Question: MACS2 run error
0
gravatar for shambyross
23 months ago by
shambyross10
shambyross10 wrote:

Hello to anyone willing to help,

I tried running Bowtie2 bam files on MACS2 to get peaks, however got the following error:

Traceback (most recent call last): File "/Users/rossshamby/galaxy/lib/galaxy/jobs/runners/__init__.py", line 170, in prepare_job job_wrapper.prepare() File "/Users/rossshamby/galaxy/lib/galaxy/jobs/__init__.py", line 897, in prepare self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build() File "/Users/rossshamby/galaxy/lib/galaxy/tools/evaluation.py", line 433, in build raise e ValueError: invalid literal for int() with base 10: '3000000000.0'

I do understand that this problem has been reported/asked before. It was suggested that it is the quality of sequencing data that might be the problem. Therefore, I ran FASTQC on the fastq files and indeed got some poor quality data.

However, I am trying to repeat publicly available data that has been used for publication.

Does this mean that they have used other program than MACS2? Their data is not reliable? or am I doing something wrong?

Thank you, This forum has been very helpful, Ross

chip-seq • 667 views
ADD COMMENTlink modified 23 months ago by Jennifer Hillman Jackson25k • written 23 months ago by shambyross10
0
gravatar for Jennifer Hillman Jackson
23 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

This looks like a python problem. What version are you running? 2.7 is the supported version. Switch to that and see if a test rerun resolves the issue.

https://wiki.galaxyproject.org/Admin/Python

Best, Jen, Galaxy team

ADD COMMENTlink written 23 months ago by Jennifer Hillman Jackson25k

Still get the same error. I have checked and I am indeed running python 2.7.12

Any other suggestions?

Thank you,

Ross

ADD REPLYlink written 23 months ago by shambyross10
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