{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1510","repository_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1510/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1510/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1510/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1510","id":170505282,"number":1510,"title":"STAR aligner using only one thread","user":{"login":"KanduriC","id":8395053,"avatar_url":"https://avatars.githubusercontent.com/u/8395053?v=3","gravatar_id":"","url":"https://api.github.com/users/KanduriC","html_url":"https://github.com/KanduriC","followers_url":"https://api.github.com/users/KanduriC/followers","following_url":"https://api.github.com/users/KanduriC/following{/other_user}","gists_url":"https://api.github.com/users/KanduriC/gists{/gist_id}","starred_url":"https://api.github.com/users/KanduriC/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/KanduriC/subscriptions","organizations_url":"https://api.github.com/users/KanduriC/orgs","repos_url":"https://api.github.com/users/KanduriC/repos","events_url":"https://api.github.com/users/KanduriC/events{/privacy}","received_events_url":"https://api.github.com/users/KanduriC/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-08-10T20:01:08Z","updated_at":"2016-08-10T20:05:32Z","closed_at":null,"body":"Hi,\r\n\r\nI was trying to run a RNA-seq pipeline with STAR as aligner. Irrespective of the instructions to use 16 cores for star aligner (specified through sample configuration file), I find that star is being instructed to use only 1 thread through command line. I am running the job on a cluster where each node contains 16 cores and at least 56G free memory. My sample configuration file and bcbio-nextgen-commands.log are shown below. Could you help me figure out the problem? Thanks.\r\n\r\n```\r\nmore ../rnaseq-seqc.yaml\r\n# Template for human RNA-seq using Illumina prepared samples\r\n---\r\ndetails:\r\n  - analysis: RNA-seq\r\n    files: [input/SRR950080_1.fastq.gz, input/SRR950080_2.fastq.gz]\r\n    description: rna_seq_example_run\r\n    resources:\r\n      star:\r\n        cores: 16\r\n        memory: 3G\r\n        options: [--runThreadN, 16]\r\n    genome_build: GRCh37\r\n    algorithm:\r\n      quality_format: Standard\r\n      aligner: star\r\n      strandedness: unstranded\r\nupload:\r\n  dir: ../final\r\n```\r\n**bcbio-nextgen-commands.log**\r\n```\r\nmore bcbio-nextgen-commands.log \r\n[2016-08-10T15:55Z] /cluster/home/skanduri/bcbio/galaxy/../anaconda/bin/STAR --g\r\nenomeDir /cluster/home/skanduri/bcbio/genomes/Hsapiens/GRCh37/star/ --readFilesI\r\nn /work/jobs/15294111.d/seqc-test/input/SRR950080_1.fastq.gz /work/jobs/15294111\r\n.d/seqc-test/input/SRR950080_2.fastq.gz **--runThreadN 1** --outFileNamePrefix /work\r\n/jobs/15294111.d/seqc-test/align/rna_seq_example_run/rna_seq_example_run --outRe\r\nadsUnmapped Fastx --outFilterMultimapNmax 10 --outStd SAM  --outSAMunmapped With\r\nin --outSAMattributes NH HI NM MD AS  --sjdbGTFfile /cluster/home/skanduri/bcbio\r\n/genomes/Hsapiens/GRCh37/rnaseq/ref-transcripts.gtf  --sjdbOverhang 100  --readF\r\nilesCommand zcat  --outSAMattrRGline ID:rna_seq_example_run PL:illumina PU:rna_s\r\neq_example_run SM:rna_seq_example_run  --outSAMstrandField intronMotif  --quantM\r\node TranscriptomeSAM  | /cluster/home/skanduri/bcbio/galaxy/../anaconda/bin/samt\r\nools sort -@ 1 -m 1G  -T /work/jobs/15294111.d/seqc-test/align/rna_seq_example_r\r\nun/rna_seq_example_run_star/tx/tmpvvZ5vP/rna_seq_example_run-sorttmp -o /work/jo\r\nbs/15294111.d/seqc-test/align/rna_seq_example_run/rna_seq_example_run_star/tx/tm\r\npvvZ5vP/rna_seq_example_run.bam /dev/stdin\r\n```\r\n**bcbio-nextgen-debug.log**\r\n```\r\nmore bcbio-nextgen-debug.log\r\n[2016-08-10T15:55Z] System YAML configuration: /cluster/home/skanduri/bcbio/gala\r\nxy/bcbio_system.yaml\r\n[2016-08-10T15:55Z] Resource requests: picard; memory: 3.50; cores: 1\r\n[2016-08-10T15:55Z] Configuring 1 jobs to run, using 1 cores each with 3.50g of \r\nmemory reserved for each job\r\n[2016-08-10T15:55Z] run local -- checkpoint passed: trimming\r\n[2016-08-10T15:55Z] Timing: organize samples\r\n[2016-08-10T15:55Z] multiprocessing: organize_samples\r\n[2016-08-10T15:55Z] Using input YAML configuration: /work/jobs/15294111.d/seqc-t\r\nest/rnaseq-seqc.yaml\r\n[2016-08-10T15:55Z] Checking sample YAML configuration: /work/jobs/15294111.d/se\r\nqc-test/rnaseq-seqc.yaml\r\n[2016-08-10T15:55Z] Testing minimum versions of installed programs\r\n[2016-08-10T15:55Z] multiprocessing: prepare_sample\r\n[2016-08-10T15:55Z] Preparing rna_seq_example_run\r\n[2016-08-10T15:55Z] Resource requests: picard, star; memory: 3.50, 3.00; cores: \r\n1, 16\r\n[2016-08-10T15:55Z] Configuring 1 jobs to run, using 16 cores each with 56.1g of\r\n memory reserved for each job\r\n[2016-08-10T15:55Z] run local -- checkpoint passed: alignment\r\n[2016-08-10T15:55Z] Timing: alignment\r\n[2016-08-10T15:55Z] multiprocessing: disambiguate_split\r\n[2016-08-10T15:55Z] multiprocessing: process_alignment\r\n[2016-08-10T15:55Z] Aligning lane rna_seq_example_run with star aligner\r\n[2016-08-10T15:55Z] Running STAR aligner on /work/jobs/15294111.d/seqc-test/inpu\r\nt/SRR950080_1.fastq.gz and /cluster/home/skanduri/bcbio/genomes/Hsapiens/GRCh37/\r\nstar/\r\n\r\n```"},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/238987233","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1510#issuecomment-238987233","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1510","id":238987233,"user":{"login":"roryk","id":414586,"avatar_url":"https://avatars.githubusercontent.com/u/414586?v=3","gravatar_id":"","url":"https://api.github.com/users/roryk","html_url":"https://github.com/roryk","followers_url":"https://api.github.com/users/roryk/followers","following_url":"https://api.github.com/users/roryk/following{/other_user}","gists_url":"https://api.github.com/users/roryk/gists{/gist_id}","starred_url":"https://api.github.com/users/roryk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/roryk/subscriptions","organizations_url":"https://api.github.com/users/roryk/orgs","repos_url":"https://api.github.com/users/roryk/repos","events_url":"https://api.github.com/users/roryk/events{/privacy}","received_events_url":"https://api.github.com/users/roryk/received_events","type":"User","site_admin":false},"created_at":"2016-08-10T20:05:32Z","updated_at":"2016-08-10T20:05:32Z","body":"Hi Chakravarthi,\r\n\r\nIt looks like the alignment has already finished, this line:\r\n\r\n`run local -- checkpoint passed: alignment`\r\n\r\nis skipping spinning up the complete resources because it thinks the alignment is finished already. The checkpoint files are in the `work/checkpoints` directory. If you nuke the alignment one, it will spin up the full resources. The checkpoint file shouldn't be written unless the entire alignment step finished properly, by any chance did this complete once already and more samples got added or the alignment directory was deleted?"}}
{"actor":{"display_login":"roryk"}}