building multiz by lastz160way

[Ho, Eric]

Hi,

I want to build a multiz track for my viral genomes like eboVir3.

I used lastz160way.txt as the template to build a new shell script to fit my machine's file structure.

I made it all the way to the doBlastzChainNet.pl call. Below is my script:

echo "time (${gbdir}/bed/doBlastzChainNet.pl ./DEF \\
-ignoreSelf -stop=net -noDbNameCheck -fileServer=biology2 \\
-tRepeats=windowmaskerSdust -qRepeats=windowmaskerSdust \\
-chainMinScore=10 -chainLinearGap=loose \\
-workhorse=biology2 -smallClusterHub=biology2 -bigClusterHub=biology2)

biology2 is my node name.

I went down to a pair of genomes to see the do.log, E.g. lastz160way/MSV/pairs/WDV-Enk1 (MSV is my reference genome). Among all error messages, I identified two fatal issues:

1. Can't exec "/cluster/bin/scripts/fileServer": No such file or directory

I'd symlinked fileServer to the same location as lastz160way.sh, why did the script still refer to hardcoded location?

2. Can't ssh via port 22. My server bars this port for security reason.

# ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' biology2 nice /home/ericho/kenthome/data/genomes/masVir1/lastz160way/MSV/pairs/WDV-Enk1/run.blastz/doPartition.bash
ssh: connect to host biology2 port 22: Connection refused

I'm wondering how to circumvent these things. I appreciate a simple solution as I only have 200+ genomes and they are small (~3kbps).

Thanks for any helps.

Eric.

[Eric Ho]

I used commands all_bz and tba to generate a maf file.

I tried to load it to my mirror database by hgLoadMaf and
hgLoadMafSummary but I encountered this error:

$ hgLoadMaf masVir1 multiz -pathPrefix=/gbdb/masVir1/multiz -loadFile=tba.maf
Indexing and tabulating ./tba.maf
Couldn't find masVir1. sequence line 1929 of ./tba.maf

multiz is my table name. It was created in mysql. I have no clue what
hgLoadMaf is complaining about. Can anyone help?

Appreciated.

Eric.

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[Christopher Lee]

Hi Eric,

hgLoadMaf expects the name of the first sequence in every MAF block to be <nameOfReference>.<chromName>.
So in this case, since the reference is masVir1, the first sequence in every MAF block needs to begin
with "masVir1.".

Please let us know if you run into further problems with your 160way track!

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further
questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived
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to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute

[Ho, Eric]

I'm not fully understand your point. Could you send me an example MAF file and how to put nameOfReference in the first sequence of a MAF block?

[Cath Tyner]

Hi Eric, 

Here is an example MAF which may be helpful, where the first sequence in every MAF block is <nameOfReference>.<chromName>:

http://hgdownload.cse.ucsc.edu/goldenPath/eboVir3/multiz160way/

Where some example lines are:

##maf version=1 scoring=roast.v3.3

a score=183000.000000

s eboVir3.KM034562v1      0 1 + 18957 C

s Guinea_Kissidougou-C15_2014.Guinea_Kissidougou-C15_2014   0 1 + 18959 C

i Guinea_Kissidougou-C15_2014.Guinea_Kissidougou-C15_2014   N 0 C 0

s Guinea_Gueckedou-C07_2014.Guinea_Gueckedou-C07_2014   0 1 + 18959 C

i Guinea_Gueckedou-C07_2014.Guinea_Gueckedou-C07_2014   N 0 C 0

s Guinea_Gueckedou-C05_2014.Guinea_Gueckedou-C05_2014   0 1 + 18959 C

i Guinea_Gueckedou-C05_2014.Guinea_Gueckedou-C05_2014   N 0 C 0

s G3713v2_2014.G3713v2_2014   0 1 + 18956 C

i G3713v2_2014.G3713v2_2014   N 0 C 0

s G3770v1_2014.G3770v1_2014   0 1 + 18958 C

i G3770v1_2014.G3770v1_2014   N 0 C 0

s G3770v2_2014.G3770v2_2014   0 1 + 18959 C

i G3770v2_2014.G3770v2_2014   N 0 C 0

s G3834_2014.G3834_2014   0 1 + 18921 C

Please respond to this list if you have further questions!

Thank you again for your inquiry and for using the UCSC Genome Browser. 

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​Enjoy,​

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

[Ho, Eric]

Cath,

I figured out myself in that way too.

Thanks, Eric.

----- Original Message -----
From: "Cath Tyner" <ca...@ucsc.edu>
To: "Ho, Eric" <h...@lafayette.edu>
Cc: "Christopher Lee" <chm...@ucsc.edu>, "chumho" <chu...@gmail.com>, "genome-mirror" <genome...@soe.ucsc.edu>
Sent: Friday, July 22, 2016 3:40:14 PM
Subject: Re: [genome-mirror] building multiz by lastz160way

Hi Eric,

Here is an example MAF which may be helpful, where the first sequence in
every MAF block is <nameOfReference>.<chromName>:

http://hgdownload.cse.ucsc.edu/goldenPath/eboVir3/multiz160way/

Where some example lines are:

##maf version=1 scoring=roast.v3.3

a score=183000.000000

s eboVir3.KM034562v1 0 1 + 18957 C

s Guinea_Kissidougou-C15_2014.Guinea_Kissidougou-C15_2014 0 1 + 18959 C

i Guinea_Kissidougou-C15_2014.Guinea_Kissidougou-C15_2014 N 0 C 0

s Guinea_Gueckedou-C07_2014.Guinea_Gueckedou-C07_2014 0 1 + 18959 C

i Guinea_Gueckedou-C07_2014.Guinea_Gueckedou-C07_2014 N 0 C 0

s Guinea_Gueckedou-C05_2014.Guinea_Gueckedou-C05_2014 0 1 + 18959 C

i Guinea_Gueckedou-C05_2014.Guinea_Gueckedou-C05_2014 N 0 C 0

s G3713v2_2014.G3713v2_2014 0 1 + 18956 C

i G3713v2_2014.G3713v2_2014 N 0 C 0

s G3770v1_2014.G3770v1_2014 0 1 + 18958 C

i G3770v1_2014.G3770v1_2014 N 0 C 0

s G3770v2_2014.G3770v2_2014 0 1 + 18959 C

i G3770v2_2014.G3770v2_2014 N 0 C 0

s G3834_2014.G3834_2014 0 1 + 18921 C

Please respond to this list if you have further questions!

Thank you again for your inquiry and for using the UCSC Genome Browser.
Please send new and follow-up questions to one of our UCSC Genome Browser
mailing lists below:

* * Post to the Public Help Forum: E*
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Enjoy,
Cath
. . .
Cath Tyner
UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute <https://genomics.soe.ucsc.edu/>
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