Difficulty reading BAMs from PIPE after qsub

Hi,

Following the example workflow, I have successfully got expected results using one of my data set. However, using the same pipeline, when I tried to 'qsub' the similar jobs to computing clusters, I got similar figures as shown in Issue #26 as reported by @Juncqyz . After a quick check, it seems there are some security issues with the subprocess.Popen when shell=True is in use as described here. Therefore, it run well directly without qsub, but for some security reason, the input BAM cannot be read when the job was submit to clusters (maybe only in some situation). If this is the case, I would be great if the authors can revise the way it read a BAM file.

Thanks,

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