{"action":"created","issue":{"url":"https://api.github.com/repos/sdparekh/zUMIs/issues/56","repository_url":"https://api.github.com/repos/sdparekh/zUMIs","labels_url":"https://api.github.com/repos/sdparekh/zUMIs/issues/56/labels{/name}","comments_url":"https://api.github.com/repos/sdparekh/zUMIs/issues/56/comments","events_url":"https://api.github.com/repos/sdparekh/zUMIs/issues/56/events","html_url":"https://github.com/sdparekh/zUMIs/issues/56","id":352110374,"node_id":"MDU6SXNzdWUzNTIxMTAzNzQ=","number":56,"title":"Mixed Species Use","user":{"login":"dylanmr","id":12213489,"node_id":"MDQ6VXNlcjEyMjEzNDg5","avatar_url":"https://avatars0.githubusercontent.com/u/12213489?v=4","gravatar_id":"","url":"https://api.github.com/users/dylanmr","html_url":"https://github.com/dylanmr","followers_url":"https://api.github.com/users/dylanmr/followers","following_url":"https://api.github.com/users/dylanmr/following{/other_user}","gists_url":"https://api.github.com/users/dylanmr/gists{/gist_id}","starred_url":"https://api.github.com/users/dylanmr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dylanmr/subscriptions","organizations_url":"https://api.github.com/users/dylanmr/orgs","repos_url":"https://api.github.com/users/dylanmr/repos","events_url":"https://api.github.com/users/dylanmr/events{/privacy}","received_events_url":"https://api.github.com/users/dylanmr/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":7,"created_at":"2018-08-20T12:19:33Z","updated_at":"2018-08-28T13:06:30Z","closed_at":null,"author_association":"NONE","body":"Hi again, \r\n\r\nI am working on generating data from a split-seq mixed species experiment. I first renamed the mouse and human dna assembly fastas to differentiate the files and then concatenated. I then downloaded the matching GTF files, renamed the chromosomes and concatenated them. I then generated new STAR genome indices with the concatenated fasta file without splice junctions.  When I then attempt to run zUMIs I get through the filtering step but hit this error: \r\n\r\nproject: mixed_species\r\nsequence_files:\r\nproject: mixed_species\r\nsequence_files:\r\n  file1:\r\n    name: /nfsdata/data/sc-splitseq/180403-splitseq_optimization/splitseq_dualspecies/fastq/splitseq_S1_R1_001.fastq.gz\r\n    base_definition: cDNA(1-66)\r\n  file2:\r\n    name: /nfsdata/data/sc-splitseq/180403-splitseq_optimization/splitseq_dualspecies/fastq/splitseq_S1_R2_001.fastq.gz\r\n\r\n\r\n You provided these parameters:\r\n YAML file:\tmixed_species.yaml\r\n zUMIs directory:\t\t/raid5/projects/dylan/splitseq/zUMIs\r\n STAR executable\t\t/projects/dylan/splitseq/star/star_for_zumis/STAR-2.5.4a/STAR\r\n samtools executable\t\tsamtools\r\n pigz executable\t\tpigz\r\n Rscript executable\t\tRscript\r\n RAM limit:   0\r\n zUMIs version 2.0\r\n\r\n\r\nFiltering...\r\n[W::bam_merge_core2] No @HD tag found.\r\nMapping...\r\nError in data.table::fread(paste(samtools, \"view\", filtered_bam, \"| cut -f10 | head -n 100\"),  :\r\n  File is empty: /tmp/Rtmpzztrfc/file82222aebfd6d\r\nExecution [halted]\r\n\r\nIt looks as though the bam file is empty. I am unsure if you have any troubleshooting recommendations, but any help would be appreciated. I have also attached my yaml file\r\n[mixed_species.txt](https://github.com/sdparekh/zUMIs/files/2302313/mixed_species.txt)\r\n\r\n\r\n\r\nBest,\r\nDylan\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/sdparekh/zUMIs/issues/comments/416576878","html_url":"https://github.com/sdparekh/zUMIs/issues/56#issuecomment-416576878","issue_url":"https://api.github.com/repos/sdparekh/zUMIs/issues/56","id":416576878,"node_id":"MDEyOklzc3VlQ29tbWVudDQxNjU3Njg3OA==","user":{"login":"LittleFrogHill","id":34407101,"node_id":"MDQ6VXNlcjM0NDA3MTAx","avatar_url":"https://avatars1.githubusercontent.com/u/34407101?v=4","gravatar_id":"","url":"https://api.github.com/users/LittleFrogHill","html_url":"https://github.com/LittleFrogHill","followers_url":"https://api.github.com/users/LittleFrogHill/followers","following_url":"https://api.github.com/users/LittleFrogHill/following{/other_user}","gists_url":"https://api.github.com/users/LittleFrogHill/gists{/gist_id}","starred_url":"https://api.github.com/users/LittleFrogHill/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/LittleFrogHill/subscriptions","organizations_url":"https://api.github.com/users/LittleFrogHill/orgs","repos_url":"https://api.github.com/users/LittleFrogHill/repos","events_url":"https://api.github.com/users/LittleFrogHill/events{/privacy}","received_events_url":"https://api.github.com/users/LittleFrogHill/received_events","type":"User","site_admin":false},"created_at":"2018-08-28T13:06:30Z","updated_at":"2018-08-28T13:06:30Z","author_association":"NONE","body":"Hi Christoph,\r\n\r\nA \"Warning\" turn to my log file, it makes the Rplots.pdf in my result broken.\r\n\r\ntail of log file:\r\n[bam_sort_core] merging from 60 files and 30 in-memory blocks...\r\n[1] \"Here are the detected subsampling options:\"\r\n[1] \"Automatic downsampling\"\r\n[1] \"Working on barcode chunk 1 out of 1\"\r\n[1] \"Processing 873 barcodes in this chunk...\"\r\n[1] \"2018-08-24 21:12:35 CST\"\r\n[1] \"I am done!! Look what I produced.../home/Share01/GaoShan/zUMIs/zUMIs_SRR6750059/zUMIs_output/\"\r\n            used   (Mb) gc trigger    (Mb)   max used    (Mb)\r\nNcells   7781635  415.6   20417335  1090.5   49847012  2662.2\r\nVcells 557872918 4256.3 1641481170 12523.6 2051851442 15654.4\r\nDescriptive statistics...\r\n[1] \"I am loading useful packages for plotting...\"\r\n[1] \"2018-08-24 21:12:42 CST\"\r\nWarning messages:\r\n1: In bind_rows_(x, .id) : Unequal factor levels: coercing to character\r\n2: In bind_rows_(x, .id) :\r\n  binding character and factor vector, coercing into character vector\r\n3: In bind_rows_(x, .id) :\r\n  binding character and factor vector, coercing into character vector\r\n4: In bind_rows_(x, .id) :\r\n  binding character and factor vector, coercing into character vector\r\nWarning messages:\r\n1: In bind_rows_(x, .id) : Unequal factor levels: coercing to character\r\n2: In bind_rows_(x, .id) :\r\n  binding character and factor vector, coercing into character vector\r\n3: In bind_rows_(x, .id) :\r\n  binding character and factor vector, coercing into character vector\r\n4: In bind_rows_(x, .id) :\r\n  binding character and factor vector, coercing into character vector\r\nWarning message:\r\nIn bind_rows_(x, .id) :\r\n  binding character and factor vector, coercing into character vector\r\n            used   (Mb) gc trigger    (Mb)   max used    (Mb)\r\nNcells   1842537   98.5   20293757  1083.9   17327516   925.4\r\nVcells 148358974 1131.9 2100043451 16022.1 2607827140 19896.2\r\n\r\nBest,\r\nShan Gao"}}
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