Paired-End Reads not being correctly analyzed

[Former user]

When I submit two fastq.gz files (as shown below), MAGeCK-VISPR doesn't appear to be able to analyze the second set of reads - the Trim function completely fails, 0% of the reads map, I receive a GINI score of approximately -1.0, and I cannot trust the subsequent results. When I remove the second set of reads, VISPR works well: the Trim function works, ~85% of the reads map, and the GINI score is closer to expected (~0.1). Am I doing something incorrectly? Is something broken? Any guidance would be appreciated.

samples: plasmid: - mpg_...S4_R1_001.fastq.gz - mpg...S4_R2_001.fastq.gz Sample1: - mpg...S1_R1_001.fastq.gz - mpg...S1_R2_001.fastq.gz Sample2: - mpg...S2_R1_001.fastq.gz - mpg...S2_R1_001.fastq.gz Sample3: - mpg...S3_R1_001.fastq.gz - mpg..._S3_R2_001.fastq.gz