Fatal fdiffact1 error when using --semisupervised and --validation-coords together

[EricR86]

Original report (BitBucket issue) by Francis Nguyen (Bitbucket: Francis Nguyen).

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When running segway train with --semisupervised and --validation-coords=<x> together, segway will submit jobs, but then fail with the following error:

ERROR: observation file 1 needs an -fdiffact1 that truncates (ts, te) or expands (rf, rl, se) because the observation files have different lengths for segment 0. All files must be truncated to 5 frames or expanded to 10 frames.

ERROR: observation file 1 needs an -fdiffact1 that truncates (ts, te) or expands (rf, rl, se) because the observation files have different lengths for segment 0. All files must be truncated to 5 frames or expanded to 10 frames.

This error can be replicated by taking the simplesemisupervised example in test/semisupervised, adding the line --validation-coords="../validate-coords.bed" \ after line 32 of run.sh, and creating a validate-coords.bed file in that directory, with contents:

chr1    1000    1100

[EricR86]

Original comment by Eric Roberts (Bitbucket: ericr86, GitHub: ericr86).

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A probable cause is that validation coords are not storing the supervised observations. I believe -of1 does refer to the int observations.