Error during deviaTE_prep step: ValueError: more than one primary alignment

[Ajinkya-IISERB]

I used the following command using WGS Illumina sequencing reads and RepeatModeler libraries as input. deviaTE_prep --input Arthir.fastq --library Arthir-families.fa --threads 64 --quality_encoding phred+33

I get this output on the screen: Trimming reads.

Reads processed: 474519376 Reads passed filtering: 474519375 5p poly-N sequences trimmed: 12048 3p poly-N sequences trimmed: 0 Reads discarded during 'remaining N filtering': 0 Reads discarded during length filtering: 1 Reads trimmed during quality filtering: 38317741

Mapping reads. Detecting internal deletions.

[bam_sort_core] merging from 214 files and 1 in-memory blocks... Traceback (most recent call last): File "/home/morpheus/.local/bin/deviaTE_fuse", line 56, in raise ValueError('more than one primary alignment') ValueError: more than one primary alignment

Can you please help me through this error? I am not able to figure out what is causing this error.

Thank you. Ajinkya