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<general>
input_format=sam
sv_type=all
mates_orientation=RF
read1_length=35
read2_length=35
mates_file=/scratch/#####/<USERNAME>/GVA_sv_tutorial/61FTVAAXX.ab.sam
cmap_file=/scratch/#####/<USERNAME<USERNAME>/GVA_sv_tutorial/NC_012967.1.lengths
num_threads=48
</general>

<detection>
split_mate_file=0
window_size=2000
step_length=1000
</detection>

<filtering>
split_link_file=0
nb_pairs_threshold=3
strand_filtering=1
</filtering>

<bed>
  <colorcode>
    255,0,0=1,4
    0,255,0=5,10
    0,0,255=11,100000
  </colorcode>
</bed>

In reviewing these tutorials these commands were not executing for me in idev sessions for unknown reasons. By chance I had an idev session time out with me noticing and I noticed it did run on the head node. Try the above commands 1 at a time, but if you see error messages like the following logout of your idev session with the logout command, and then execute them 1 at a time on the head node. While this is not the best citizenship, the program gave no indications of being a problem.

Feedback from other students says this is not a problem limited to me and that multiple people are experiencing the same problem. Running these commands on the head node should be acceptable, for reasons that will be discussed in zoom.

Config/General.pm did not return a true value at /corral-repl/utexas/BioITeam/bin/SVDetect line 48.
BEGIN failed--compilation aborted at /corral-repl/utexas/BioITeam/bin/SVDetect line 48.

.