I have a problem like this too with android studio.
Now I realized the difference in classpath between AndroidStudio3 and console invocation of a task:
Android Studio takes some jars from “.gradle/caches/jars-3/” where as console takes everything from “.gradle/caches/modules-2”,
Console:
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.android.tools.build/gradle/3.0.1/cfa107d4db0c11c11f445a11e768adf61c72ce06/gradle-3.0.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.jetbrains.kotlin/kotlin-gradle-plugin/1.1.60/dc7acce581312f418c1ad55932ab770da61e205d/kotlin-gradle-plugin-1.1.60.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.android.tools.build/gradle-core/3.0.1/c2945119335b491ca56e4042f7c8c55dccf5c9c2/gradle-core-3.0.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.jetbrains.kotlin/kotlin-gradle-plugin-api/1.1.60/97a69272b6dc47f9ca1f523859e4819a1c61cb39/kotlin-gradle-plugin-api-1.1.60.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.jetbrains.kotlin/kotlin-annotation-processing-gradle/1.1.60/8f2d3fef4c0d7ecfc85fa51744153f399cdeb3a2/kotlin-annotation-processing-gradle-1.1.60.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.jetbrains.kotlin/kotlin-android-extensions/1.1.60/3b6a750e48ac6a4ca5f0fba633385825610dce3e/kotlin-android-extensions-1.1.60.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.jetbrains.kotlin/kotlin-compiler-runner/1.1.60/d2586f88979235b4b102348c431d888bdd2cf63f/kotlin-compiler-runner-1.1.60.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.jetbrains.kotlin/kotlin-compiler-embeddable/1.1.60/e0ea7c24d46acc433ece025023868bf9ffe5e437/kotlin-compiler-embeddable-1.1.60.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.android.tools.build/builder/3.0.1/1f896967507729bb35ac727c03d3b9306fe87b7d/builder-3.0.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.android.tools.lint/lint/26.0.1/541bfb082a95a3b55d0158d69b067f1d7c623122/lint-26.0.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.android.tools.lint/lint-checks/26.0.1/a5df32c64598e190808accaa03820fb9db9f8201/lint-checks-26.0.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.android.tools.lint/lint-api/26.0.1/2d4dd9f4676fbb152e4baf6f6f4cbbb868521832/lint-api-26.0.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.android.tools.build/manifest-merger/26.0.1/700cbb1ed4066f48d4970f5669c44a51bd03142/manifest-merger-26.0.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.android.tools/sdk-common/26.0.1/9ddd2fa552e7b49548c421c0be4e65dc9a245f69/sdk-common-26.0.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.android.tools/sdklib/26.0.1/bdb4723f8e3791f1d3911b1f191acf25840f352a/sdklib-26.0.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.android.tools/repository/26.0.1/bc0dfe02af8d075f6b7ad63a202ed4c63a6a647d/repository-26.0.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.jetbrains.kotlin/kotlin-reflect/1.1.60/af5cabae2d352850b076213f358dc2150b14a812/kotlin-reflect-1.1.60.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.jetbrains.kotlin/kotlin-stdlib/1.1.60/ac63d0e86e690fe4eded7f1f8998996c28499989/kotlin-stdlib-1.1.60.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.android.tools.external.org-jetbrains/uast/26.0.1/663906c592ce867fa2e9bcbffbe2130397078132/uast-26.0.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.android.tools.build/gradle-api/3.0.1/92640ae3c543aa3faee7b954ce641d03949d4401/gradle-api-3.0.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.android.databinding/compilerCommon/3.0.1/7f51b3e1636063e491131a0b0436512131cb1bdc/compilerCommon-3.0.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.android.tools.build/transform-api/2.0.0-deprecated-use-gradle-api/47f6c56527c42425742fa9b56ffd3fd80763fe03/transform-api-2.0.0-deprecated-use-gradle-api.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.ow2.asm/asm-analysis/5.1/6d1bf8989fc7901f868bee3863c44f21aa63d110/asm-analysis-5.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.ow2.asm/asm-commons/5.1/25d8a575034dd9cfcb375a39b5334f0ba9c8474e/asm-commons-5.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.ow2.asm/asm-util/5.1/b60e33a6bd0d71831e0c249816d01e6c1dd90a47/asm-util-5.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.ow2.asm/asm-tree/5.1/87b38c12a0ea645791ead9d3e74ae5268d1d6c34/asm-tree-5.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.ow2.asm/asm/5.1/5ef31c4fe953b1fd00b8a88fa1d6820e8785bb45/asm-5.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.jacoco/org.jacoco.report/0.7.4.201502262128/5c6bb5f95ae695dc4510b95f7d5ad0397e4881ad/org.jacoco.report-0.7.4.201502262128.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.jacoco/org.jacoco.core/0.7.4.201502262128/31482f50411a3a5769b6c78fa9b97ba731c205e7/org.jacoco.core-0.7.4.201502262128.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/net.sf.jopt-simple/jopt-simple/4.9/ee9e9eaa0a35360dcfeac129ff4923215fd65904/jopt-simple-4.9.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/net.sf.proguard/proguard-gradle/5.3.3/ad23a0505f58d0dfc95bb1472decc397460406c9/proguard-gradle-5.3.3.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.android.tools.analytics-library/tracker/26.0.1/15f0c0560c8a97700651d2dd5219937baa80c166/tracker-26.0.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.android.tools.analytics-library/shared/26.0.1/5cfc3811c2fd6cddfce2ec1bb5fbbec87e0fc462/shared-26.0.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.android.tools.analytics-library/protos/26.0.1/7719e7ed7498e25ec555bdfcb7a4de0e88a47ea/protos-26.0.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.google.protobuf/protobuf-java/3.0.0/6d325aa7c921661d84577c0a93d82da4df9fa4c8/protobuf-java-3.0.0.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.jetbrains.kotlin/kotlin-script-runtime/1.1.60/64c9714b95a3c6cc662c0b4185c6651d5bfb86c6/kotlin-script-runtime-1.1.60.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.jetbrains.kotlin/kotlin-build-common/1.1.60/5d80ca486fd5be2ad431a12295c110de77af9d9b/kotlin-build-common-1.1.60.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.jetbrains.kotlin/kotlin-daemon-client/1.1.60/e614c9c3352a6c0faf9fe1344cfb1d9f5789dcd4/kotlin-daemon-client-1.1.60.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.android.tools.build/builder-model/3.0.1/e9de7e34339a8eb90fda30ac6bf580d5f2c4f282/builder-model-3.0.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.android.tools.build/builder-test-api/3.0.1/5f084a2888a7f638c4c89c3278760345b1fb4c8/builder-test-api-3.0.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.android.tools.ddms/ddmlib/26.0.1/d4bcdb3a578812688ccc34f1359702601fea955d/ddmlib-26.0.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.android.tools.layoutlib/layoutlib-api/26.0.1/4eb1f46803873ff996f2457d1dd64c5c305818d8/layoutlib-api-26.0.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.android.tools/dvlib/26.0.1/46f3eeaf812811374b4ea2c49ad52687a7ff6a87/dvlib-26.0.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.android.tools/common/26.0.1/38e362a43a905b6745d609bea37faddb0c5bffab/common-26.0.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.android.tools.build/apksig/3.0.1/535b9323a1bd47e3a9c860d11f4e11a80db13f2b/apksig-3.0.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.squareup/javawriter/2.5.0/81241ff7078ef14f42ea2a8995fa09c096256e6b/javawriter-2.5.0.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.bouncycastle/bcpkix-jdk15on/1.56/4648af70268b6fdb24674fb1fd7c1fcc73db1231/bcpkix-jdk15on-1.56.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.bouncycastle/bcprov-jdk15on/1.56/a153c6f9744a3e9dd6feab5e210e1c9861362ec7/bcprov-jdk15on-1.56.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/it.unimi.dsi/fastutil/7.2.0/5ad3a2bb04143f70aa0765fc29fc29571a7d6b34/fastutil-7.2.0.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.googlecode.json-simple/json-simple/1.1/5e303a03d04e6788dddfa3655272580ae0fc13bb/json-simple-1.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.eclipse.jdt.core.compiler/ecj/4.6.1/5555607add54eb79c5a0729134e663fe2e6300c2/ecj-4.6.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.google.jimfs/jimfs/1.1/8fbd0579dc68aba6186935cc1bee21d2f3e7ec1c/jimfs-1.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.android.tools.external.lombok/lombok-ast/0.2.3/528b6f8bde3157f17530aa366631f2aad2a6cf9/lombok-ast-0.2.3.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.google.guava/guava/22.0/3564ef3803de51fb0530a8377ec6100b33b0d073/guava-22.0.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.android.databinding/baseLibrary/3.0.1/cc0483d84342e82c261aeb5fd0ef2f876b587489/baseLibrary-3.0.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.antlr/antlr4/4.5.3/f35db7e4b2446e4174ba6a73db7bd6b3e6bb5da1/antlr4-4.5.3.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/commons-io/commons-io/2.4/b1b6ea3b7e4aa4f492509a4952029cd8e48019ad/commons-io-2.4.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.googlecode.juniversalchardet/juniversalchardet/1.0.3/cd49678784c46aa8789c060538e0154013bb421b/juniversalchardet-1.0.3.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.android.tools/annotations/26.0.1/29012758503f56c7dc0714eda494f7f140fd3db8/annotations-26.0.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/net.sf.proguard/proguard-base/5.3.3/988b6b0636ce343d4962b3b37f6319dcc6e99a61/proguard-base-5.3.3.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.google.code.gson/gson/2.3/5fc52c41ef0239d1093a1eb7c3697036183677ce/gson-2.3.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.apache.commons/commons-compress/1.12/84caa68576e345eb5e7ae61a0e5a9229eb100d7b/commons-compress-1.12.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.apache.httpcomponents/httpclient/4.2.6/e4ca30a6a3a075053a61c6fc850d2432dc012ba7/httpclient-4.2.6.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.apache.httpcomponents/httpmime/4.1/9ba2dcdf94ce35c8a8e9bff242db0618ca932e92/httpmime-4.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/net.sf.kxml/kxml2/2.3.0/ccbc77a5fd907ef863c29f3596c6f54ffa4e9442/kxml2-2.3.0.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.google.code.findbugs/jsr305/1.3.9/40719ea6961c0cb6afaeb6a921eaa1f6afd4cfdf/jsr305-1.3.9.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.google.errorprone/error_prone_annotations/2.0.18/5f65affce1684999e2f4024983835efc3504012e/error_prone_annotations-2.0.18.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.google.j2objc/j2objc-annotations/1.1/ed28ded51a8b1c6b112568def5f4b455e6809019/j2objc-annotations-1.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.codehaus.mojo/animal-sniffer-annotations/1.14/775b7e22fb10026eed3f86e8dc556dfafe35f2d5/animal-sniffer-annotations-1.14.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.intellij/annotations/12.0/bbcf6448f6d40abe506e2c83b70a3e8bfd2b4539/annotations-12.0.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.apache.httpcomponents/httpcore/4.2.5/472f0f5f8dba5d1962cb9d7739feed739a31c30d/httpcore-4.2.5.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/commons-logging/commons-logging/1.1.1/5043bfebc3db072ed80fbd362e7caf00e885d8ae/commons-logging-1.1.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/commons-codec/commons-codec/1.6/b7f0fc8f61ecadeb3695f0b9464755eee44374d4/commons-codec-1.6.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/com.android.tools.external.com-intellij/intellij-core/26.0.1/a373ed549821cb9a932b87c79792790f6d018727/intellij-core-26.0.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.jetbrains.trove4j/trove4j/20160824/33c3e174a9c8368d93761d3d12712db18e903959/trove4j-20160824.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.jetbrains/annotations/13.0/919f0dfe192fb4e063e7dacadee7f8bb9a2672a9/annotations-13.0.jar
Android Studio 3
:file:/Users/fabian/.gradle/caches/jars-3/5c3c987e568a7e2d3123b7ee57cbfba4/gradle-3.0.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.jetbrains.kotlin/kotlin-gradle-plugin/1.1.60/dc7acce581312f418c1ad55932ab770da61e205d/kotlin-gradle-plugin-1.1.60.jar
:file:/Users/fabian/.gradle/caches/jars-3/fe69a7a42fede0fe8676722d0d7cf970/gradle-core-3.0.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.jetbrains.kotlin/kotlin-gradle-plugin-api/1.1.60/97a69272b6dc47f9ca1f523859e4819a1c61cb39/kotlin-gradle-plugin-api-1.1.60.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.jetbrains.kotlin/kotlin-annotation-processing-gradle/1.1.60/8f2d3fef4c0d7ecfc85fa51744153f399cdeb3a2/kotlin-annotation-processing-gradle-1.1.60.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.jetbrains.kotlin/kotlin-android-extensions/1.1.60/3b6a750e48ac6a4ca5f0fba633385825610dce3e/kotlin-android-extensions-1.1.60.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.jetbrains.kotlin/kotlin-compiler-runner/1.1.60/d2586f88979235b4b102348c431d888bdd2cf63f/kotlin-compiler-runner-1.1.60.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.jetbrains.kotlin/kotlin-compiler-embeddable/1.1.60/e0ea7c24d46acc433ece025023868bf9ffe5e437/kotlin-compiler-embeddable-1.1.60.jar
:file:/Users/fabian/.gradle/caches/jars-3/a8f9cc8f57e57275dd7e0e4f887563b1/builder-3.0.1.jar
:file:/Users/fabian/.gradle/caches/jars-3/d25ae0a93cc8161073ed411ccf2f15f2/lint-26.0.1.jar
:file:/Users/fabian/.gradle/caches/jars-3/071188ed2a50fef0d4b8e73b6b538d10/lint-checks-26.0.1.jar
:file:/Users/fabian/.gradle/caches/jars-3/340d79f490a37a2e826af11e3f4356ec/lint-api-26.0.1.jar
:file:/Users/fabian/.gradle/caches/jars-3/15dc424ff5261869cedb4c0e5a20e245/manifest-merger-26.0.1.jar
:file:/Users/fabian/.gradle/caches/jars-3/f391b93f631315d2bdf9d377b80e5b91/sdk-common-26.0.1.jar
:file:/Users/fabian/.gradle/caches/jars-3/9f07ffbf4dbdecd6e41e9ee00501122c/sdklib-26.0.1.jar
:file:/Users/fabian/.gradle/caches/jars-3/5c35e0a9d78e5d47cd8822b1bf46921d/repository-26.0.1.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.jetbrains.kotlin/kotlin-reflect/1.1.60/af5cabae2d352850b076213f358dc2150b14a812/kotlin-reflect-1.1.60.jar
:file:/Users/fabian/.gradle/caches/modules-2/files-2.1/org.jetbrains.kotlin/kotlin-stdlib/1.1.60/ac63d0e86e690fe4eded7f1f8998996c28499989/kotlin-stdlib-1.1.60.jar
:file:/Users/fabian/.gradle/caches/jars-3/316e5431a2b687ac56c7f6dbcc1c9494/uast-26.0.1.jar
:file:/Users/fabian/.gradle/caches/jars-3/a639f12d6f35274aeb5b84917d018543/gradle-api-3.0.1.jar
:file:/Users/fabian/.gradle/caches/jars-3/5a815f3f93ee3ea5fddb0b336108fdb3/compilerCommon-3.0.1.jar
:file:/Users/fabian/.gradle/caches/jars-3/985172a195bdfbab4cdfffc88b22ac93/transform-api-2.0.0-deprecated-use-gradle-api.jar
:file:/Users/fabian/.gradle/caches/jars-3/0c311c56cf8ab286a5dc313445596433/asm-analysis-5.1.jar
:file:/Users/fabian/.gradle/caches/jars-3/08cdd41fe1f26baeb39b42fea9560740/asm-commons-5.1.jar
:file:/Users/fabian/.gradle/caches/jars-3/01be4c5f22346cb9b30cf8da870a55d5/asm-util-5.1.jar
:file:/Users/fabian/.gradle/caches/jars-3/bc49c094a2443fb7fadba7269dffb02a/asm-tree-5.1.jar
:file:/Users/fabian/.gradle/caches/jars-3/0ede7333fe09a80fbc4fe1a0c9b586cd/asm-5.1.jar
:file:/Users/fabian/.gradle/caches/jars-3/6a74a1be83056603e80b6cb9e0149ecc/org.jacoco.report-0.7.4.201502262128.jar
:file:/Users/fabian/.gradle/caches/jars-3/ca06f182421af2dc08b18e644cc5b319/org.jacoco.core-0.7.4.201502262128.jar
:file:/Users/fabian/.gradle/caches/jars-3/c93e74da8ceb3a75ff5456599f439b40/jopt-simple-4.9.jar
:file:/Users/fabian/.gradle/caches/jars-3/aef91c30517375c16ce5441e84be0f5e/proguard-gradle-5.3.3.jar
:file:/Users/fabian/.gradle/caches/jars-3/c3b9ad2921cb4003eeaddbb23f1bfb23/tracker-26.0.1.jar
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