running finished without output files!

[Unalibun]

Dear NGS TE mapper2 Team,

I am running ngs_te_mapper2 for six isolates, including the genome and TE library from the reference species. Unfortunately, the output folder does not have either not ref.bed and ref.bed files. Log file does not reflect any error,

07/20/2023 10:03:10: INFO: CMD: /home/sami/micromamba/envs/ngs_te_mapper2/bin/ngs_te_mapper2 -f /data1/sami/p_ulei_new/pre_fastqc/p_ulei3_caqueta_1.fq,/data1/sami/p_ulei_new/pre_fastqc/p_ulei3_caqueta_2.fq -l P.ulei_combined_library.fasta -r p_ulei_scaf.mod.fa -o /data2/sami/ngs_TE_mapper2/output_ngs_te_mapper2//p_ulei3_caqueta.out
07/20/2023 10:03:10: INFO: Parsing input files...
07/20/2023 21:18:43: INFO: Start alignment...
07/20/2023 21:18:43: INFO: Alignment finished in 0 seconds
07/20/2023 21:18:43: INFO: Detecting insertions...

However std.out file has many "No depth info" lines and

[Errno 2] could not open alignment file /path/to/main/folder/family-specific/tRNA-Leu-TTA(m)/tRNA-Leu-TTA(m).te.cigar.bam: No such file or directory

Could you please give some guidance?