error tool Bowtie2

Question: error tool Bowtie2

3.2 years ago by

Noè • 0

European Union

Noè • 0 wrote:

Goodmornig,

I have a problem with Galaxy, I am using Bowtie2 tool and the output at the end of analysis is:

Settings:
Output files: "genome.*.bt2"
Line rate: 6 (line is 64 bytes)
Lines per side: 1 (side is 64 bytes)
Offset rate: 4 (one in 16)
FTable chars: 10
Strings: unpacked
Max bucket size: default
Max bucket size, sqrt multiplier: default

There is indicated to display at UCSC or at Ensembl, but:

- UCSC reports: Error in TCP non-blocking connect() 111 - Connection refused
Couldn't open http://127.0.0.1:8080/display_application/6a65222fe2393f8f/ucsc_bam/main/776a4e075f8e7604/param/track

- Ensembl reports: The URL used to reach this page may be incomplete or out-of-date. A location is required to build this page. For example, chromosomal coordinates:http://www.ensembl.org/Homo_sapiens/Location/View?r=17:63973115-64437414 You can also browse this genome via its karyotype

What is the problem?

Thank you very much in advance

ensembl ucsc mapping bowtie2 • 907 views

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modified 3.2 years ago • written 3.2 years ago by Noè • 0

3.2 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

There is a problem with visualizing a BAM dataset at UCSC/Emsembl? Is the dataset intact? Try running a few other simple tools that accept BAM input to test the dataset (statistic tools from the samtools or picard group would be a good choices - these will often report exactly what is wrong with the dataset). Do this unless there is already a clear yellow message in the dataset's box about a metadata problem. If that is present, first try to correct the issue by resetting metadata in Edit Attributes (click on the pencil icon to reach these functions).

Please let us know if this does not help you to resolve the problem, Jen, Galaxy team

ADD COMMENT • link written 3.2 years ago by Jennifer Hillman Jackson ♦ 25k

3.2 years ago by

Noè • 0

European Union

Noè • 0 wrote:

Thank you very much for your help. I have tried Bam coverage statistic tool and it has run correcty

ADD COMMENT • link written 3.2 years ago by Noè • 0

Where are you using Galaxy? External display links are functioning correctly at http://usegalaxy.org from testing. This could be an issue with your internet service if outbound connections are problematic. Jen

ADD REPLY • link written 3.2 years ago by Jennifer Hillman Jackson ♦ 25k

Thank you very much for your help, I am using Galaxy in local, I don't have problem with internet... so I do not understand what is the problem :(

ADD REPLY • link written 3.2 years ago by Noè • 0

Are you setting up Galaxy with the production server configuration? If using a web proxy, the configuration may need tuning. Please see the wiki here for help if this is the case: https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Using_a_proxy_server

ADD REPLY • link written 3.2 years ago by Jennifer Hillman Jackson ♦ 25k

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