{"action":"created","issue":{"url":"https://api.github.com/repos/ablab/spades/issues/202","repository_url":"https://api.github.com/repos/ablab/spades","labels_url":"https://api.github.com/repos/ablab/spades/issues/202/labels{/name}","comments_url":"https://api.github.com/repos/ablab/spades/issues/202/comments","events_url":"https://api.github.com/repos/ablab/spades/issues/202/events","html_url":"https://github.com/ablab/spades/issues/202","id":375548594,"node_id":"MDU6SXNzdWUzNzU1NDg1OTQ=","number":202,"title":"metaspades - number of errors on not found files","user":{"login":"GeoMicroSoares","id":14272488,"node_id":"MDQ6VXNlcjE0MjcyNDg4","avatar_url":"https://avatars3.githubusercontent.com/u/14272488?v=4","gravatar_id":"","url":"https://api.github.com/users/GeoMicroSoares","html_url":"https://github.com/GeoMicroSoares","followers_url":"https://api.github.com/users/GeoMicroSoares/followers","following_url":"https://api.github.com/users/GeoMicroSoares/following{/other_user}","gists_url":"https://api.github.com/users/GeoMicroSoares/gists{/gist_id}","starred_url":"https://api.github.com/users/GeoMicroSoares/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/GeoMicroSoares/subscriptions","organizations_url":"https://api.github.com/users/GeoMicroSoares/orgs","repos_url":"https://api.github.com/users/GeoMicroSoares/repos","events_url":"https://api.github.com/users/GeoMicroSoares/events{/privacy}","received_events_url":"https://api.github.com/users/GeoMicroSoares/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-10-30T15:25:27Z","updated_at":"2018-10-31T11:01:25Z","closed_at":null,"author_association":"NONE","body":"Hi there,\r\nRunning spades on an HPC and am getting the following error in ca. 1min after the submission:\r\n```\r\n[user@sl2 metaspades_assembly]$ cat bench.out.28552 \r\nCommand line: /opt/SPAdes-3.13.0-Linux/bin/spades.py\t--meta\t-k\t21,33,55,77,99,127\t--tmp-dir\t/scratch/user\t-o\t/home/user/metagenomes/data/analysis/assembly/metaspades_assembly\t-1\t/home/user/metagenomes/data/analysis/qc_trimmed_data/S117_M_004_S4_trimqc_R1_001.fastq.gz\t-2\t/home/user/metagenomes/data/analysis/qc_trimmed_data/S117_M_004_S4_trimqc_R2_001.fastq.gz\t\r\n\r\nSystem information:\r\n  SPAdes version: 3.13.0\r\n  Python version: 2.7.15\r\n  OS: Linux-3.10.0-693.21.1.el7.x86_64-x86_64-with-Ubuntu-18.04-bionic\r\n\r\nOutput dir: /home/user/metagenomes/data/analysis/assembly/metaspades_assembly\r\nMode: read error correction and assembling\r\nDebug mode is turned OFF\r\n\r\nDataset parameters:\r\n  Metagenomic mode\r\n  Reads:\r\n    Library number: 1, library type: paired-end\r\n      orientation: fr\r\n      left reads: ['/home/user/metagenomes/data/analysis/qc_trimmed_data/S117_M_004_S4_trimqc_R1_001.fastq.gz']\r\n      right reads: ['/home/user/metagenomes/data/analysis/qc_trimmed_data/S117_M_004_S4_trimqc_R2_001.fastq.gz']\r\n      interlaced reads: not specified\r\n      single reads: not specified\r\n      merged reads: not specified\r\nRead error correction parameters:\r\n  Iterations: 1\r\n  PHRED offset will be auto-detected\r\n  Corrected reads will be compressed\r\nAssembly parameters:\r\n  k: [21, 33, 55, 77, 99, 127]\r\n  Repeat resolution is enabled\r\n  Mismatch careful mode is turned OFF\r\n  MismatchCorrector will be SKIPPED\r\n  Coverage cutoff is turned OFF\r\nOther parameters:\r\n  Dir for temp files: /scratch/user\r\n  Threads: 16\r\n  Memory limit (in Gb): 250\r\n\r\n\r\n======= SPAdes pipeline started. Log can be found here: /home/user/metagenomes/data/analysis/assembly/metaspades_assembly/spades.log\r\n\r\n[Errno 2] No such file or directory: '/home/user/metagenomes/data/analysis/assembly/metaspades_assembly/configs/corrector/corrector.info'\r\nTraceback (most recent call last):\r\n  File \"/opt/SPAdes-3.13.0-Linux/bin/spades.py\", line 756, in main\r\n    dir_util.copy_tree(os.path.join(spades_home, \"configs\"), tmp_configs_dir, preserve_times=False, preserve_mode=False)\r\n  File \"/usr/lib/python2.7/distutils/dir_util.py\", line 163, in copy_tree\r\n    verbose=verbose, dry_run=dry_run))\r\n  File \"/usr/lib/python2.7/distutils/dir_util.py\", line 167, in copy_tree\r\n    dry_run=dry_run)\r\n  File \"/usr/lib/python2.7/distutils/file_util.py\", line 156, in copy_file\r\n    _copy_file_contents(src, dst)\r\n  File \"/usr/lib/python2.7/distutils/file_util.py\", line 44, in _copy_file_contents\r\n    fdst = open(dst, 'wb')\r\nIOError: [Errno 2] No such file or directory: '/home/user/metagenomes/data/analysis/assembly/metaspades_assembly/configs/corrector/corrector.info'\r\n\r\n\r\n== Error ==  exception caught: <type 'exceptions.IOError'>\r\n\r\nIn case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru\r\nor report an issue on our GitHub repository github.com/ablab/spades\r\nPlease provide us with params.txt and spades.log files from the output directory.\r\nCommand line: /opt/SPAdes-3.13.0-Linux/bin/spades.py\t--meta\t-k\t21,33,55,77,99,127\t--tmp-dir\t/scratch/user\t-o\t/home/user/metagenomes/data/analysis/assembly/metaspades_assembly\t-1\t/home/user/metagenomes/data/analysis/qc_trimmed_data/S117_M_007_S7_trimqc_R1_001.fastq.gz\t-2\t/home/user/metagenomes/data/analysis/qc_trimmed_data/S117_M_007_S7_trimqc_R2_001.fastq.gz\t\r\n\r\nSystem information:\r\n  SPAdes version: 3.13.0\r\n  Python version: 2.7.15\r\n  OS: Linux-3.10.0-693.21.1.el7.x86_64-x86_64-with-Ubuntu-18.04-bionic\r\n\r\nOutput dir: /home/user/metagenomes/data/analysis/assembly/metaspades_assembly\r\nMode: read error correction and assembling\r\nDebug mode is turned OFF\r\n\r\nDataset parameters:\r\n  Metagenomic mode\r\n  Reads:\r\n    Library number: 1, library type: paired-end\r\n      orientation: fr\r\n      left reads: ['/home/user/metagenomes/data/analysis/qc_trimmed_data/S117_M_007_S7_trimqc_R1_001.fastq.gz']\r\n      right reads: ['/home/user/metagenomes/data/analysis/qc_trimmed_data/S117_M_007_S7_trimqc_R2_001.fastq.gz']\r\n      interlaced reads: not specified\r\n      single reads: not specified\r\n      merged reads: not specified\r\nRead error correction parameters:\r\n  Iterations: 1\r\n  PHRED offset will be auto-detected\r\n  Corrected reads will be compressed\r\nAssembly parameters:\r\n  k: [21, 33, 55, 77, 99, 127]\r\n  Repeat resolution is enabled\r\n  Mismatch careful mode is turned OFF\r\n  MismatchCorrector will be SKIPPED\r\n  Coverage cutoff is turned OFF\r\nOther parameters:\r\n  Dir for temp files: /scratch/user\r\n  Threads: 16\r\n  Memory limit (in Gb): 250\r\n\r\n\r\n======= SPAdes pipeline started. Log can be found here: /home/user/metagenomes/data/analysis/assembly/metaspades_assembly/spades.log\r\n\r\n[Errno 39] Directory not empty: '/home/user/metagenomes/data/analysis/assembly/metaspades_assembly/configs/debruijn'\r\nTraceback (most recent call last):\r\n  File \"/opt/SPAdes-3.13.0-Linux/bin/spades.py\", line 751, in main\r\n    shutil.rmtree(tmp_configs_dir)\r\n  File \"/usr/lib/python2.7/shutil.py\", line 261, in rmtree\r\n    rmtree(fullname, ignore_errors, onerror)\r\n  File \"/usr/lib/python2.7/shutil.py\", line 270, in rmtree\r\n    onerror(os.rmdir, path, sys.exc_info())\r\n  File \"/usr/lib/python2.7/shutil.py\", line 268, in rmtree\r\n    os.rmdir(path)\r\nOSError: [Errno 39] Directory not empty: '/home/user/metagenomes/data/analysis/assembly/metaspades_assembly/configs/debruijn'\r\n\r\n\r\n== Error ==  exception caught: <type 'exceptions.OSError'>\r\n\r\nIn case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru\r\nor report an issue on our GitHub repository github.com/ablab/spades\r\nPlease provide us with params.txt and spades.log files from the output directory.\r\n```\r\nI'm not sure why this is happening, what more information can I provide to get to the bottom of this?\r\n\r\nThanks!"},"comment":{"url":"https://api.github.com/repos/ablab/spades/issues/comments/434645419","html_url":"https://github.com/ablab/spades/issues/202#issuecomment-434645419","issue_url":"https://api.github.com/repos/ablab/spades/issues/202","id":434645419,"node_id":"MDEyOklzc3VlQ29tbWVudDQzNDY0NTQxOQ==","user":{"login":"GeoMicroSoares","id":14272488,"node_id":"MDQ6VXNlcjE0MjcyNDg4","avatar_url":"https://avatars3.githubusercontent.com/u/14272488?v=4","gravatar_id":"","url":"https://api.github.com/users/GeoMicroSoares","html_url":"https://github.com/GeoMicroSoares","followers_url":"https://api.github.com/users/GeoMicroSoares/followers","following_url":"https://api.github.com/users/GeoMicroSoares/following{/other_user}","gists_url":"https://api.github.com/users/GeoMicroSoares/gists{/gist_id}","starred_url":"https://api.github.com/users/GeoMicroSoares/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/GeoMicroSoares/subscriptions","organizations_url":"https://api.github.com/users/GeoMicroSoares/orgs","repos_url":"https://api.github.com/users/GeoMicroSoares/repos","events_url":"https://api.github.com/users/GeoMicroSoares/events{/privacy}","received_events_url":"https://api.github.com/users/GeoMicroSoares/received_events","type":"User","site_admin":false},"created_at":"2018-10-31T11:01:25Z","updated_at":"2018-10-31T11:01:25Z","author_association":"NONE","body":"Hi @asl I do, just checked..."}}
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