sauloal / introgressionbrowser Goto Github PK

Hi,

I tried the standalone pull just now, which terminated with an error. Any ideas ?

Thanks,
Colin

~/docker/introgressionbrowser$ docker run -it --rm \

-v $PWD/data:/var/www/ibrowser/data
-v $PWD/access.log:/var/log/apache2/access.log
-v $PWD/error.log:/var/log/apache2/error.log
-p 127.0.0.1:10000:10000
--name ibrowser
sauloal/introgressionbrowser
Unable to find image 'sauloal/introgressionbrowser:latest' locally
latest: Pulling from sauloal/introgressionbrowser
c87d97ed7d49: Pull complete
3ed890b0e33e: Pull complete
e9938c931006: Pull complete
ab57dbafeeea: Pull complete
d3e1d2f95336: Pull complete
f3e0f3de8f08: Pull complete
9c3467a5df1a: Pull complete
71cf24ad09a8: Pull complete
a475be933374: Pull complete
264f0baa5ab3: Already exists
Digest: sha256:5192dedc77f2e48312bea736a8ac800bf106eda2877995676d6694283b5e73f7
Status: Downloaded newer image for sauloal/introgressionbrowser:latest

Timestamp: 2015-09-01 09:42:15.805461273 +0200 CEST
Code: System error

Message: not a directory

Frames:

0: setupRootfs
Package: github.com/docker/libcontainer

File: rootfs_linux.go@37

1: Init
Package: github.com/docker/libcontainer.(*linuxStandardInit)

File: standard_init_linux.go@52

2: StartInitialization
Package: Error response from daemon: Cannot start container 1d4388fb71eb90c70351cca995814bc82c38a65e354ae653f17765270f27805e: [8] System error: not a directory
~/docker/introgressionbrowser$ ls
access.log data error.log README.txt

when I ran /vcfmerger/vcf_walk_ram.py -t 12 --pickle -d R01R08
The screen shows COORD DOES NOT EXISTS R01R08/chrA01/PASS_filter_hund_rape_r03_raw_SNP.vcf.nc.list.csv.vcf.gz.simplified.filter.vcf.gz.filtered.vcf.gz.chrA01.000023250001-000023300000.Frag_chrA01g50000_023250001_023300000.vcf.gz.chrA01.chrA01.fasta.coords
then I cd R01R08/chrA01 ; only find a file name
R01R08/chrA01/PASS_filter_hund_rape_r03_raw_SNP.vcf.nc.list.csv.vcf.gz.simplified.filter.vcf.gz.filtered.vcf.gz.chrA01.000023250001-000023300000.Frag_chrA01g50000_023250001_023300000.vcf.gz.chrA01.fasta.coords
There are two "chrA01" in the filename which vcf_walk_ram.py try to find ,but only one "chrA01"
in the true file
Maybe something is wrong with the vcf_walk_ram.py script, but I don't know how to revise it

I can't open the URL of the data:
https://s3.eu-central-1.amazonaws.com/saulo.ibrowser/index.html
and I try another computer , fail again; is there anything wrong with the URL?

I'm trying to run vcfsimplify.py to filter snps from a VCF file, but it keeps returning an error (see below). Any help with this would be much appreciated.

andrea@T3610-U:~/introgressionbrowser$ vcfmerger/vcfsimplify.py -i /home/andrea/introgressionbrowser/data/PvTFL1y_refV2_Chr01.recode.vcf -o simp_snp
VCF Heap Translation None
simplifying :: SNP [ 2, 1] True
simplifying :: Heterozygous [ 4, 2] True
simplifying :: Homozygous [ 8, 3] True
simplifying :: Indel [ 16, 4] True
simplifying :: Singleton [ 32, 5] True
Progress Legend:
print every : 1000
Heterozygous Dest : h
Homozygous : o
Heterozygous Indel: I
Homozygous Indel : i
Source Indel : s
Singleton 1 : 1
Singleton 2 : 2
Singleton 3 : 3
Ok : .
2018-09-25T12:26:21.947195
saving to simp_snp
adding file to heap
vcf file /home/andrea/introgressionbrowser/data/PvTFL1y_refV2_Chr01.recode.vcf does exists
creating vcf handler
created vcf handler
getting first register
got first register
added to heap

STARTING CHROMOSOME Chr01
heterozygous: ACTCTCTCTCTCTC,ACTCTCTCTCTCTCTC
heterozygous: C,G
heterozygous: G,T
heterozygous: A,T
heterozygous: A,G
heterozygous: C,T
heterozygous: A,T
heterozygous: A,G
heterozygous: C,T
Traceback (most recent call last):
File "vcfmerger/vcfsimplify.py", line 127, in
main(sys.argv[1:])
File "vcfmerger/vcfsimplify.py", line 105, in main
lines.append( str( val ) )
File "/home/andrea/introgressionbrowser/vcfmerger/vcfmerger.py", line 362, in str
vcfResult.simpliStats['Homozygous Indel'] += 1
KeyError: 'Homozygous Indel'