{"action":"created","issue":{"url":"https://api.github.com/repos/mossmatters/HybPiper/issues/10","repository_url":"https://api.github.com/repos/mossmatters/HybPiper","labels_url":"https://api.github.com/repos/mossmatters/HybPiper/issues/10/labels{/name}","comments_url":"https://api.github.com/repos/mossmatters/HybPiper/issues/10/comments","events_url":"https://api.github.com/repos/mossmatters/HybPiper/issues/10/events","html_url":"https://github.com/mossmatters/HybPiper/issues/10","id":177530783,"number":10,"title":"Issue running test data - error with SPAdes assembly","user":{"login":"CharlesBarden","id":22246635,"avatar_url":"https://avatars.githubusercontent.com/u/22246635?v=3","gravatar_id":"","url":"https://api.github.com/users/CharlesBarden","html_url":"https://github.com/CharlesBarden","followers_url":"https://api.github.com/users/CharlesBarden/followers","following_url":"https://api.github.com/users/CharlesBarden/following{/other_user}","gists_url":"https://api.github.com/users/CharlesBarden/gists{/gist_id}","starred_url":"https://api.github.com/users/CharlesBarden/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/CharlesBarden/subscriptions","organizations_url":"https://api.github.com/users/CharlesBarden/orgs","repos_url":"https://api.github.com/users/CharlesBarden/repos","events_url":"https://api.github.com/users/CharlesBarden/events{/privacy}","received_events_url":"https://api.github.com/users/CharlesBarden/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-09-16T22:11:23Z","updated_at":"2016-09-20T20:24:42Z","closed_at":null,"body":"I'm using Linux Redhat and am simply trying to run the tutorial with the test data set. Any tips or help will be much appreciated. The following is the command I entered and the resulting error message:\r\n\r\n[test_dataset]$ ../reads_first.py -b test_targets.fasta -r NZ281_R*_test.fastq --prefix NZ281 --bwa\r\n\r\n...\r\n\r\n\r\ntime parallel --eta spades.py --only-assembler --threads 1 --cov-cutoff 8 --12 {}/{}_interleaved.fasta -o {}/{}_spades :::: spades_genelist.txt > spades.log\r\n/bin/sh: parallel: command not found\r\n\r\nreal\t0m0.001s\r\nuser\t0m0.001s\r\nsys\t0m0.000s\r\nERROR: One or more genes had an error with SPAdes assembly. This may be due to low coverage. No contigs found for the following genes:\r\ngene660\r\ngene461\r\ngene293\r\ngene001\r\ngene026\r\ngene002\r\ngene111\r\ngene074\r\ngene298\r\ngene079\r\ngene006\r\ngene012\r\ngene030\r\nTraceback (most recent call last):\r\n  File \"/home/berendzen/HybPiper/spades_runner.py\", line 166, in <module>\r\n    if __name__ == \"__main__\":main()\r\n  File \"/home/berendzen/HybPiper/spades_runner.py\", line 160, in main\r\n    spades_failed,spades_duds = rerun_spades(\"failed_spades.txt\",cov_cutoff=args.cov_cutoff,paired=is_paired)\r\n  File \"/home/berendzen/HybPiper/spades_runner.py\", line 82, in rerun_spades\r\n    all_kmers = [int(x[1:]) for x in os.listdir(os.path.join(gene,\"{}_spades\".format(gene))) if x.startswith(\"K\")]\r\nOSError: [Errno 2] No such file or directory: 'gene660/gene660_spades'\r\nWARNING: Something went wrong with the assemblies! Check for failed assemblies and re-run! \r\nERROR: No genes had assembled contigs! Exiting!\r\n"},"comment":{"url":"https://api.github.com/repos/mossmatters/HybPiper/issues/comments/248423000","html_url":"https://github.com/mossmatters/HybPiper/issues/10#issuecomment-248423000","issue_url":"https://api.github.com/repos/mossmatters/HybPiper/issues/10","id":248423000,"user":{"login":"CharlesBarden","id":22246635,"avatar_url":"https://avatars.githubusercontent.com/u/22246635?v=3","gravatar_id":"","url":"https://api.github.com/users/CharlesBarden","html_url":"https://github.com/CharlesBarden","followers_url":"https://api.github.com/users/CharlesBarden/followers","following_url":"https://api.github.com/users/CharlesBarden/following{/other_user}","gists_url":"https://api.github.com/users/CharlesBarden/gists{/gist_id}","starred_url":"https://api.github.com/users/CharlesBarden/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/CharlesBarden/subscriptions","organizations_url":"https://api.github.com/users/CharlesBarden/orgs","repos_url":"https://api.github.com/users/CharlesBarden/repos","events_url":"https://api.github.com/users/CharlesBarden/events{/privacy}","received_events_url":"https://api.github.com/users/CharlesBarden/received_events","type":"User","site_admin":false},"created_at":"2016-09-20T20:24:42Z","updated_at":"2016-09-20T20:24:42Z","body":"Thank you for your help. I think I've fixed the previous problem but when I run the program I'm encountering some different errors. Any idea what the issue is?\r\n\r\npython2.7env/lib/python2.7/site-packages/Bio/Seq.py:2071: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future.\r\n  BiopythonWarning)\r\n0 proteins had no good matches.\r\n\r\nreal\t0m0.127s\r\nuser\t0m0.112s\r\nsys\t0m0.016s\r\nRunning SPAdes on 13 genes\r\ntime parallel --eta spades.py --only-assembler --threads 1 --cov-cutoff 8 -s {}/{}_interleaved.fasta -o {}/{}_spades :::: spades_genelist.txt > spades.log\r\n\r\neal\t0m8.477s\r\nuser\t0m44.894s\r\nsys\t0m5.240s\r\nERROR: One or more genes had an error with SPAdes assembly. This may be due to low coverage. No contigs found for the following genes:\r\ngene293\r\ngene026\r\ngene002\r\ngene079\r\ngene006\r\ngene012\r\ngene030\r\nWARNING: All Kmers failed for gene079!\r\nWARNING: All Kmers failed for gene030!\r\nRe-running SPAdes for 5 genes\r\nparallel --eta :::: redo_spades_commands.txt > spades_redo.log\r\n\r\n** (process:18798): WARNING **: Compiled with assertion checking - will run slowly\r\n**\r\nERROR:protein2genome.c:25:Protein2Genome_Data_create: assertion failed: (target->alphabet->type == Alphabet_Type_DNA)\r\n/bin/sh: line 1: 18798 Aborted                 exonerate -m protein2genome --showalignment no --showvulgar no -V 0 --ryo \">%ti,%qi,%qab,%qae,%pi,(%tS),%tab,%tae\\n%tcs\\n\" gene111/gene111_baits.fasta gene111/gene111_contigs.fasta > gene111/NZ874/exonerate_results.fasta\r\nThere were 0 exonerate hits for gene111/gene111_baits.fasta.\r\n\r\nreal\t0m0.347s\r\nuser\t0m1.085s\r\nsys\t0m0.334s\r\nGenerated sequences from 0 genes!\r\nWARNING: Potential paralogs detected for 0 genes!Making nucleotide bwa index in current directory.\r\n"}}
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