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Issue with obligate_essentiality_analysis.R

Hello, I was trying to use Tn-seq doccker version on my dataset and I 'm stuck with the following error

Error:

Error in mutate_impl(.data, dots) :
  contrasts can be applied only to factors with 2 or more levels
Calls: %>% ... mutate -> mutate_ -> mutate_.tbl_df -> mutate_impl -> .Call
Execution halted

To replicate the error here is the needed files:

TSV files created with khturner/tn-seq process_reads.py attached
gff file attached
reference genome attached

download files here:
https://drive.switch.ch/index.php/s/86FDiZBJ4HNB7Hk

command used:

/root/Tn-seq/py/obligate_essentiality_analysis.py -r /data/F72C_mycoplasma.fasta -g M.hyopneumoniae.gff -f CDS -3 10 -i 100 -o obligate_essentiality -c 1_S271_R1_001.sites.tsv 2_S283_R1_001.sites.tsv

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