FastQ Screen fails to clean up after itself

[FelixKrueger]

In --bisulfite mode, FastQ Screen seem to leave some files behind, e.g.:

Cat.lane1_another_sample_R2_trimmed.fq.gz_temp_subset.fastq_C_to_T.fastq
Cat.lane1_another_sample_R2_trimmed.fq.gz_temp_subset.fastq_G_to_A.fastq
lane1_another_sample_R2_trimmed.fq.gz_temp_subset.fastq
lane1_other_sample_R1_trimmed.fq.gz_temp_subset.fastq
lane1_other_sample_R2_trimmed.fq.gz_temp_subset.fastq
lane1_some_sample_R2_trimmed.fq.gz_temp_subset.fastq
Opossum.lane1_other_sample_R1_trimmed.fq.gz_temp_subset.fastq_C_to_T.fastq
Opossum.lane1_other_sample_R1_trimmed.fq.gz_temp_subset.fastq_G_to_A.fastq
Opossum.lane1_other_sample_R2_trimmed.fq.gz_temp_subset_bismark_bt2.bam
Opossum.lane1_other_sample_R2_trimmed.fq.gz_temp_subset_bismark_bt2_SE_report.txt
Opossum.lane1_other_sample_R2_trimmed.fq.gz_temp_subset.fastq_ambiguous_reads.fq.gz
Opossum.lane1_other_sample_R2_trimmed.fq.gz_temp_subset.fastq_C_to_T.fastq
Opossum.lane1_other_sample_R2_trimmed.fq.gz_temp_subset.fastq_G_to_A.fastq
Opossum.lane1_some_sample_R2_trimmed.fq.gz_temp_subset.fastq_C_to_T.fastq
Opossum.lane1_some_sample_R2_trimmed.fq.gz_temp_subset.fastq_G_to_A.fastq

Not sure why this happens.

[StevenWingett]

When I ran FastQ Screen (the latest development version) in --bisulfite mode, processing the Bismark Test Dataset, the software did clean up after itself. Please let me know if there is a specific example in which this is a problem or else I'll have to assume FastQ Screen is working correctly.

Thanks.