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Achilles Error: Line 5460 did not have 6 elements

I am trying to run Achilles on our most recent refresh of our cdm and am getting this error. I have no other error reports in the log and every individual query seems to complete before hitting this error on the merge step.
Here is the full error report:
Thread: Main

Message: line 5460 did not have 6 elements

Level: FATAL

Time: 2024-05-06 17:22:16

Stack trace:

9: h(simpleError(msg, call))

8: .handleSimpleError(function (condition)


if (is(condition, "error")) {

7: scan(file = file, what = what, sep = sep, quote = quote, dec = dec, nmax =

6: utils::read.table(file = file.path(outputFolder, "log_achilles.txt"), heade

5: .parseLogs(outputFolder)

4: .mergeAchillesScratchTables(resultsTable = table, connectionDetails = conne

3: FUN(X[[i]], ...)

2: lapply(resultsTablesToMerge, function(table) {


1: achilles(cdmVersion = "5.4", connectionDetails = connectionDetails, cdmData

R version:

R version 4.4.0 (2024-04-24)



Attached base packages:

- stats

- graphics

- grDevices

- utils

- datasets

- methods

- base

Other attached packages:

- Achilles (1.7.2)

- DatabaseConnector (6.3.2)

I wonder if I am missing something here?

Please let me know if I can provide anything else in order to help with troubleshooting.


Hi, We have the same issue. Did you manage to solve it?

Thanks in advance.

Hi Ana,

The error is related to the number of threads we were using and this causing the corruption of the log files as we understood it. We were also getting issues in some of the queries that caused a problem.

Reducing the thread used as well as correcting any underlying query errors solved it for us.