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unexpected operator 3-align/index.sh #244

Closed rfinkers closed 3 months ago

rfinkers commented 3 months ago

in the folder 3-align, script index.sh (Linux ubuntu 22); the following error is thrown:

./index.sh: 10: [: False: unexpected operator

this results in an empty diploid.index; pipeline continues as normal.

As I don't fully understand the impact of this; e.g. what is the effect of execution of the first part of the test (diploid="--diploid-heuristic 21 31 --diploid-heuristic-cache ../3-align/diploid.index"), rather than the touch diploid.index; I have trouble know if/what the impact of this on my assembly might be. This besides the possible bug in this script.

brianwalenz commented 3 months ago

Ouch! The error is the double-equal-sign == in index.sh; Ubuntu's /bin/sh seems particularly strict but we don't have any instances to test on. index.sh is generated by ${VERKKO_INSTALL_DIR}/lib/verkko/Snakefiles/3-alignONT.sm. Changing == to = on lines 59 and 131 will fix the problem.

The bigger issue is that unless you ran with --haploid, you're assembly isn't correct. You can recover some of the lost compute by removing (or renaming) directories [45678]*, 3-alignTips, the assembly.* outputs and everything in 3-align EXCEPT the split* files/directory.

rfinkers commented 3 months ago

confirmed that this workaround did do the trick.