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