tool_test_output.json

{"tests": [{"data": {"status": "failure", "tool_id": "barcode_splitter", "time_seconds": 38.440266132354736, "inputs": {"runinterface|seqfiles_0|nameinterface|readtype": "single", "runinterface|seqfiles_1|nameinterface|readtype": "singleindex", "runinterface|seqfiles_1|nameinterface|readname": "read2", "barcodes_at_end": false, "runinterface|seqfiles_0|input": {"src": "hda", "id": "5729865256bc2525"}, "runinterface|seqfiles_0|nameinterface|readname": "read1", "bcfile": {"src": "hda", "id": "2891970512fa2d5a"}, "runinterface|seqfiles_1|input": {"src": "hda", "id": "54f2a3a23292eb07"}, "runinterface|seqfiles_2|input": {"src": "hda", "id": "8155e4b4bf1581ff"}, "mismatches": "2", "runinterface|run_type": "flexible", "split_all": true, "runinterface|seqfiles_2|nameinterface|readname": "index2", "runinterface|seqfiles_2|nameinterface|readtype": "index"}, "tool_version": "0.18.4.0", "output_problems": [""], "job": {"inputs": {"runinterface|seqfiles_2|input": {"src": "hda", "id": "8155e4b4bf1581ff", "uuid": "0e1a53f5-451d-4b22-b925-b4f4f9f20656"}, "bcfile": {"src": "hda", "id": "2891970512fa2d5a", "uuid": "ac543d2d-2bcb-4ec2-a4d4-4bf20ae6afdc"}, "runinterface|seqfiles_0|input": {"src": "hda", "id": "5729865256bc2525", "uuid": "75791d34-d2f7-4c0e-8ac5-f055401c7c03"}, "runinterface|seqfiles_1|input": {"src": "hda", "id": "54f2a3a23292eb07", "uuid": "cb9af93a-3134-48c2-9d09-b987af0b0e9f"}}, "update_time": "2019-03-13T14:47:18.926613", "tool_id": "barcode_splitter", "outputs": {"__new_primary_file_split_output_multi|multimatched read2__": {"src": "hda", "id": "440a6c2b5d9efe20", "uuid": "029dc3a7-984d-45b1-895c-11b2ca4475d3"}, "__new_primary_file_index_only|BC4 index2__": {"src": "hda", "id": "c18708cec3343c17", "uuid": "f211899c-d2f0-4b97-b0d9-5d38ecdc336b"}, "__new_primary_file_split_output_multi|BC2 read1__": {"src": "hda", "id": "a90a30fafe298e1e", "uuid": "f2a98286-bb65-47c8-93e7-6557e98ada20"}, "__new_primary_file_split_output_multi|BC4 read2__": {"src": "hda", "id": "b54fb481e575bccc", "uuid": "d163ea0f-fd14-4f7c-96dc-9fa3da3e8a73"}, "__new_primary_file_split_output_multi|BC3 read2__": {"src": "hda", "id": "9ce08b2254e4d5ed", "uuid": "dcf190af-295b-420e-be37-3095fe8dd2e8"}, "__new_primary_file_split_output_multi|BC1 read2__": {"src": "hda", "id": "683bc220e21425bb", "uuid": "7e4a2a92-df5d-4802-a83b-40a852253872"}, "__new_primary_file_index_only|unmatched index2__": {"src": "hda", "id": "3e4e8de146a035f5", "uuid": "129c0998-bf23-4c9e-aaf9-f8e701b4badb"}, "__new_primary_file_index_only|BC3 index2__": {"src": "hda", "id": "b28067233c6d9fa0", "uuid": "74c85471-f058-4433-b942-2e1ddb5d4d3f"}, "__new_primary_file_split_output_multi|BC2 read2__": {"src": "hda", "id": "b842d972534ccb3e", "uuid": "5a13027a-f5b5-4da4-9f18-172211881ef8"}, "summary": {"src": "hda", "id": "7b55dbb89df8f4e5", "uuid": "92f8ee63-a198-4a52-a36a-603c0f4418bc"}, "__new_primary_file_split_output_multi|unmatched read1__": {"src": "hda", "id": "ea0b941dfbe636f8", "uuid": "8216b581-f729-46f0-8b31-ecdde64211f7"}, "__new_primary_file_split_output_multi|BC4 read1__": {"src": "hda", "id": "80b8022ff3f677b7", "uuid": "bdb597c2-59ee-4972-a0be-f6505aa3abe7"}, "__new_primary_file_split_output_multi|BC1 read1__": {"src": "hda", "id": "fa6d20d0fb68383f", "uuid": "9d1b601f-10ed-4f43-98c1-9edfb674e205"}, "__new_primary_file_index_only|BC2 index2__": {"src": "hda", "id": "d5b3e51b7b790121", "uuid": "6bf28195-5d42-47bb-ba2b-5a0a3e45f3f1"}, "__new_primary_file_index_only|multimatched index2__": {"src": "hda", "id": "5ca39fba41b940d1", "uuid": "9e9a7f06-9911-433c-ab7c-ad58c0c5393d"}, "__new_primary_file_index_only|BC1 index2__": {"src": "hda", "id": "61f03d5eef6f1538", "uuid": "7c4e4a6d-8a22-417f-b280-c9469c97c63b"}, "__new_primary_file_split_output_multi|BC3 read1__": {"src": "hda", "id": "5449172d6ff5669b", "uuid": "02878c13-38e9-4945-96ed-1f4f75421651"}, "__new_primary_file_split_output_multi|unmatched read2__": {"src": "hda", "id": "27ee89e2e3d631e0", "uuid": "d7468596-0833-45aa-8e03-4e12aa9d8465"}, "__new_primary_file_split_output_multi|multimatched read1__": {"src": "hda", "id": "1ae74d26531588b0", "uuid": "5ca4e883-a8bc-442e-b997-83d2268dc652"}}, "stdout": "total 120\ndrwxr-xr-x  20 rleach  staff   640B Mar 13 10:47 ./\ndrwxr-xr-x   4 rleach  staff   128B Mar 13 10:47 ../\n-rw-r--r--   1 rleach  staff   360B Mar 13 10:47 BC1 index2 index 0.fastq\n-rw-r--r--   1 rleach  staff   480B Mar 13 10:47 BC1 read1 single 0.fastq\n-rw-r--r--   1 rleach  staff   360B Mar 13 10:47 BC1 read2 single 0.fastq\n-rw-r--r--   1 rleach  staff   864B Mar 13 10:47 BC2 index2 index 0.fastq\n-rw-r--r--   1 rleach  staff   1.1K Mar 13 10:47 BC2 read1 single 0.fastq\n-rw-r--r--   1 rleach  staff   864B Mar 13 10:47 BC2 read2 single 0.fastq\n-rw-r--r--   1 rleach  staff   648B Mar 13 10:47 BC3 index2 index 0.fastq\n-rw-r--r--   1 rleach  staff   864B Mar 13 10:47 BC3 read1 single 0.fastq\n-rw-r--r--   1 rleach  staff   648B Mar 13 10:47 BC3 read2 single 0.fastq\n-rw-r--r--   1 rleach  staff     0B Mar 13 10:47 BC4 index2 index 0.fastq\n-rw-r--r--   1 rleach  staff     0B Mar 13 10:47 BC4 read1 single 0.fastq\n-rw-r--r--   1 rleach  staff     0B Mar 13 10:47 BC4 read2 single 0.fastq\n-rw-r--r--   1 rleach  staff   432B Mar 13 10:47 multimatched index2 index 0.fastq\n-rw-r--r--   1 rleach  staff   576B Mar 13 10:47 multimatched read1 single 0.fastq\n-rw-r--r--   1 rleach  staff   432B Mar 13 10:47 multimatched read2 single 0.fastq\n-rw-r--r--   1 rleach  staff   576B Mar 13 10:47 unmatched index2 index 0.fastq\n-rw-r--r--   1 rleach  staff   768B Mar 13 10:47 unmatched read1 single 0.fastq\n-rw-r--r--   1 rleach  staff   576B Mar 13 10:47 unmatched read2 single 0.fastq\n", "command_line": "mkdir split && barcode_splitter  --bcfile '/private/var/folders/8d/z84mms353qb2n0r3n2jhww0m0000gq/T/tmpvQzdYV/files/000/dataset_1.dat' --mismatches '2' --galaxy  --prefix 'split/'     '/private/var/folders/8d/z84mms353qb2n0r3n2jhww0m0000gq/T/tmpvQzdYV/files/000/dataset_2.dat' '/private/var/folders/8d/z84mms353qb2n0r3n2jhww0m0000gq/T/tmpvQzdYV/files/000/dataset_3.dat' '/private/var/folders/8d/z84mms353qb2n0r3n2jhww0m0000gq/T/tmpvQzdYV/files/000/dataset_4.dat'   --idxread '2' '3'   --format 'fastq' --suffix '.fastq' --split_all  > '/private/var/folders/8d/z84mms353qb2n0r3n2jhww0m0000gq/T/tmpvQzdYV/files/000/dataset_5.dat';   rc=0;      for f in split/*-read-'1'.'fastq'; do if [ -e \"$f\" ]; then mv \"$f\" \"${f/-read-1/ read1 single 0}\" || rc=$?; fi; done;    for f in split/*-read-'2'.'fastq'; do if [ -e \"$f\" ]; then mv \"$f\" \"${f/-read-2/ read2 single 0}\" || rc=$?; fi; done;    for f in split/*-read-'3'.'fastq'; do if [ -e \"$f\" ]; then mv \"$f\" \"${f/-read-3/ index2 index 0}\" || rc=$?; fi; done;   ls -halF split;  [ $rc == 0 ];", "exit_code": 0, "state": "ok", "create_time": "2019-03-13T14:47:13.079118", "params": {"mismatches": "\"2\"", "barcodes_at_end": "\"false\"", "runinterface": "{\"run_type\": \"flexible\", \"seqfiles\": [{\"__index__\": 0, \"nameinterface\": {\"readtype\": \"single\", \"readname\": \"read1\", \"__current_case__\": 0}, \"input\": {\"values\": [{\"src\": \"hda\", \"id\": 2}]}}, {\"__index__\": 1, \"nameinterface\": {\"readtype\": \"singleindex\", \"readname\": \"read2\", \"__current_case__\": 1}, \"input\": {\"values\": [{\"src\": \"hda\", \"id\": 3}]}}, {\"__index__\": 2, \"nameinterface\": {\"readtype\": \"index\", \"readname\": \"index2\", \"__current_case__\": 2}, \"input\": {\"values\": [{\"src\": \"hda\", \"id\": 4}]}}], \"__current_case__\": 2}", "dbkey": "\"?\"", "chromInfo": "\"/private/var/folders/8d/z84mms353qb2n0r3n2jhww0m0000gq/T/tmpvQzdYV/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "split_all": "\"true\""}, "stderr": "WARNING: More than one barcode matches @CSHL_3_FC042AGLLWW:1:2:7:203, moving to multimatched category\nWARNING: More than one barcode matches @CSHL_3_FC042AGLLWW:1:2:7:203, moving to multimatched category\nWARNING: More than one barcode matches @CSHL_3_FC042AGLLWW:1:2:7:203, moving to multimatched category\nWARNING: More than one barcode matches @CSHL_3_FC042AGLLWW:1:2:7:203, moving to multimatched category\nWARNING: More than one barcode matches @CSHL_3_FC042AGLLWW:1:2:7:203, moving to multimatched category\nWARNING: More than one barcode matches @CSHL_3_FC042AGLLWW:1:2:7:203, moving to multimatched category\nERROR: Index ID mismatch: @CSHL_3_FC042AGLLWW:1:2:7:203/2 does not match @CSHL_3_FC042AGLLWW:1:2:7:203/1\nERROR: Index ID mismatch: @HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 3:N:0: does not match @HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 1:N:0:\n", "job_metrics": [], "model_class": "Job", "external_id": "29493", "id": "7b55dbb89df8f4e5", "user_email": "test@bx.psu.edu"}, "problem_log": "Traceback (most recent call last):\n  File \"/usr/local/Cellar/python@2/2.7.15_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/unittest/case.py\", line 329, in run\n    testMethod()\n  File \"/private/var/folders/8d/z84mms353qb2n0r3n2jhww0m0000gq/T/tmpvQzdYV/galaxy-dev/test/functional/test_toolbox.py\", line 88, in test_tool\n    self.do_it(tool_version=tool_version, test_index=test_index)\n  File \"/private/var/folders/8d/z84mms353qb2n0r3n2jhww0m0000gq/T/tmpvQzdYV/galaxy-dev/test/functional/test_toolbox.py\", line 41, in do_it\n    verify_tool(tool_id, self.galaxy_interactor, resource_parameters=resource_parameters, test_index=test_index, tool_version=tool_version, register_job_data=register_job_data)\n  File \"/private/var/folders/8d/z84mms353qb2n0r3n2jhww0m0000gq/T/tmpvQzdYV/galaxy-dev/lib/galaxy/tools/verify/interactor.py\", line 689, in verify_tool\n    raise e\nJobOutputsError\n", "test_index": 5, "problem_type": "galaxy.tools.verify.interactor.JobOutputsError"}, "id": "functional.test_toolbox.TestForTool_barcode_splitter.test_tool_000005", "has_data": true}], "version": "0.1", "exit_code": 1, "summary": {"num_skips": 0, "num_errors": 0, "num_failures": 1, "num_tests": 1}}