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Pass cTWAS weight paths to ctwas_assemble.R through a list file - #1436
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A genome-scale chromosome joins thousands of weight paths into one --twas-weights argument (229 KB on chr19 for MSBB eQTL), past the 128 KB per-argument limit, so the assemble step fails with exit code 126. The notebook now writes the paths to <output>.weights.txt and ctwas_assemble.R accepts a text file listing the paths; comma-separated input still works.
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The cTWAS step of
twas_ctwas.ipynbjoins every per-gene weight RDS path into one comma-separated--twas-weightsargument. On a genome-scale run this exceeds Linux's 128 KB limit for a single argument, soctwas_assemble.Rnever starts (exit code 126). For MSBB eQTL weights the argument was 229 KB on chr19 (1,350 genes), and 11 of 22 chromosomes failed this way.Changes:
twas_ctwas.ipynb: write the weight paths to<output>.weights.txt(one per line) and pass that file to--twas-weights.ctwas_assemble.R:--twas-weightsalso accepts a text file listing the paths. Comma-separated paths still work as before.Tested on SCC with pecotmr 0.9.5: MSBB eQTL chr19 now writes the 1,350-path list and passes assemble and prior estimation.