{"action":"created","issue":{"url":"https://api.github.com/repos/pachterlab/kallisto/issues/95","repository_url":"https://api.github.com/repos/pachterlab/kallisto","labels_url":"https://api.github.com/repos/pachterlab/kallisto/issues/95/labels{/name}","comments_url":"https://api.github.com/repos/pachterlab/kallisto/issues/95/comments","events_url":"https://api.github.com/repos/pachterlab/kallisto/issues/95/events","html_url":"https://github.com/pachterlab/kallisto/issues/95","id":122461118,"number":95,"title":"Kallisto freezes ","user":{"login":"olegs","id":75644,"avatar_url":"https://avatars.githubusercontent.com/u/75644?v=3","gravatar_id":"","url":"https://api.github.com/users/olegs","html_url":"https://github.com/olegs","followers_url":"https://api.github.com/users/olegs/followers","following_url":"https://api.github.com/users/olegs/following{/other_user}","gists_url":"https://api.github.com/users/olegs/gists{/gist_id}","starred_url":"https://api.github.com/users/olegs/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/olegs/subscriptions","organizations_url":"https://api.github.com/users/olegs/orgs","repos_url":"https://api.github.com/users/olegs/repos","events_url":"https://api.github.com/users/olegs/events{/privacy}","received_events_url":"https://api.github.com/users/olegs/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":18,"created_at":"2015-12-16T09:21:55Z","updated_at":"2016-04-04T15:40:23Z","closed_at":null,"body":"We try to launch kallisto to compute tpm abundance of the following fastq.gz file. \r\nUnfortunally it performs em algorithm and freezes, i.e. no output for more than 6 hours.\r\n`kallisto quant -i /mnt/stripe/Bioinformatics/data/genomes/hg19/hg19.cdna.all.fa.idx -o /mnt/stripe/Bioinformatics/data/experiments/cache/kallisto/kallisto_hg19_IMR90 cell line_SRR020295 -b 100 -t 32 --single -l 200 -s 600 /mnt/stripe/Bioinformatics/data/raw-data/roadmapepigenomics/SRX007167/SRR020295/SRR020295.fastq.gz`\r\n\r\nAs you may see from the command line above we launch kallisto for roadmap epigenomics data. http://sra.dnanexus.com/runs/SRR020292/experiments\r\nLater we've converted it to `fastq.gz` using `fastq-dump` from `sratoolkit.2.3.3-4-centos_linux64` with --gzip argument.\r\n\r\n```\r\n[2015-12-15 18:17:04] [quant] fragment length distribution is truncate gaussian with mean = 200, sd = 600\r\n[2015-12-15 18:17:04] [index] k-mer length: 31\r\n[2015-12-15 18:17:04] [index] number of targets: 196,317\r\n[2015-12-15 18:17:04] [index] number of k-mers: 119,100,823\r\n[2015-12-15 18:17:27] [index] number of equivalence classes: 797,045\r\n[2015-12-15 18:17:30] [quant] running in single-end mode\r\n[2015-12-15 18:17:30] [quant] will process file 1: /mnt/stripe/Bioinformatics/data/raw-data/roadmapepigenomics/SRX007167/SRR020295/SRR020295.fastq.gz\r\n[2015-12-15 18:20:50] [quant] finding pseudoalignments for the reads ... done\r\n[2015-12-15 18:20:50] [quant] processed 9,936,500 reads, 5,068,932 reads pseudoaligned\r\n[2015-12-15 18:21:26] [   em] quantifying the abundances ... done\r\n[2015-12-15 18:21:26] [   em] the Expectation-Maximization algorithm ran for 1,223 rounds\r\n```\r\n\r\nPlease note that other files are being processed correctly, so indeces are ok. Thanks a lot for the great tool, hope this will be resolved soon."},"comment":{"url":"https://api.github.com/repos/pachterlab/kallisto/issues/comments/205356138","html_url":"https://github.com/pachterlab/kallisto/issues/95#issuecomment-205356138","issue_url":"https://api.github.com/repos/pachterlab/kallisto/issues/95","id":205356138,"user":{"login":"atsky","id":145728,"avatar_url":"https://avatars.githubusercontent.com/u/145728?v=3","gravatar_id":"","url":"https://api.github.com/users/atsky","html_url":"https://github.com/atsky","followers_url":"https://api.github.com/users/atsky/followers","following_url":"https://api.github.com/users/atsky/following{/other_user}","gists_url":"https://api.github.com/users/atsky/gists{/gist_id}","starred_url":"https://api.github.com/users/atsky/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/atsky/subscriptions","organizations_url":"https://api.github.com/users/atsky/orgs","repos_url":"https://api.github.com/users/atsky/repos","events_url":"https://api.github.com/users/atsky/events{/privacy}","received_events_url":"https://api.github.com/users/atsky/received_events","type":"User","site_admin":false},"created_at":"2016-04-04T15:40:23Z","updated_at":"2016-04-04T15:40:23Z","body":"@pmelsted, I had some other process run in parallel, so it finished in reasonable time. "}}