{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":558466703,"defaultBranch":"main","name":"genome_skimming_LAB","ownerLogin":"trippster08","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2022-10-27T15:49:28.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/20462653?v=4","public":true,"private":false,"isOrgOwned":false},"refInfo":{"name":"","listCacheKey":"v0:1712920932.0","currentOid":""},"activityList":{"items":[{"before":"1397f1948b37b5d4ce13226c2da2efe95456df4c","after":"1348d0efeffa4a8f9c8e1c98164a1d9bca248195","ref":"refs/heads/main","pushedAt":"2024-09-20T15:10:45.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"increased memory requested","shortMessageHtmlLink":"increased memory requested"}},{"before":"c8046364b81a9920fc45569dd062104f3f051513","after":"1397f1948b37b5d4ce13226c2da2efe95456df4c","ref":"refs/heads/main","pushedAt":"2024-09-19T18:55:36.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"edited information about raw read formatting","shortMessageHtmlLink":"edited information about raw read formatting"}},{"before":"cdde52aef4fd541cce445c2c82952c954d5330bf","after":"c8046364b81a9920fc45569dd062104f3f051513","ref":"refs/heads/main","pushedAt":"2024-09-19T15:18:31.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"removed line breaks from spades contigs fasta\n\nSPAdes assembly contig fastas have line breaks, which isn't always useful for downstream analyses, so I've changed from copying and renaming the contigs.fasta files to copying, renaming, and de-linebreaking the contigs.fasta files","shortMessageHtmlLink":"removed line breaks from spades contigs fasta"}},{"before":"4baf1bc88efbfcad20fdb0aaaa9a7b6d5ace9f21","after":"cdde52aef4fd541cce445c2c82952c954d5330bf","ref":"refs/heads/main","pushedAt":"2024-09-19T15:09:21.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"Updated using awk instead of grep\n\nawk searches faster, so I have updated this script","shortMessageHtmlLink":"Updated using awk instead of grep"}},{"before":"9641abeeda9cc13cc36917c47a0db9af0f32c0cf","after":"4baf1bc88efbfcad20fdb0aaaa9a7b6d5ace9f21","ref":"refs/heads/main","pushedAt":"2024-09-19T15:07:30.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"Don't need this anymore\n\nI have incorporated this into spades_loop.job, so I don't need this separate script","shortMessageHtmlLink":"Don't need this anymore"}},{"before":"328fd4675fe5cd8a23e8029f632bd609ceced6e6","after":"9641abeeda9cc13cc36917c47a0db9af0f32c0cf","ref":"refs/heads/main","pushedAt":"2024-09-13T18:08:44.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"added new sh and job for checking spades contigs for circularity\n\nI've added a new shell script and job file for checking circularity in spades contigs. It takes all contigs from a fasta file and searches to see if the first 50 bp of a sequence can be found anywhere in the last 200 bp of that sequence, and outputs all sequences in which this is true into a new fasta file","shortMessageHtmlLink":"added new sh and job for checking spades contigs for circularity"}},{"before":"a506dc75a8add00743e2a1e1c955854689424365","after":"328fd4675fe5cd8a23e8029f632bd609ceced6e6","ref":"refs/heads/main","pushedAt":"2024-09-13T12:36:36.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"added short sleep between each job submission","shortMessageHtmlLink":"added short sleep between each job submission"}},{"before":"cff72988a8104a374bddc91c050c016be399b533","after":"a506dc75a8add00743e2a1e1c955854689424365","ref":"refs/heads/main","pushedAt":"2024-07-23T14:32:58.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"forgot to make this results directory","shortMessageHtmlLink":"forgot to make this results directory"}},{"before":"aacd9b86d48452d0ea2339ff8721ee55f71d9cf4","after":"cff72988a8104a374bddc91c050c016be399b533","ref":"refs/heads/main","pushedAt":"2024-07-11T15:33:08.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"replaced trimmed_sequences with trimmed_reads","shortMessageHtmlLink":"replaced trimmed_sequences with trimmed_reads"}},{"before":"bbb8c5bc4c15cd850b350b3c8c0d65de535c75ca","after":"aacd9b86d48452d0ea2339ff8721ee55f71d9cf4","ref":"refs/heads/main","pushedAt":"2024-07-11T15:30:37.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"replaced \"seqences\" wth \"reads\" for trimmed directories","shortMessageHtmlLink":"replaced \"seqences\" wth \"reads\" for trimmed directories"}},{"before":"e802b13617ef601dde843f051dde51c68da93fc3","after":"bbb8c5bc4c15cd850b350b3c8c0d65de535c75ca","ref":"refs/heads/main","pushedAt":"2024-06-28T20:08:56.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"clarified and expanded description of scripts","shortMessageHtmlLink":"clarified and expanded description of scripts"}},{"before":"1386935ccf76414a62d6f6adaf94461541ed9809","after":"e802b13617ef601dde843f051dde51c68da93fc3","ref":"refs/heads/main","pushedAt":"2024-06-18T12:41:50.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"updated description of script","shortMessageHtmlLink":"updated description of script"}},{"before":"134a3aabee371bad4941608836d50f94f7ec157a","after":"1386935ccf76414a62d6f6adaf94461541ed9809","ref":"refs/heads/main","pushedAt":"2024-06-14T19:39:25.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"add 0.1 second sleep to loop; formatted\n\nI added a 0.1 second sleep to the loop to delay between job submissions. Our qmaster (qsub controller) doesn't work right with Hydra7, and can only allow 20 job submissions per second, so this should allow all jobs to be submitted.\nI also made the format more consistent regarding spacing and indenting","shortMessageHtmlLink":"add 0.1 second sleep to loop; formatted"}},{"before":"b281459c92b10b8051c7303aee2b1b9cea99f258","after":"134a3aabee371bad4941608836d50f94f7ec157a","ref":"refs/heads/main","pushedAt":"2024-05-29T21:40:49.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"removed incomplete sentence and spades reference","shortMessageHtmlLink":"removed incomplete sentence and spades reference"}},{"before":"75543b7e00553062995b68af87cc23560b200f8e","after":"b281459c92b10b8051c7303aee2b1b9cea99f258","ref":"refs/heads/main","pushedAt":"2024-05-28T17:42:27.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"fixed path to fastp module","shortMessageHtmlLink":"fixed path to fastp module"}},{"before":"d1125cda5559111d752266a5a4b6b0a652f9f671","after":"75543b7e00553062995b68af87cc23560b200f8e","ref":"refs/heads/main","pushedAt":"2024-05-22T13:45:43.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"removed max memory","shortMessageHtmlLink":"removed max memory"}},{"before":"dad674e8c70f1be1e1255decabf88b968e521040","after":"d1125cda5559111d752266a5a4b6b0a652f9f671","ref":"refs/heads/main","pushedAt":"2024-05-17T20:01:56.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"Fixed path names","shortMessageHtmlLink":"Fixed path names"}},{"before":"b6958dddd23710a73e83cb45f2528b45bb19655d","after":"dad674e8c70f1be1e1255decabf88b968e521040","ref":"refs/heads/main","pushedAt":"2024-05-17T13:54:07.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"changed threads requested","shortMessageHtmlLink":"changed threads requested"}},{"before":"1755107cdb7a68d2c8a5fbdc2d45743759d53c6c","after":"b6958dddd23710a73e83cb45f2528b45bb19655d","ref":"refs/heads/main","pushedAt":"2024-05-17T13:50:46.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"increased memory requested","shortMessageHtmlLink":"increased memory requested"}},{"before":"16b5650f6c0d0d336f2bc843a2b64545152e5845","after":"1755107cdb7a68d2c8a5fbdc2d45743759d53c6c","ref":"refs/heads/main","pushedAt":"2024-05-17T13:48:39.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"changed command for name variable","shortMessageHtmlLink":"changed command for name variable"}},{"before":"9064e1243a119ac2926d5018af26af2bd6faf921","after":"16b5650f6c0d0d336f2bc843a2b64545152e5845","ref":"refs/heads/main","pushedAt":"2024-05-16T15:52:56.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"increase vmem requested","shortMessageHtmlLink":"increase vmem requested"}},{"before":"ec5771fb9f1a0f9af4a009b9ee8538950b7584c1","after":"9064e1243a119ac2926d5018af26af2bd6faf921","ref":"refs/heads/main","pushedAt":"2024-05-15T21:34:07.000Z","pushType":"push","commitsCount":10,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"removed jobs","shortMessageHtmlLink":"removed jobs"}},{"before":"e74a3843c58e0c4bc5876932be173316639c5fb9","after":"ec5771fb9f1a0f9af4a009b9ee8538950b7584c1","ref":"refs/heads/main","pushedAt":"2024-05-14T13:24:51.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"moved spades-related files","shortMessageHtmlLink":"moved spades-related files"}},{"before":"248f8dc2dec2cdd9d30e8f0053adc3a1d9091d28","after":"e74a3843c58e0c4bc5876932be173316639c5fb9","ref":"refs/heads/main","pushedAt":"2024-05-14T12:38:47.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"Change memory, results copying\n\nI increased the memory because the new version of Mitofinder uses java, which uses more memory. I also changed where the results are saved, and also copied the log into the results directory","shortMessageHtmlLink":"Change memory, results copying"}},{"before":"bed7b2f2648f1cf6641d6a5e748a476a290a9487","after":"248f8dc2dec2cdd9d30e8f0053adc3a1d9091d28","ref":"refs/heads/main","pushedAt":"2024-05-13T18:55:54.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"changed env and added copy logs step","shortMessageHtmlLink":"changed env and added copy logs step"}},{"before":"1c97ee366882e0786ab516702f141bad9df5c669","after":"bed7b2f2648f1cf6641d6a5e748a476a290a9487","ref":"refs/heads/main","pushedAt":"2024-05-09T15:05:26.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"started multiparameters job and shell","shortMessageHtmlLink":"started multiparameters job and shell"}},{"before":"3f2cdd3c322ba2ac669444d7ec0520d5fe5dbcfc","after":"1c97ee366882e0786ab516702f141bad9df5c669","ref":"refs/heads/main","pushedAt":"2024-05-08T16:29:50.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"created getorganellee_plus sh and job\n\ncreated a new job and shell script for getorganelle. If getorganelle sucessfully finds a complete mitogenome, it will then create a read coverage graph","shortMessageHtmlLink":"created getorganellee_plus sh and job"}},{"before":"b5cf8741d42896372325207e16e5a80504ca2f03","after":"3f2cdd3c322ba2ac669444d7ec0520d5fe5dbcfc","ref":"refs/heads/main","pushedAt":"2024-05-07T22:37:20.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"added organelle to getorganelle","shortMessageHtmlLink":"added organelle to getorganelle"}},{"before":"3f812e720649c04e4c26067043fe3436ef218a59","after":"b5cf8741d42896372325207e16e5a80504ca2f03","ref":"refs/heads/main","pushedAt":"2024-05-07T22:36:44.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"removed period from code","shortMessageHtmlLink":"removed period from code"}},{"before":"a1f7a8d86e68c73814cfbd9f1be526cb369fb464","after":"3f812e720649c04e4c26067043fe3436ef218a59","ref":"refs/heads/main","pushedAt":"2024-05-07T22:36:15.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trippster08","name":"Tripp Macdonald","path":"/trippster08","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20462653?s=80&v=4"},"commit":{"message":"expanded getorganelle description","shortMessageHtmlLink":"expanded getorganelle description"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"startCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wOS0yMFQxNToxMDo0NS4wMDAwMDBazwAAAAS8GccQ","endCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wNS0wN1QyMjozNjoxNS4wMDAwMDBazwAAAAREDq97"}},"title":"Activity ยท trippster08/genome_skimming_LAB"}