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Old 03-20-2018, 02:17 AM   #21
DrYak
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Hi,

Can I use reformat or any other bbtools script to split my fasta file into sub-files?

eg X.fa (100 sequences) -> X01.fa X02.fa....X10.fa (each with 10 sequences)?

I don't mind whether I need to select the number of sequences per file or total number of files and it doesn't really matter what order the sequences are in as long as there is no duplication of sequences.

Cheers,
Dave
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Old 03-20-2018, 04:58 AM   #22
GenoMax
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faSplit from Jim Kent's utilities is a much better option for splitting fasta files.

Run faSplit to look at inline help for multiple options available.
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Old 03-20-2018, 10:07 AM   #23
Brian Bushnell
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Reformat won't do that, but you can use partition.sh:

Code:
partition.sh in=X.fa out=X%.fa ways=10
That will produce 10 output files with an equal number of sequences and no duplication.
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Old 08-01-2018, 06:47 PM   #24
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Hi Brian Bushnell,
when I used mapPacBio.sh for mapping pacbio reads. I met the errors as following:
Exception in thread "Thread-23" java.lang.AssertionError: Read 20, length 10550, exceeds the limit of 6019
You can map the reads in chunks by reformatting to fasta, then mapping with the setting 'fastareadlen=6019'
at align2.AbstractMapThread.run(AbstractMapThread.java:480)

But I did not find how I can reformat it.
Could you help me figure out this issue?
Thanks,
Fuyou
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Old 08-02-2018, 06:08 AM   #25
GenoMax
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You can use
Code:
reformat.sh in=your_file.fastq out=newfile.fa
to convert the reads to fasta format.

That said I think mapPacBio.sh should automatically split reads longer than 6k when it does mapping. Is that not working?
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Old 08-02-2018, 06:29 AM   #26
sunnycqcn
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Quote:
Originally Posted by GenoMax View Post
You can use
Code:
reformat.sh in=your_file.fastq out=newfile.fa
to convert the reads to fasta format.

That said I think mapPacBio.sh should automatically split reads longer than 6k when it does mapping. Is that not working?
It is not working. I used fasta format.
Thanks,
Fuyou
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Old 01-30-2019, 01:54 PM   #27
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hello folks, I am trying to work on a FASTQ file using reformat.sh, although I have correctly installed Java and tested it in the command line, I still can't get it to work. It seems the problem is that I don't have the FASTQ file in the same directory as the BBMap folder, could that be an issue?
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Old 01-30-2019, 03:20 PM   #28
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pepe84, do you provide a path to the file? Please copy your command as tried, and then copy the error message.
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Old 01-31-2019, 05:26 AM   #29
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here is the command:
java -cp C:\BBMap\current\jgi.ReformatReads in=C:\BBMap\resources\SRRXXXXX.fastq out1=EFB_R1.fq out2=EFB_R2.fq

And here is the error:
Error: Could not find or load main class in=C:\BBMap\resources\SRRXXXXX.fastq

Just an FYI I am using the command line on windows.

Thanks, I appreciate any help


Quote:
Originally Posted by SNPsaurus View Post
pepe84, do you provide a path to the file? Please copy your command as tried, and then copy the error message.
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Old 02-14-2019, 12:14 AM   #30
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Default deinterleave with singletons

Hi!

I have a interleaved fastq containing unmapped reads produced by segemehl -u. I want to deinterleave it into the two mate pair files as well as removing/saving the singletons into a separate file.

Currently, reformat.sh cannot deal with it, even if I give outsingle= as parameter. The header contains the strand information (i. e. 2:N:0:2).

Is there some way to get at least the pairing reads extracted without singletons in between?

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Kind regards,
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Old 02-14-2019, 06:50 AM   #31
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You could use `repair.sh` to separate the singletons out afterwards.
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Old 02-15-2019, 12:45 AM   #32
tolot27
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Quote:
Originally Posted by GenoMax View Post
You could use `repair.sh` to separate the singletons out afterwards.
Thanks for pointing me into this direction. Unfortunately, repair.sh did not produce well ordered files. Fortunately, bbsplitpairs.sh could be used instead of the reformat.sh/repair.sh combination and extracted the correct pairing reads as well as singletons into a separate file.
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Old 02-26-2019, 11:29 AM   #33
milw
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Default I'm confused about sam/bam options

In version 37.52, the parameters under Sam and bam processing options are confusing to me
Sam and bam processing options:

mappedonly=f Toss unmapped reads.
unmappedonly=f Toss mapped reads.
pairedonly=f Toss reads that are not mapped as proper pairs.
unpairedonly=f Toss reads that are mapped as proper pairs.
primaryonly=f Toss secondary alignments. Set this to true for sam to fastq conversion.

if 'mappedonly' is false, shouldn't that mean to KEEP unmapped plus mapped reads?
Likewise, 'pairedonly' false (to me) means KEEP unpaired and paired

In the end, I want my bam to only contain paired reads, so I've been running it with 'pairedonly=t' , but reformat.sh says 'input is being processed as unpaired' for my bam file.
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Old 09-25-2019, 01:45 AM   #34
Oomjah
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Default Could not find or load main class

Hi,

first time poster so my apologies for any horrid faux pas', and also for the thread necromancy!

I'm trying to convert fastq's to an unmapped SAM (ultimately to a cram to test space saving and to check no loss of data when it's reconverted back to fastq's again) and I saw a thread suggesting BBMAP. However I'm having the same issue as pepe84.

The command:
reformat.sh in=/opt/science/blah.fastq.gz out=/opt/science/blah.sam

results in:
"java -ea -Xm200m -cp /opt/science/BBMap/sh/current/ jgi.ReformatReads in=/opt/science/blah.fastq.gz out=/opt/science/blah.sam
Error: Could not find or load main class jgi.ReformatReads"

When I copy/paste the full java line quoted in the error but remove the space between "/current/" and "jgi.ReformatReads" I instead get:
"Error: Could not find or load main class in=.opt.science.blah.fastq.gz"

I've tried it with the fastq file both in and out of the BBMap directory to see if it would help, but got the same error.

Any advice would be gratefully accepted

Roy.

Quote:
Originally Posted by pepe84 View Post
here is the command:
java -cp C:\BBMap\current\jgi.ReformatReads in=C:\BBMap\resources\SRRXXXXX.fastq out1=EFB_R1.fq out2=EFB_R2.fq

And here is the error:
Error: Could not find or load main class in=C:\BBMap\resources\SRRXXXXX.fastq

Just an FYI I am using the command line on windows.

Thanks, I appreciate any help
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Old 09-26-2019, 03:55 AM   #35
quokka
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Hi,

I'm trying to use BBMap version 38.08 to retrieve fastq sequences from a bam file. However, I keep getting a problem where the quality output is merely: JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ

Here's some lines from the bam file:

Code:
HISEQ:378:C7F64ANXX:3:1207:13039:83924	97	smaller_kp_promoter_region_upstream_of_atg_with_chloroplast_insertion_removed_1814_upstream_of_insertion_and_1089_downstream_upstream__5_prime_end_adjacent_to_a_stretch_of_n_residues	15	60	125M	=	644	754	GGGGGAGTGATAAAAATATATTTATTTCATCTAACTGATGAAATAACGTTTTTGCTCTTACAACTAATAGTTAAATACAACAGAACTTGGATGATGGGTATGTGTTTGAGTTTTTAAAATGTTGA	bbbbbfffffffffffffffffffffffffffffffffffffbffffffffef_ebffffffffffffffdfcefffffbfffffffbbfffffffdfefd_\ebOdefOWZW_bWefffdWce[	NM:i:0	MD:Z:125	MC:Z:125M	AS:i:125	XS:i:0
HISEQ:378:C7F64ANXX:3:1106:10647:86342	97	smaller_kp_promoter_region_upstream_of_atg_with_chloroplast_insertion_removed_1814_upstream_of_insertion_and_1089_downstream_upstream__5_prime_end_adjacent_to_a_stretch_of_n_residues	30	60	125M	=	669	764	ATATATTTATTTCATCTAACTGATGAAATAACGTTTTTGCTCTTACAACTAATAGTTAAATACAACAGAACTTGGATGATGGGTATGTGTTTGAGTTTTTAAAATGTTGAGAGTGGGAGTTTGAG	aabbbbffffffffffffffbbeffffffffffePaaebcfeefffffffeffYeffff\efPe]PePPPbc\bbPedP^PeaP]\dYbc]edcfOPOYd_bfeOcfOYOZ\\OdefffNObeOf	NM:i:0	MD:Z:125	MC:Z:125M	AS:i:125	XS:i:0
HISEQ:378:C7F64ANXX:3:1208:17933:95359	97	smaller_kp_promoter_region_upstream_of_atg_with_chloroplast_insertion_removed_1814_upstream_of_insertion_and_1089_downstream_upstream__5_prime_end_adjacent_to_a_stretch_of_n_residues	32	60	125M	=	620	713	ATATTTATTTCATCCAATTGATGAAATGATGTTTTTGCTCTTACAACTAATAGCTAAATACAGTAGAACTTGGATAATGCGTATGTGTTTGAGTTTTTAAAATATTGAGAGTGGAAGTTTGAGAA	aab_`dedbefe]ZPPP^PePdZbbPPY_cbffbfffdfPePPbPP[d][effdfffcebbffcbYPbP\P[PYdb\d]Pd\NdP]P]\eaP[aeePec_OYYOOOYea\O]_O_^dW]edcfef	NM:i:11	MD:Z:14T2C9A1C23T8A0C11G3G23G10G10	MC:Z:125M	AS:i:70	XS:i:0
HISEQ:378:C7F64ANXX:3:2305:17850:4846	97	smaller_kp_promoter_region_upstream_of_atg_with_chloroplast_insertion_removed_1814_upstream_of_insertion_and_1089_downstream_upstream__5_prime_end_adjacent_to_a_stretch_of_n_residues	52	60	125M	=	625	690	ATGAAATGATGTTTTTGCTCTTACAACTAATAGCTAAATACAGTAGAACTTGGATAATGCGTATGTGTTTGAGTTTTTAAAATATTGAGAGTGGAAGTTTGAGAATGCATCAAACCTTGGGAAGG	abbbbffffffffffffffffffffffffffffeffffffffffffeffffff]db\aeffffffffffffffP]ecaeffff]efffeeff_fffffffffffeffffffffffffffffffef	NM:i:9	MD:Z:7A1C23T8A0C11G3G23G10G30	MC:Z:117M8S	AS:i:80	XS:i:0
HISEQ:378:C7F64ANXX:3:2205:15096:32122	97	smaller_kp_promoter_region_upstream_of_atg_with_chloroplast_insertion_removed_1814_upstream_of_insertion_and_1089_downstream_upstream__5_prime_end_adjacent_to_a_stretch_of_n_residues	59	60	125M	=	675	741	AACGTTTTTGCTCTTACAACTAATAGTTAAATACAACAGAACTTGGATGATGGGTATGTGTTTGAGTTTTTAAAATGTTGAGAGTGGGAGGTTGAGGATGCATCAAACCTTGGGAAGGAATAAGT	`aa_`ffaefP^Z\bPdP^_cebPPYbadfffbfbecac_a_Pef]P\Y[PbedPP[e\ed_facYPefff_efePbYYbP]\PP[deO\NN]e[aOOZbOOYaeef]bcb_OeOWb]ZWbOObO	NM:i:2	MD:Z:90T5A28	MC:Z:125M	AS:i:115	XS:i:0
HISEQ:378:C7F64ANXX:3:1307:17567:99979	97	smaller_kp_promoter_region_upstream_of_atg_with_chloroplast_insertion_removed_1814_upstream_of_insertion_and_1089_downstream_upstream__5_prime_end_adjacent_to_a_stretch_of_n_residues	68	60	125M	=	718	775	GCTCTTACAACTAATAGTTAAATACAACAGAACTTGGATGATGGGTATGTGTTTGAGTTTTTAAAATGTTGAGAGTGGGAGTTTGAGAATGCATCAAACCTTGGGAAGGAATAAGTCTTTTGGCC	ababbfffffffffffffffffffffffffffffffffffcffdfeffff]efffffefcffffffffefffffffecfffaefffffffffffffffffffeffffffffffffffb]e]fa]e	NM:i:0	MD:Z:125	MC:Z:125M	AS:i:125	XS:i:0
HISEQ:378:C7F64ANXX:3:2211:20485:88833	97	smaller_kp_promoter_region_upstream_of_atg_with_chloroplast_insertion_removed_1814_upstream_of_insertion_and_1089_downstream_upstream__5_prime_end_adjacent_to_a_stretch_of_n_residues	68	60	125M	=	654	711	GCTCTTACAACTAATAGTTAAATACAACAGAACTTGGATGATGGGTATGTGTTTGAGTTTTTAAAATGTTGAGAGTGGGAGTTTGAGAATGCATCAAACCTTGGGAAGGAATAAGTCTTTTGGCC	aabaaecfffffffffffffffffffffffffffffdefffffefffffffdeffffdefffffffffdffffefffffffefffffffff]cfdfdffffffffffcffffffffbeffffeff	NM:i:0	MD:Z:125	MC:Z:125M	AS:i:125	XS:i:0
HISEQ:378:C7F64ANXX:3:1212:7300:28109	97	smaller_kp_promoter_region_upstream_of_atg_with_chloroplast_insertion_removed_1814_upstream_of_insertion_and_1089_downstream_upstream__5_prime_end_adjacent_to_a_stretch_of_n_residues	71	60	125M	=	636	690	CTTACAACTAATAGCTAAATACAGTAGAACTTGGATAATGCGTATGTGTTTGAGTTTTTAAAATATTGAGAGTGGAAGTTTGAGAATGCATCAAACCTTGGGAAGGAATAAGTCTTTTGGCCTTC	bbbbbfffffffffffffffffffffffffffffffffffffaffffeefffff^efffffffffcffPeff]efffffffffffefffffffffffffffdfffffdfffff]bfdffffffff	NM:i:7	MD:Z:14T8A0C11G3G23G10G49	MC:Z:125M	AS:i:90	XS:i:0
HISEQ:378:C7F64ANXX:3:2303:16430:40702	97	smaller_kp_promoter_region_upstream_of_atg_with_chloroplast_insertion_removed_1814_upstream_of_insertion_and_1089_downstream_upstream__5_prime_end_adjacent_to_a_stretch_of_n_residues	72	60	125M	=	694	747	TTACAACTAATAGTTAAATACAACAGAACTTGGATGATGGGTATGTGTTTGAGTTTTTAAAATGTTGAGAGTGGGAGTTTGAGAATGCATCAAACCTTGGGAAGGAATAAGTCTTTTGGCCTTCC	abbbaffffffffffffdffffffeffffffffffeefffeffffefffefffcffffffffffdffffff_fffffaefffffff]edfffffffff]fffffffffdffcefffffff]ae_b	NM:i:0	MD:Z:125	MC:Z:125M	AS:i:125	XS:i:0
HISEQ:378:C7F64ANXX:3:2116:16496:33002	97	smaller_kp_promoter_region_upstream_of_atg_with_chloroplast_insertion_removed_1814_upstream_of_insertion_and_1089_downstream_upstream__5_prime_end_adjacent_to_a_stretch_of_n_residues	95	60	125M	=	722	752	CAGAACTTGGATGATGGGTATGTGTTTGAGTTTTTAAAATGTTGAGAGTGGGAGTTTGAGAATGCATCAAACCTTGGGAAGGAATAAGTCTTTTGGCCTTCCAAAACTATATAGATAGATAGAGC	bbbbbffffffffffffdffffeeffffffdffffffeffffffffffdfffff]ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff	NM:i:0	MD:Z:125	MC:Z:125M	AS:i:125	XS:i:0
Here's the command and STDERR (NB in this case I was using qin=64 qout=33 for troubleshooting but I get the same result without these flags):

Code:
/home/xub/host/opt/bbmap/bbmap/reformat.sh qin=64 qout=33 requiredbits=16 overwrite=t in=/home/xub/host/opt/findMatesAndRepair/output/150901_80_small/150901_80_small.bothEndsMapped.1.bam out=/home/xub/host/opt/findMatesAndRepair/output/150901_80_small/150901_80_small.bothEndsMapped.reverse.1.fq.gz
java -ea -Xmx200m -cp /home/xub/host/opt/bbmap/bbmap/current/ jgi.ReformatReads qin=64 qout=33 requiredbits=16 overwrite=t in=/home/xub/host/opt/findMatesAndRepair/output/150901_80_small/150901_80_small.bothEndsMapped.1.bam out=/home/xub/host/opt/findMatesAndRepair/output/150901_80_small/150901_80_small.bothEndsMapped.reverse.1.fq.gz
Executing jgi.ReformatReads [qin=64, qout=33, requiredbits=16, overwrite=t, in=/home/xub/host/opt/findMatesAndRepair/output/150901_80_small/150901_80_small.bothEndsMapped.1.bam, out=/home/xub/host/opt/findMatesAndRepair/output/150901_80_small/150901_80_small.bothEndsMapped.reverse.1.fq.gz]

Could not find sambamba.
Found samtools 1.8
Input is being processed as unpaired
Input:                  	464 reads          	58000 bases
Output:                 	230 reads (49.57%) 	28750 bases (49.57%)

Time:                         	0.634 seconds.
Reads Processed:         464 	0.73k reads/sec
Bases Processed:       58000 	0.09m bases/sec


Here's some of the output:

Code:
@HISEQ:378:C7F64ANXX:3:2205:16922:87749
CAAATGACAACCTAAATTGTAAACTGTTTTTTTAAAATCTACTAACCCAAACTGAATCATTTTATAAACCAAATCAAACTATAATTTTTAAATGGTTTGGTCCGATTTTATAATTTGAGCCTATT
+
JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ
@HISEQ:378:C7F64ANXX:3:1210:20568:23121
AAATTTATCCAAATGACAACCTAAATTGTAAACTGTTTTTTTAAAATCTACTAACCCAAACTGAATCATTTTATAAACCAAATCAAACTATAATTTTTAAATGGTTTGGTCCGATTTTATAATTT
+
JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ
@HISEQ:378:C7F64ANXX:3:2212:11893:40357
GGTTTATGGTTTGACTTGGTTTGAAATTTATCCAAATGACAACCTAAATTGTAAACTGTTTTTTTAAAATCTACTAACCCAAACTGAATCATTTTATAAACCAAATCAAACTATAATTTTTAAAT
+
JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ
@HISEQ:378:C7F64ANXX:3:2210:7117:7877
GGTTTGACTTGGTTTGAAATTTATCCAAATGACAACCTAAATTGTAAACTGTTTTTTTAAAATCTACTAACCCAAACTGAATCATTTTATAAACCAAATCAAACTATAATTTTTAAATGGTTTGG
+
JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ

Thanks for any advice.

Cheers.
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Old 09-26-2019, 04:18 AM   #36
GenoMax
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Did you move any of the bbmap folder contents after you downloaded and uncompressed bbmap code?

Make sure the top level directory with BBMap is in your $PATH. Something like
Code:
export PATH=$PATH:/opt/science/BBMap
would work.


Quote:
Originally Posted by Oomjah View Post
Hi,

first time poster so my apologies for any horrid faux pas', and also for the thread necromancy!

I'm trying to convert fastq's to an unmapped SAM (ultimately to a cram to test space saving and to check no loss of data when it's reconverted back to fastq's again) and I saw a thread suggesting BBMAP. However I'm having the same issue as pepe84.

The command:
reformat.sh in=/opt/science/blah.fastq.gz out=/opt/science/blah.sam

results in:
"java -ea -Xm200m -cp /opt/science/BBMap/sh/current/ jgi.ReformatReads in=/opt/science/blah.fastq.gz out=/opt/science/blah.sam
Error: Could not find or load main class jgi.ReformatReads"

When I copy/paste the full java line quoted in the error but remove the space between "/current/" and "jgi.ReformatReads" I instead get:
"Error: Could not find or load main class in=.opt.science.blah.fastq.gz"

I've tried it with the fastq file both in and out of the BBMap directory to see if it would help, but got the same error.

Any advice would be gratefully accepted

Roy.
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