-rw-r--r-- 1 skimble5 sds154        3703 May  3 11:17 dDocent.15908963.comet-25-40.1node24cores.out

-rw-r--r-- 1 skimble5 sds154         348 May  3 11:31 dDocent.sb

-rw-r--r-- 1 skimble5 sds154         968 May  3 11:32 namelist

-rw-r--r-- 1 skimble5 sds154        7758 May  3 11:32 dDocent.runs

-rw-r--r-- 1 skimble5 sds154         199 May  3 11:36 uniqseq.data

-rw-r--r-- 1 skimble5 sds154  9314122122 May  3 11:46 uniqCperindv

-rw-r--r-- 1 skimble5 sds154         371 May  3 11:47 uniqseq.peri.data

-rw-r--r-- 1 skimble5 sds154  9314122122 May  3 11:48 uniq.k..c..seqs

-rw-r--r-- 1 skimble5 sds154 12142159622 May  3 11:55 uniq.full.fasta

-rw-r--r-- 1 skimble5 sds154 19371082096 May  3 12:36 dDocent_main.LOG

-rw-r--r-- 1 skimble5 sds154 11984519841 May  3 12:38 uniq.fasta

-rw-r--r-- 1 skimble5 sds154  8946114018 May  3 12:38 totaluniqseq

-rw-r--r-- 1 skimble5 sds154 11984229626 May  3 12:46 uniq.F.fasta

-rw-r--r-- 1 skimble5 sds154 19471762653 May  5 11:31 cdhit.log

-rw-r--r-- 1 skimble5 sds154        8474 May  5 11:32 dDocent.15909140.comet-22-14.1node24cores.out



and finally the .out file:

dDocent 2.2.25 

Contact jpu...@gmail.com with any problems 

 
Checking for required software

All required software is installed!

dDocent run started Thu May 3 11:32:45 PDT 2018 

dDocent will require input during the assembly stage.  Please wait until prompt says it is safe to move program to the background.
                       Number of Unique Sequences with More than X Coverage (Counted within individuals)

  3.5e+07 +-+---------+-----------+----------+-----------+-----------+-----------+----------+-----------+---------+-+
          +           +           +          +           +           +           +          +           +           +
          |                                                                                                         |
    3e+07 +-+                                                                                                     +-+
          | |                                                                                                       |
          |  |                                                                                                      |
          |  |                                                                                                      |
  2.5e+07 +-+ |                                                                                                   +-+
          |    |                                                                                                    |
          |     +-                                                                                                  |
    2e+07 +-+     -                                                                                               +-+
          |        --                                                                                               |
          |          -                                                                                              |
  1.5e+07 +-+                                                                                                     +-+
          |           +----                                                                                         |
          |                -                                                                                        |
    1e+07 +-+               +----                                                                                 +-+
          |                      -                                                                                  |
          |                       +----                                                                             |
          |                            +-----                                                                       |
    5e+06 +-+                                +-----                                                               +-+
          |                                        +-----+-----                                                     |
          +           +           +          +           +     +-----+-----+-----+-----+----+-----      +           +
        0 +-+---------+-----------+----------+-----------+-----------+-----------+----------+-----------+---------+-+
          2           4           6          8           10          12          14         16          18          20
                                                           Coverage

Please choose data cutoff.  In essence, you are picking a minimum (within individual) coverage level for a read (allele) to be used in the reference assembly
                                Number of Unique Sequences present in more than X Individuals

  7e+06 +-+-----------+------------+-------------+------------+-------------+------------+-------------+----------+-+
        +    |        +            +             +            +             +            +             +            +
        |     |                                                                                                     |
  6e+06 +-+   |                                                                                                   +-+
        |     |                                                                                                     |
        |      |                                                                                                    |
        |      |                                                                                                    |
  5e+06 +-+    |                                                                                                  +-+
        |      |                                                                                                    |
        |       |                                                                                                   |
  4e+06 +-+     +                                                                                                 +-+
        |        +                                                                                                  |
        |         +                                                                                                 |
  3e+06 +-+        +--                                                                                            +-+
        |                                                                                                           |
        |             +-                                                                                            |
  2e+06 +-+             +--+--                                                                                    +-+
        |                     +-+--                                                                                 |
        |                          +--+-+--+--                                                                      |
        |                                     +--+-+--+--+-+--                                                      |
  1e+06 +-+                                                   +--+-+--+--+--+-                                    +-+
        |                                                                     +--+--+-+--+--+-                      |
        +             +            +             +            +             +            +    +--+--+--+-+--+       +
      0 +-+-----------+------------+-------------+------------+-------------+------------+-------------+----------+-+
        0             5            10            15           20            25           30            35           40
                                                    Number of Individuals

Please choose data cutoff.  Pick point right before the assymptote. A good starting cutoff might be 10% of the total number of individuals
At this point, all configuration information has been entered and dDocent may take several hours to run.
It is recommended that you move this script to a background operation and disable terminal input and output.
All data and logfiles will still be recorded.
To do this:
Press control and Z simultaneously
Type 'bg' without the quotes and press enter
Type 'disown -h' again without the quotes and press enter

Now sit back, relax, and wait for your analysis to finish.
TrimmomaticSE: Started with arguments: -threads 24 -phred33 uniq.fq uniq.fq1 ILLUMINACLIP:/home/skimble5/installs/dreqs/TruSeq2-PE.fa:2:30:10 MINLEN:0
Using PrefixPair: 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT'
Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT'
Using Long Clipping Sequence: 'AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG'
Using Long Clipping Sequence: 'TTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC'
Using Long Clipping Sequence: 'TTTTTTTTTTCAAGCAGAAGACGGCATACGA'
Using Long Clipping Sequence: 'CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT'
Using Long Clipping Sequence: 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT'
ILLUMINACLIP: Using 1 prefix pairs, 6 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Input Reads: 122532739 Surviving: 121084756 (98.82%) Dropped: 1447983 (1.18%)
TrimmomaticSE: Completed successfully
slurmstepd: *** JOB 15909140 ON comet-22-14 CANCELLED AT 2018-05-05T11:32:00 DUE TO TIME LIMIT ***


After looking at some other questions on the google group, I also peaked at the cdhit.log:


$head -100 cdhit.log

================================================================

Program: CD-HIT, V4.6 (+OpenMP), Mar 20 2018, 11:09:22

Command: cd-hit-est -i uniq.F.fasta -o xxx -c 0.8 -T 0 -M 0 -g

         1 -d 100


Started: Thu May  3 12:46:07 2018

================================================================

                            Output                              

----------------------------------------------------------------

total number of CPUs in the system is 24

Actual number of CPUs to be used: 24


Warning: from file "uniq.F.fasta",

Discarding invalid sequence or sequence without identifier and description!


>dDocent_Contig_1

EEEEEEEEEEEEEEEEEAEEEAEEEEE/EEEEEAEAEEEE///EAEEEAEEEAEEEA/EEEEEEEEEAEEA6/

Warning: from file "uniq.F.fasta",

Discarding invalid sequence or sequence without identifier and description!


>dDocent_Contig_3

EEAEEEEEEEEE6EEEEEEEEEEEAEEEE/E/EEAEEEEAEAEEEEEEEEEEEEEEEAEEEEEEEA<EEEAEE

Warning: from file "uniq.F.fasta",

Discarding invalid sequence or sequence without identifier and description!


>dDocent_Contig_4

EEEEEE//E/E/E/AEEAEE//AEEEEEEEE/EE//E<E<EEEEAE/EE/EEEEAEEEEEEEEEEAEEEEEEE

Warning: from file "uniq.F.fasta",

Discarding invalid sequence or sequence without identifier and description!


>dDocent_Contig_7

6AEE/EEEAEEEEAA/EE<AA/A6///EE/EAEEE/E/EEEAEE/EEE/E///<A/<<E/EEE6EEEEA<EE/

Warning: from file "uniq.F.fasta",

Discarding invalid sequence or sequence without identifier and description!


...


>dDocent_Contig_23

EEEEEEEAA/EEEE/EEE/EAA/E/EAEE///AEEEE/EE//<EE/E//E/EEE<<EEEE//E6AEE6///</

Warning: from file "uniq.F.fasta",

Discarding invalid sequence or sequence without identifier and description!



and



$tail -100 cdhit.log


..........  2240000  finished     783120  clusters

..........  2250000  finished     785674  clusters

..........  2260000  finished     788198  clusters

..........  2270000  finished     790631  clusters

..........  2280000  finished     793134  clusters

100.0%---------- new table with   106732 representatives

# comparing sequences from    2283154  to    2708552

..........  2290000  finished     795710  clusters

..........  2300000  finished     798228  clusters

..........  2310000  finished     800775  clusters

..........  2320000  finished     803253  clusters

..........  2330000  finished     805705  clusters

..........  2340000  finished     808213  clusters

..........  2350000  finished     810736  clusters

..........  2360000  finished     813288  clusters

..........  2370000  finished     815757  clusters

..........  2380000  finished     818253  clusters

..........  2390000  finished     820691  clusters

..........  2400000  finished     823132  clusters

..........  2410000  finished     825567  clusters

..........  2420000  finished     828075  clusters

..........  2430000  finished     830567  clusters

..........  2440000  finished     833020  clusters

..........  2450000  finished     835391  clusters

..........  2460000  finished     837794  clusters

..........  2470000  finished     840255  clusters

..........  2480000  finished     842628  clusters

..........  2490000  finished     845060  clusters

..........  2500000  finished     847535  clusters

..........  2510000  finished     849968  clusters

..........  2520000  finished     852343  clusters

..........  2530000  finished     854734  clusters

..........  2540000  finished     857187  clusters

..........  2550000  finished     859591  clusters

..........  2560000  finished     861961  clusters

..........  2570000  finished     864346  clusters

..........  2580000  finished     866784  clusters

..........  2590000  finished     869107  clusters

..........  2600000  finished     871485  clusters

..........  2610000  finished     873917  clusters

..........  2620000  finished     876316  clusters

..........  2630000  finished     878698  clusters

..........  2640000  finished     881136  clusters

..........  2650000  finished     883491  clusters

..........  2660000  finished     885927  clusters

..........  2670000  finished     888244  clusters

..........  2680000  finished     890512  clusters

..........  2690000  finished     892787  clusters

..........  2700000  finished     895173  clusters



These appear to differ from what I've seen posted elsewhere, but I'm not sure how to use them to help me predict running time. 1.) Is there a way to use cdhit.log to predict the run time for assembling? and 2.) Is the assembling working properly?

Thanks for you time,
Steve


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Steven J.A. Kimble, PhD
Visiting Assistant Professor, Department of Biological Sciences
Towson University
ski...@towson.edu
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