{"action":"created","issue":{"url":"https://api.github.com/repos/alexdobin/STAR/issues/527","repository_url":"https://api.github.com/repos/alexdobin/STAR","labels_url":"https://api.github.com/repos/alexdobin/STAR/issues/527/labels{/name}","comments_url":"https://api.github.com/repos/alexdobin/STAR/issues/527/comments","events_url":"https://api.github.com/repos/alexdobin/STAR/issues/527/events","html_url":"https://github.com/alexdobin/STAR/issues/527","id":383682385,"node_id":"MDU6SXNzdWUzODM2ODIzODU=","number":527,"title":"Mapping issue with STAR","user":{"login":"sagnikbanerjee15","id":23457977,"node_id":"MDQ6VXNlcjIzNDU3OTc3","avatar_url":"https://avatars1.githubusercontent.com/u/23457977?v=4","gravatar_id":"","url":"https://api.github.com/users/sagnikbanerjee15","html_url":"https://github.com/sagnikbanerjee15","followers_url":"https://api.github.com/users/sagnikbanerjee15/followers","following_url":"https://api.github.com/users/sagnikbanerjee15/following{/other_user}","gists_url":"https://api.github.com/users/sagnikbanerjee15/gists{/gist_id}","starred_url":"https://api.github.com/users/sagnikbanerjee15/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sagnikbanerjee15/subscriptions","organizations_url":"https://api.github.com/users/sagnikbanerjee15/orgs","repos_url":"https://api.github.com/users/sagnikbanerjee15/repos","events_url":"https://api.github.com/users/sagnikbanerjee15/events{/privacy}","received_events_url":"https://api.github.com/users/sagnikbanerjee15/received_events","type":"User","site_admin":false},"labels":[{"id":381875797,"node_id":"MDU6TGFiZWwzODE4NzU3OTc=","url":"https://api.github.com/repos/alexdobin/STAR/labels/issue","name":"issue","color":"5319e7","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-11-23T01:26:16Z","updated_at":"2018-11-25T12:39:22Z","closed_at":null,"author_association":"NONE","body":"Hello Alex,\r\n\r\nI currently working with a genome fasta file which has 264085 references. The length of the genome is 587450705. Plugging those numbers in, I calculated the value of genomeSAindexNbases as 13 and genomeChrBinNbits as 11. The genome index generation step was completed without any errors. I have attached the Log.out file. I proceeded to map paired ended reads which resulted in an error. Here is what I got from the STAR run.\r\n\r\nEXITING because of FATAL error, could not open file /work/LAS/rpwise-lab/sagnik/quality_check_genome_annotations/data/STAR_index_combined_all_reads_transcripts/sjdbInfo.txt\r\nSOLUTION: check that the path to genome files, specified in --genomeDir is correct and the files are present, and have user read permsissions\r\n\r\nPlease note that I do not have any GTF file associated with the genome. The command I used for mapping the reads is - \r\nnohup STAR  --runThreadN 20  --genomeDir /work/LAS/rpwise-lab/sagnik/quality_check_genome_annotations/data/STAR_index_combined_all_reads_transcripts  --readFilesIn /work/LAS/rpwise-lab/sagnik/maize_gene_annotations/data/raw_fastq/SRR5488463_adapter_trimmed_1.fastq  --outFileNamePrefix /work/LAS/rpwise-lab/sagnik/quality_check_genome_annotations/data/STAR_SRR5488463_ \r\n\r\nThank you.\r\n\r\n[Log.out.txt.zip](https://github.com/alexdobin/STAR/files/2609488/Log.out.txt.zip)\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/alexdobin/STAR/issues/comments/441437589","html_url":"https://github.com/alexdobin/STAR/issues/527#issuecomment-441437589","issue_url":"https://api.github.com/repos/alexdobin/STAR/issues/527","id":441437589,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0MTQzNzU4OQ==","user":{"login":"sagnikbanerjee15","id":23457977,"node_id":"MDQ6VXNlcjIzNDU3OTc3","avatar_url":"https://avatars1.githubusercontent.com/u/23457977?v=4","gravatar_id":"","url":"https://api.github.com/users/sagnikbanerjee15","html_url":"https://github.com/sagnikbanerjee15","followers_url":"https://api.github.com/users/sagnikbanerjee15/followers","following_url":"https://api.github.com/users/sagnikbanerjee15/following{/other_user}","gists_url":"https://api.github.com/users/sagnikbanerjee15/gists{/gist_id}","starred_url":"https://api.github.com/users/sagnikbanerjee15/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sagnikbanerjee15/subscriptions","organizations_url":"https://api.github.com/users/sagnikbanerjee15/orgs","repos_url":"https://api.github.com/users/sagnikbanerjee15/repos","events_url":"https://api.github.com/users/sagnikbanerjee15/events{/privacy}","received_events_url":"https://api.github.com/users/sagnikbanerjee15/received_events","type":"User","site_admin":false},"created_at":"2018-11-25T12:39:22Z","updated_at":"2018-11-25T12:39:22Z","author_association":"NONE","body":"Hi Alex,\r\n\r\nThanks for your reply. I will try out the patch. Please find attached the log file from the mapping.\r\nCould you also please explain the difference between Linux_x86_64 and Linux_x86_64_static?\r\n\r\nThank you.\r\n[STAR_SRR5488454_Log.out.zip](https://github.com/alexdobin/STAR/files/2613065/STAR_SRR5488454_Log.out.zip)\r\n"}}
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