{"action":"created","issue":{"url":"https://api.github.com/repos/sdparekh/zUMIs/issues/53","repository_url":"https://api.github.com/repos/sdparekh/zUMIs","labels_url":"https://api.github.com/repos/sdparekh/zUMIs/issues/53/labels{/name}","comments_url":"https://api.github.com/repos/sdparekh/zUMIs/issues/53/comments","events_url":"https://api.github.com/repos/sdparekh/zUMIs/issues/53/events","html_url":"https://github.com/sdparekh/zUMIs/issues/53","id":350371697,"node_id":"MDU6SXNzdWUzNTAzNzE2OTc=","number":53,"title":"[main_samview] truncated file","user":{"login":"MaxKman","id":30081989,"node_id":"MDQ6VXNlcjMwMDgxOTg5","avatar_url":"https://avatars1.githubusercontent.com/u/30081989?v=4","gravatar_id":"","url":"https://api.github.com/users/MaxKman","html_url":"https://github.com/MaxKman","followers_url":"https://api.github.com/users/MaxKman/followers","following_url":"https://api.github.com/users/MaxKman/following{/other_user}","gists_url":"https://api.github.com/users/MaxKman/gists{/gist_id}","starred_url":"https://api.github.com/users/MaxKman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MaxKman/subscriptions","organizations_url":"https://api.github.com/users/MaxKman/orgs","repos_url":"https://api.github.com/users/MaxKman/repos","events_url":"https://api.github.com/users/MaxKman/events{/privacy}","received_events_url":"https://api.github.com/users/MaxKman/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-08-14T10:35:45Z","updated_at":"2018-08-14T14:43:09Z","closed_at":null,"author_association":"NONE","body":"Unfortunately I ran into another issue. The zUMIs pipeline now works with the example data set but not with my own fastq file. Yaml file:\r\n[MB_new.yaml.txt](https://github.com/sdparekh/zUMIs/files/2286550/MB_new.yaml.txt)\r\n\r\nHere is the output:\r\n\r\n> You provided these parameters:\r\n>  YAML file:     MB_new.yaml\r\n>  zUMIs directory:               /home/makaufm/apps/zUMIs\r\n>  STAR executable                /home/makaufm/apps/STAR_2.5.4a/bin/Linux_x86_64/STAR\r\n>  samtools executable            /home/makaufm/apps/samtools_1.9/bin/samtools\r\n>  pigz executable                pigz\r\n>  Rscript executable             Rscript\r\n>  RAM limit:   0\r\n>  zUMIs version 2.0\r\n> \r\n> \r\n> Filtering...\r\n> [W::sam_read1] Parse error at line 1\r\n> [main_samview] truncated file.\r\n> [W::sam_read1] Parse error at line 1\r\n> [main_samview] truncated file.\r\n> [W::sam_read1] Parse error at line 3\r\n> [main_samview] truncated file.\r\n> [W::sam_read1] Parse error at line 1\r\n> [main_samview] truncated file.\r\n> [W::sam_read1] Parse error at line 3\r\n> [main_samview] truncated file.\r\n> [W::sam_read1] Parse error at line 1\r\n> [main_samview] truncated file.\r\n> [W::sam_read1] Parse error at line 2\r\n> [main_samview] truncated file.\r\n> [W::sam_read1] Parse error at line 3\r\n> [main_samview] truncated file.\r\n> [W::sam_read1] Parse error at line 4\r\n> [main_samview] truncated file.\r\n> [W::sam_read1] Parse error at line 4\r\n> [main_samview] truncated file.\r\n> [W::sam_read1] Parse error at line 4\r\n> [main_samview] truncated file.\r\n> [W::sam_read1] Parse error at line 5\r\n> [main_samview] truncated file.\r\n> [W::sam_read1] Parse error at line 3\r\n> [main_samview] truncated file.\r\n> [W::sam_read1] Parse error at line 1\r\n> [main_samview] truncated file.\r\n> [W::sam_read1] Parse error at line 1\r\n> [main_samview] truncated file.\r\n> [W::sam_read1] Parse error at line 3\r\n> [main_samview] truncated file.\r\n> [W::sam_read1] Parse error at line 2\r\n> [main_samview] truncated file.\r\n> [W::sam_read1] [W::sam_read1] Parse error at line 3\r\n> [main_samview] truncated file.\r\n> Parse error at line 1\r\n> [main_samview] truncated file.\r\n> [W::sam_read1] Parse error at line 4\r\n> [main_samview] truncated file.\r\n> [W::sam_read1] Parse error at line 3\r\n> [main_samview] truncated file.\r\n> [W::sam_read1] Parse error at line 3\r\n> [main_samview] truncated file.\r\n> [W::sam_read1] Parse error at line 4\r\n> [main_samview] truncated file.\r\n> [W::sam_read1] Parse error at line 3\r\n> [main_samview] truncated file.\r\n> [W::sam_read1] Parse error at line 2\r\n> [main_samview] truncated file.\r\n> [W::sam_read1] Parse error at line 1\r\n> [main_samview] truncated file.\r\n> [W::sam_read1] Parse error at line 2\r\n> [main_samview] truncated file.\r\n> [W::sam_read1] Parse error at line 1\r\n> [main_samview] truncated file.\r\n> [W::bam_merge_core2] No @HD tag found.\r\n> cat: /data/max/01_projects/03_MadeleineB/zUMIs_out/zUMIs_output/.tmpMerge//MB.*.BCstats.txt: No such file or directory\r\n> \r\n\r\nThe result is a bam file, which only contains 41 lines:\r\n[MB.filtered.tagged.txt](https://github.com/sdparekh/zUMIs/files/2286389/MB.filtered.tagged.txt)\r\n\r\nThe input fastq files looks perfectly normal to me.\r\n\r\nAny idea what could be going on?\r\n\r\nBest Max\r\n"},"comment":{"url":"https://api.github.com/repos/sdparekh/zUMIs/issues/comments/412896727","html_url":"https://github.com/sdparekh/zUMIs/issues/53#issuecomment-412896727","issue_url":"https://api.github.com/repos/sdparekh/zUMIs/issues/53","id":412896727,"node_id":"MDEyOklzc3VlQ29tbWVudDQxMjg5NjcyNw==","user":{"login":"cziegenhain","id":16579427,"node_id":"MDQ6VXNlcjE2NTc5NDI3","avatar_url":"https://avatars2.githubusercontent.com/u/16579427?v=4","gravatar_id":"","url":"https://api.github.com/users/cziegenhain","html_url":"https://github.com/cziegenhain","followers_url":"https://api.github.com/users/cziegenhain/followers","following_url":"https://api.github.com/users/cziegenhain/following{/other_user}","gists_url":"https://api.github.com/users/cziegenhain/gists{/gist_id}","starred_url":"https://api.github.com/users/cziegenhain/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cziegenhain/subscriptions","organizations_url":"https://api.github.com/users/cziegenhain/orgs","repos_url":"https://api.github.com/users/cziegenhain/repos","events_url":"https://api.github.com/users/cziegenhain/events{/privacy}","received_events_url":"https://api.github.com/users/cziegenhain/received_events","type":"User","site_admin":false},"created_at":"2018-08-14T14:43:09Z","updated_at":"2018-08-14T14:43:09Z","author_association":"COLLABORATOR","body":"Hey Max,\r\n\r\nHmm okay that confirms my theory, thanks for checking so quickly!\r\n\r\nUnfortunately I have to say I don't have an immediate solution. \r\nOf course we will implement this type of variable cDNA length soon. \r\n\r\nFor now, you would need to stick with the shortest read length found or with the previous version of zUMIs.\r\n\r\nI will keep this issue open for other users until we have changed this handling. \r\n\r\nBest\r\n\r\nChristoph"}}
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