Question: BWA-MEM mapping Taking longer time
gravatar for abidraheel
18 months ago by
abidraheel0 wrote:

Hi Folks,

I am trying to run BWA-MEM mapping, its taking longer time. Can you please look into it. Below are details of my job

Secondly, I am wondering, as I have to perform next step of my assignment to perform stat on this generated file by using SAM tools. Should I wait to run this job till mapping is complete or I can execute the job and it will line up.

BWA-MEM Dataset Information Number: 9 Name: BWA-MEM on data 8 and data 7 (mapped reads in BAM format) Created: Sat 20 May 2017 11:24:24 AM (UTC) Filesize: ??? bytes Dbkey: ? Format: bam Job Information Galaxy Tool ID: Galaxy Tool Version: 0.1 Tool Version: None Tool Standard Output: stdout Tool Standard Error: stderr Tool Exit Code: None History Content API ID: bbd44e69cb8906b5be340f6634613d8a Job API ID: bbd44e69cb8906b55e778ac97690b10b History API ID: 7a2ba3115a492412 UUID: 3068dd9a-819c-4bb7-8d9f-f2fb653d7959 Tool Parameters Input Parameter Value Note for rerun Load reference genome from cached
Using reference genome hg38canon
Single or Paired-end reads paired
Select first set of reads 7: FASTQ Groomer on data 1
Select second set of reads 8: FASTQ Groomer on data 2
Enter mean, standerd deviation, max, and min for insert lengths. Empty.
Set read groups information? do_not_set
Select analysis mode illumina
Job Resource Parameters no
Inheritance Chain BWA-MEM on data 8 and data 7 (mapped reads in BAM format) Job Dependencies Dependency Dependency Type Version bwa tool_shed_package samtools tool_shed_package 1.1

bwa • 682 views
ADD COMMENTlink modified 18 months ago by Jennifer Hillman Jackson25k • written 18 months ago by abidraheel0
gravatar for Jennifer Hillman Jackson
18 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Update for job delays and/or cluster failures at 5-22-2017:

ADD COMMENTlink written 18 months ago by Jennifer Hillman Jackson25k
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