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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,61 @@ | ||
| collect_scatter (scatter_collect_no_array_frag_stage-0:collect) (done) job-Ggy7Y1j0yzZbZbq0k2k4B24G | ||
| rnathans 2024-03-21 19:16:39 (runtime 0:00:36) | ||
| 2024-03-21 19:18:46 collect_scatter INFO Logging initialized (priority) | ||
| 2024-03-21 19:18:46 collect_scatter INFO Logging initialized (bulk) | ||
| 2024-03-21 19:18:50 collect_scatter INFO Skipping dependency scatter_task because it is inactive in stage (function) collect | ||
| 2024-03-21 19:18:50 collect_scatter INFO Downloading bundled file dxWDLrt.tar.gz | ||
| 2024-03-21 19:18:53 collect_scatter STDOUT >>> Unpacking dxWDLrt.tar.gz to / | ||
| 2024-03-21 19:18:53 collect_scatter STDERR tar: Removing leading `/' from member names | ||
| 2024-03-21 19:19:00 collect_scatter INFO Setting SSH public key | ||
| 2024-03-21 19:19:05 collect_scatter STDOUT dxpy/0.371.0 (Linux-5.15.0-1055-aws-x86_64-with-glibc2.29) Python/3.8.10 | ||
| 2024-03-21 19:19:05 collect_scatter STDOUT bash running (job ID job-Ggy7Y1j0yzZbZbq0k2k4B24G) | ||
| 2024-03-21 19:19:05 collect_scatter STDOUT Skipping bash variables for dxCompiler | ||
| 2024-03-21 19:19:06 collect_scatter STDERR Creating JobMeta: rootDir /home/dnanexus, waitOnUpload: false | ||
| 2024-03-21 19:19:06 collect_scatter STDERR Creating WorkflowExecutor: separateOutputs false, waitOnUpload false | ||
| 2024-03-21 19:19:07 collect_scatter STDERR Creating FileSourceResolver localDirectories = /home/dnanexus/work | ||
| 2024-03-21 19:19:07 collect_scatter STDERR Discovering all files in the input values | ||
| 2024-03-21 19:19:07 collect_scatter STDERR Loading raw JSON input from /home/dnanexus/job_input.json | ||
| 2024-03-21 19:19:07 collect_scatter STDERR Raw inputs: | ||
| 2024-03-21 19:19:07 collect_scatter STDERR { | ||
| 2024-03-21 19:19:07 collect_scatter STDERR "input_string": "ooooooooooooo", | ||
| 2024-03-21 19:19:07 collect_scatter STDERR "n": 3 | ||
| 2024-03-21 19:19:07 collect_scatter STDERR } | ||
| 2024-03-21 19:19:07 collect_scatter STDERR No overrides | ||
| 2024-03-21 19:19:07 collect_scatter STDERR dxCompiler version: 2.11.6-SNAPSHOT | ||
| 2024-03-21 19:19:07 collect_scatter STDERR Executable links: Map(scatter_task -> ExecutableLink(scatter_task,Map(index -> TInt, input_string -> TString),Map(out -> TFile),DxApplet(applet-Ggy7VK00yzZvGxy45yJjvkvq,None))) | ||
| 2024-03-21 19:19:07 collect_scatter STDERR Environment: Map(input_string -> (TString,VString(ooooooooooooo)), n -> (TInt,VInt(3))) | ||
| 2024-03-21 19:19:07 collect_scatter STDERR Block Vector(0) to execute: | ||
| 2024-03-21 19:19:07 collect_scatter STDERR Block(0, ScatterOneCall) | ||
| 2024-03-21 19:19:07 collect_scatter STDERR Inputs: Vector(Int n, String input_string, Int i) | ||
| 2024-03-21 19:19:07 collect_scatter STDERR Outputs: Vector(Array[File] scatter_task.out) | ||
| 2024-03-21 19:19:07 collect_scatter STDERR Body: | ||
| 2024-03-21 19:19:07 collect_scatter STDERR scatter (i in range(n)) { | ||
| 2024-03-21 19:19:07 collect_scatter STDERR call scatter_task { input: input_string = input_string,index = i } | ||
| 2024-03-21 19:19:07 collect_scatter STDERR } | ||
| 2024-03-21 19:19:07 collect_scatter STDERR | ||
| 2024-03-21 19:19:07 collect_scatter STDERR Env: | ||
| 2024-03-21 19:19:07 collect_scatter STDERR input_string: String ooooooooooooo | ||
| 2024-03-21 19:19:07 collect_scatter STDERR n: Int 3 | ||
| 2024-03-21 19:19:07 collect_scatter STDERR | ||
| 2024-03-21 19:19:07 collect_scatter STDERR | ||
| 2024-03-21 19:19:07 collect_scatter STDERR Scatter job results: | ||
| 2024-03-21 19:19:07 collect_scatter STDERR Some(ScatterExecution(scatter_task,0,Map(out -> {"$dnanexus_link":"file-Ggy7YG00xKVxf87XQ92QjPp8"}),DxJob(job-Ggy7Y1Q0yzZXx63xzfj6227j,None))) | ||
| 2024-03-21 19:19:07 collect_scatter STDERR Some(ScatterExecution(scatter_task,1,Map(out -> {"$dnanexus_link":"file-Ggy7YVj06fk8jPYfYvVJZ5QF"}),DxJob(job-Ggy7Y1Q0yzZx9VKz79KxQj3G,None))) | ||
| 2024-03-21 19:19:07 collect_scatter STDERR Some(ScatterExecution(scatter_task,2,Map(out -> {"$dnanexus_link":"file-Ggy7YpQ0y5b2qj8Y5xVX3bP6"}),DxJob(job-Ggy7Y1Q0yzZqV9PY9Y4q3pFg,None))) | ||
| 2024-03-21 19:19:07 collect_scatter STDERR ============= flatOuts ============= Vector(DxFile(file-Ggy7YG00xKVxf87XQ92QjPp8,None), DxFile(file-Ggy7YVj06fk8jPYfYvVJZ5QF,None), DxFile(file-Ggy7YpQ0y5b2qj8Y5xVX3bP6,None)) | ||
| 2024-03-21 19:19:08 collect_scatter STDERR Bulk describing 3 unique file ids | ||
| 2024-03-21 19:19:08 collect_scatter STDERR Successfully bulk described 3 files | ||
| 2024-03-21 19:19:08 collect_scatter STDERR Scatter outputs: | ||
| 2024-03-21 19:19:08 collect_scatter STDERR scatter_task.out -> (TArray(TFile,false),VArray(Vector(VFile(dx://file-Ggy7YG00xKVxf87XQ92QjPp8::/no_array_result_0.txt,None,None,None,None,Vector(),None,None), VFile(dx://file-Ggy7YVj06fk8jPYfYvVJZ5QF::/no_array_result_1.txt,None,None,None,None,Vector(),None,None), VFile(dx://file-Ggy7YpQ0y5b2qj8Y5xVX3bP6::/no_array_result_2.txt,None,None,None,None,Vector(),None,None)))) | ||
| 2024-03-21 19:19:08 collect_scatter STDERR prepareBlockOutputs | ||
| 2024-03-21 19:19:08 collect_scatter STDERR env = Set(input_string, n) | ||
| 2024-03-21 19:19:08 collect_scatter STDERR fragResults = Set(scatter_task.out) | ||
| 2024-03-21 19:19:08 collect_scatter STDERR exportedVars = Set(scatter_task.out) | ||
| 2024-03-21 19:19:08 collect_scatter STDERR | ||
| 2024-03-21 19:19:08 collect_scatter STDERR outputLinks: | ||
| 2024-03-21 19:19:08 collect_scatter STDERR scatter_task.out -> ParameterLinkValue([{"$dnanexus_link":"file-Ggy7YG00xKVxf87XQ92QjPp8"},{"$dnanexus_link":"file-Ggy7YVj06fk8jPYfYvVJZ5QF"},{"$dnanexus_link":"file-Ggy7YpQ0y5b2qj8Y5xVX3bP6"}],TArray(TFile,false)) | ||
| 2024-03-21 19:19:08 collect_scatter STDOUT success Collect | ||
| collect_scatter (scatter_collect_no_array_frag_stage-0:collect) (done) job-Ggy7Y1j0yzZbZbq0k2k4B24G | ||
| rnathans 2024-03-21 19:16:39 (runtime 0:00:36) | ||
| Output: scatter_task___out = [ file-Ggy7YG00xKVxf87XQ92QjPp8, | ||
| file-Ggy7YVj06fk8jPYfYvVJZ5QF, file-Ggy7YpQ0y5b2qj8Y5xVX3bP6 ] |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,64 @@ | ||
| collect_scatter (scatter_collect_no_glob_frag_stage-0:collect) (done) job-Ggy7ggj0yzZvg185B7PK0x2y | ||
| rnathans 2024-03-21 19:26:39 (runtime 0:00:36) | ||
| 2024-03-21 19:28:46 collect_scatter INFO Logging initialized (priority) | ||
| 2024-03-21 19:28:46 collect_scatter INFO Logging initialized (bulk) | ||
| 2024-03-21 19:28:50 collect_scatter INFO Skipping dependency scatter_task because it is inactive in stage (function) collect | ||
| 2024-03-21 19:28:50 collect_scatter INFO Downloading bundled file dxWDLrt.tar.gz | ||
| 2024-03-21 19:28:53 collect_scatter STDOUT >>> Unpacking dxWDLrt.tar.gz to / | ||
| 2024-03-21 19:28:53 collect_scatter STDERR tar: Removing leading `/' from member names | ||
| 2024-03-21 19:29:01 collect_scatter INFO Setting SSH public key | ||
| 2024-03-21 19:29:05 collect_scatter STDOUT dxpy/0.371.0 (Linux-5.15.0-1055-aws-x86_64-with-glibc2.29) Python/3.8.10 | ||
| 2024-03-21 19:29:06 collect_scatter STDOUT bash running (job ID job-Ggy7ggj0yzZvg185B7PK0x2y) | ||
| 2024-03-21 19:29:06 collect_scatter STDOUT Skipping bash variables for dxCompiler | ||
| 2024-03-21 19:29:06 collect_scatter STDERR Creating JobMeta: rootDir /home/dnanexus, waitOnUpload: false | ||
| 2024-03-21 19:29:06 collect_scatter STDERR Creating WorkflowExecutor: separateOutputs false, waitOnUpload false | ||
| 2024-03-21 19:29:07 collect_scatter STDERR Creating FileSourceResolver localDirectories = /home/dnanexus/work | ||
| 2024-03-21 19:29:07 collect_scatter STDERR Discovering all files in the input values | ||
| 2024-03-21 19:29:07 collect_scatter STDERR Loading raw JSON input from /home/dnanexus/job_input.json | ||
| 2024-03-21 19:29:07 collect_scatter STDERR Raw inputs: | ||
| 2024-03-21 19:29:07 collect_scatter STDERR { | ||
| 2024-03-21 19:29:07 collect_scatter STDERR "input_string": "sssssssssss", | ||
| 2024-03-21 19:29:07 collect_scatter STDERR "n": 3 | ||
| 2024-03-21 19:29:07 collect_scatter STDERR } | ||
| 2024-03-21 19:29:07 collect_scatter STDERR No overrides | ||
| 2024-03-21 19:29:07 collect_scatter STDERR dxCompiler version: 2.11.6-SNAPSHOT | ||
| 2024-03-21 19:29:07 collect_scatter STDERR Executable links: Map(scatter_task -> ExecutableLink(scatter_task,Map(index -> TInt, input_string -> TString),Map(out -> TArray(TFile,false)),DxApplet(applet-Ggy7bzQ0yzZqYzXy72PF38g1,None))) | ||
| 2024-03-21 19:29:07 collect_scatter STDERR Environment: Map(input_string -> (TString,VString(sssssssssss)), n -> (TInt,VInt(3))) | ||
| 2024-03-21 19:29:08 collect_scatter STDERR Block Vector(0) to execute: | ||
| 2024-03-21 19:29:08 collect_scatter STDERR Block(0, ScatterOneCall) | ||
| 2024-03-21 19:29:08 collect_scatter STDERR Inputs: Vector(Int n, String input_string, Int i) | ||
| 2024-03-21 19:29:08 collect_scatter STDERR Outputs: Vector(Array[Array[File]] scatter_task.out) | ||
| 2024-03-21 19:29:08 collect_scatter STDERR Body: | ||
| 2024-03-21 19:29:08 collect_scatter STDERR scatter (i in range(n)) { | ||
| 2024-03-21 19:29:08 collect_scatter STDERR call scatter_task { input: input_string = input_string,index = i } | ||
| 2024-03-21 19:29:08 collect_scatter STDERR } | ||
| 2024-03-21 19:29:08 collect_scatter STDERR | ||
| 2024-03-21 19:29:08 collect_scatter STDERR Env: | ||
| 2024-03-21 19:29:08 collect_scatter STDERR input_string: String sssssssssss | ||
| 2024-03-21 19:29:08 collect_scatter STDERR n: Int 3 | ||
| 2024-03-21 19:29:08 collect_scatter STDERR | ||
| 2024-03-21 19:29:08 collect_scatter STDERR | ||
| 2024-03-21 19:29:08 collect_scatter STDERR Scatter job results: | ||
| 2024-03-21 19:29:08 collect_scatter STDERR Some(ScatterExecution(scatter_task,0,Map(out -> [{"$dnanexus_link":"file-Ggy7j2001qgx5jQjy1bYBK7J"}]),DxJob(job-Ggy7ggQ0yzZqVYY8BqxQK3VV,None))) | ||
| 2024-03-21 19:29:08 collect_scatter STDERR Some(ScatterExecution(scatter_task,1,Map(out -> [{"$dnanexus_link":"file-Ggy7j700V2JFV9PY9Y4q3pG2"}]),DxJob(job-Ggy7ggQ0yzZjjPYfYvVJZ5QQ,None))) | ||
| 2024-03-21 19:29:08 collect_scatter STDERR Some(ScatterExecution(scatter_task,2,Map(out -> [{"$dnanexus_link":"file-Ggy7jQ80XVgZk6Q7ykG58268"}]),DxJob(job-Ggy7ggQ0yzZXx63xzfj6227y,None))) | ||
| 2024-03-21 19:29:08 collect_scatter STDERR ============= flatOuts ============= Vector(DxFile(file-Ggy7j2001qgx5jQjy1bYBK7J,None), DxFile(file-Ggy7j700V2JFV9PY9Y4q3pG2,None), DxFile(file-Ggy7jQ80XVgZk6Q7ykG58268,None)) | ||
| 2024-03-21 19:29:08 collect_scatter STDERR Bulk describing 3 unique file ids | ||
| 2024-03-21 19:29:08 collect_scatter STDERR Successfully bulk described 3 files | ||
| 2024-03-21 19:29:08 collect_scatter STDERR Scatter outputs: | ||
| 2024-03-21 19:29:08 collect_scatter STDERR scatter_task.out -> (TArray(TArray(TFile,false),false),VArray(Vector(VArray(Vector(VFile(dx://file-Ggy7j2001qgx5jQjy1bYBK7J::/no_glob_result_0.txt,None,None,None,None,Vector(),None,None))), VArray(Vector(VFile(dx://file-Ggy7j700V2JFV9PY9Y4q3pG2::/no_glob_result_1.txt,None,None,None,None,Vector(),None,None))), VArray(Vector(VFile(dx://file-Ggy7jQ80XVgZk6Q7ykG58268::/no_glob_result_2.txt,None,None,None,None,Vector(),None,None)))))) | ||
| 2024-03-21 19:29:08 collect_scatter STDERR prepareBlockOutputs | ||
| 2024-03-21 19:29:08 collect_scatter STDERR env = Set(input_string, n) | ||
| 2024-03-21 19:29:08 collect_scatter STDERR fragResults = Set(scatter_task.out) | ||
| 2024-03-21 19:29:08 collect_scatter STDERR exportedVars = Set(scatter_task.out) | ||
| 2024-03-21 19:29:08 collect_scatter STDERR | ||
| 2024-03-21 19:29:08 collect_scatter STDERR outputLinks: | ||
| 2024-03-21 19:29:08 collect_scatter STDERR scatter_task.out -> ParameterLinkValue([[{"$dnanexus_link":"file-Ggy7j2001qgx5jQjy1bYBK7J"}],[{"$dnanexus_link":"file-Ggy7j700V2JFV9PY9Y4q3pG2"}],[{"$dnanexus_link":"file-Ggy7jQ80XVgZk6Q7ykG58268"}]],TArray(TArray(TFile,false),false)) | ||
| 2024-03-21 19:29:08 collect_scatter STDOUT success Collect | ||
| collect_scatter (scatter_collect_no_glob_frag_stage-0:collect) (done) job-Ggy7ggj0yzZvg185B7PK0x2y | ||
| rnathans 2024-03-21 19:26:39 (runtime 0:00:36) | ||
| Output: scatter_task___out = { ___: [ [ file-Ggy7j2001qgx5jQjy1bYBK7J ], [ | ||
| file-Ggy7j700V2JFV9PY9Y4q3pG2 ], [ file-Ggy7jQ80XVgZk6Q7ykG58268 ] ] | ||
| } | ||
| scatter_task___out___dxfiles = [ file-Ggy7j2001qgx5jQjy1bYBK7J, | ||
| file-Ggy7j700V2JFV9PY9Y4q3pG2, file-Ggy7jQ80XVgZk6Q7ykG58268 ] |
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