INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
Found 0 primers in BED file
Exiting.
[E::hts_open_format] Failed to open file "ivar_trim/1570532-IA.primertrim.bam" : No such file or directory
samtools sort: can't open "ivar_trim/1570532-IA.primertrim.bam": No such file or directory
[E::hts_open_format] Failed to open file "ivar_trim/1570532-IA.primertrim.sorted.bam" : No such file or directory
samtools index: failed to open "ivar_trim/1570532-IA.primertrim.sorted.bam": No such file or directory