{"action":"opened","issue":{"url":"https://api.github.com/repos/rvolden/C3POa/issues/2","repository_url":"https://api.github.com/repos/rvolden/C3POa","labels_url":"https://api.github.com/repos/rvolden/C3POa/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/rvolden/C3POa/issues/2/comments","events_url":"https://api.github.com/repos/rvolden/C3POa/issues/2/events","html_url":"https://github.com/rvolden/C3POa/issues/2","id":361391591,"node_id":"MDU6SXNzdWUzNjEzOTE1OTE=","number":2,"title":"Error in running C3POa.py","user":{"login":"Joon-Biogen","id":42358298,"node_id":"MDQ6VXNlcjQyMzU4Mjk4","avatar_url":"https://avatars3.githubusercontent.com/u/42358298?v=4","gravatar_id":"","url":"https://api.github.com/users/Joon-Biogen","html_url":"https://github.com/Joon-Biogen","followers_url":"https://api.github.com/users/Joon-Biogen/followers","following_url":"https://api.github.com/users/Joon-Biogen/following{/other_user}","gists_url":"https://api.github.com/users/Joon-Biogen/gists{/gist_id}","starred_url":"https://api.github.com/users/Joon-Biogen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Joon-Biogen/subscriptions","organizations_url":"https://api.github.com/users/Joon-Biogen/orgs","repos_url":"https://api.github.com/users/Joon-Biogen/repos","events_url":"https://api.github.com/users/Joon-Biogen/events{/privacy}","received_events_url":"https://api.github.com/users/Joon-Biogen/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-09-18T16:44:02Z","updated_at":"2018-09-18T16:44:02Z","closed_at":null,"author_association":"NONE","body":"Hi, I am struggling with the C3POa.py script. \r\nI was able to run the preprocessing script without an issue and able to see the expected files.\r\nBut when I try to use these files for C3POa.py, I am getting this error : \r\n\r\nrm: cannot remove `/home/jlee20/dataset/ONT/PRJNA448331/consensus//tmp1': No such file or directory\r\n/home/jlee20/dataset/ONT/PRJNA448331/raw_data/preprocessed/splint_reads/1/R2C2_raw_reads.fastq\r\nTraceback (most recent call last):\r\n  File \"/camhpc/pkg/C3POa/1.0/centos6/C3POa.py\", line 755, in <module>\r\n    main()\r\n  File \"/camhpc/pkg/C3POa/1.0/centos6/C3POa.py\", line 752, in main\r\n    analyze_reads(read_list)\r\n  File \"/camhpc/pkg/C3POa/1.0/centos6/C3POa.py\", line 713, in analyze_reads\r\n    score_list_f = split_SW(name, forward, step=True)\r\n  File \"/camhpc/pkg/C3POa/1.0/centos6/C3POa.py\", line 485, in split_SW\r\n    run_water(step, seq1, seq2, totalLen, diag_dict, diag_set)\r\n  File \"/camhpc/pkg/C3POa/1.0/centos6/C3POa.py\", line 459, in run_water\r\n    diag_set, diag_dict)\r\n  File \"/camhpc/pkg/C3POa/1.0/centos6/C3POa.py\", line 512, in parse_file\r\n    for line in open(matrix_file):\r\nFileNotFoundError: [Errno 2] No such file or directory: 'SW_PARSE.txt'\r\n\r\nCan you let me know what is going wrong? My bash script is like this :\r\n\r\noutpath=/home/jlee20/dataset/ONT/PRJNA448331/consensus/\r\npath=/camhpc/pkg/C3POa/1.0/centos6/NUC.4.4.mat\r\npath2=/camhpc/pkg/C3POa/1.0/centos6/config_file\r\npath3=/home/jlee20/dataset/ONT/PRJNA448331/raw_data/preprocessed/splint_reads\r\nfasta=consensus.fasta\r\noutput=$outpath$fasta\r\nreads=/home/jlee20/dataset/ONT/PRJNA448331/raw_data/preprocessed/splint_reads/1/R2C2_raw_reads.fastq\r\n\r\npython3 /camhpc/pkg/C3POa/1.0/centos6/C3POa.py --reads $reads --matrix $path --config $path2 --output $output -p $outpath\r\n\r\nThank you!\r\nJoon"}}
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