Unary operator expected, mergeBed errors when running test data

[heidihyang]

Hi,

I'm having an issue running the test data with the TEMP2 scripts. I've made a conda environment with bio-perl=1.6.924, samtools=1.19.2, bedtools=2.31.1, bwa=0.7.17, and R=4.2.2, and the program is finding the packages through the conda env.

Here is the command I ran:
../TEMP2 insertion -l test.1.fastq.gz -r test.2.fastq.gz -I bwa_index/chr2L -g chr2L.fa -R transposon.fa -t rmsk.bed -o test_output -c 2

I'm encountering this error first: /u/project/vlsork/hyangg/TEMP2/bin/TEMP2_insertion.sh: line 204: [: -lt: unary operator expected. I then get errors later down the line with mergeBed and others. I've attached the job log: temp2-joblog.txt

Any help / suggestions would be appreciated!

Best,
Heidi