diff --git a/CHANGELOG.md b/CHANGELOG.md index ad406eb0d70e49f2d1934b874fc2d3d7b5d17dd7..cf7c23d2d1831c7fa15946572fb22dd372b45a6a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,7 @@ All notable changes to Pantools will be documented in this file. - `pantools sequence_visualization` now requires the "sequence" rule to be set for unphased pangenomes (!226). - Fixed a number of bugs causing grouping results to slightly differ based on the order of genome or proteome input files (!223). - Fixed `pantools blast` for TBLASTN and TBLASTX where the wrong output file was written (!241). +- Fixed the KMC command needed for `pantools add_genomes` (!243). ## [4.3.1] - 08-12-2023 diff --git a/src/main/java/nl/wur/bif/pantools/construction/index/IndexDatabase.java b/src/main/java/nl/wur/bif/pantools/construction/index/IndexDatabase.java index 2d8e450e14d9af63ff38810560cb3a39a741b49e..50c343b9af4234df61ef4df78aa57b4dd42fc2ca 100755 --- a/src/main/java/nl/wur/bif/pantools/construction/index/IndexDatabase.java +++ b/src/main/java/nl/wur/bif/pantools/construction/index/IndexDatabase.java @@ -296,7 +296,7 @@ public final class IndexDatabase { // merge two indices Pantools.logger.debug("Merging two indices."); - final String merge_command = KMC + "_tools simple union " + index_path + "sorted " + index_path + "new " + index_path + "merged"; + final String merge_command = KMC + "_tools simple " + index_path + "sorted " + index_path + "new union " + index_path + "merged"; Pantools.logger.debug("KMC command: {}", merge_command); final String merge_output = runCommandWithOutput(merge_command);