{"action":"created","issue":{"url":"https://api.github.com/repos/Xinglab/rmats2sashimiplot/issues/24","repository_url":"https://api.github.com/repos/Xinglab/rmats2sashimiplot","labels_url":"https://api.github.com/repos/Xinglab/rmats2sashimiplot/issues/24/labels{/name}","comments_url":"https://api.github.com/repos/Xinglab/rmats2sashimiplot/issues/24/comments","events_url":"https://api.github.com/repos/Xinglab/rmats2sashimiplot/issues/24/events","html_url":"https://github.com/Xinglab/rmats2sashimiplot/issues/24","id":287487791,"node_id":"MDU6SXNzdWUyODc0ODc3OTE=","number":24,"title":"Error: no entries found","user":{"login":"albertoriva","id":6775418,"node_id":"MDQ6VXNlcjY3NzU0MTg=","avatar_url":"https://avatars3.githubusercontent.com/u/6775418?v=4","gravatar_id":"","url":"https://api.github.com/users/albertoriva","html_url":"https://github.com/albertoriva","followers_url":"https://api.github.com/users/albertoriva/followers","following_url":"https://api.github.com/users/albertoriva/following{/other_user}","gists_url":"https://api.github.com/users/albertoriva/gists{/gist_id}","starred_url":"https://api.github.com/users/albertoriva/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/albertoriva/subscriptions","organizations_url":"https://api.github.com/users/albertoriva/orgs","repos_url":"https://api.github.com/users/albertoriva/repos","events_url":"https://api.github.com/users/albertoriva/events{/privacy}","received_events_url":"https://api.github.com/users/albertoriva/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-01-10T16:06:44Z","updated_at":"2018-06-28T16:47:33Z","closed_at":null,"author_association":"NONE","body":"I'm trying to run rmats2sashimiplot providing the coordinates of the region I'm interested in. I used the following commandline: \r\n\r\nrmats2sashimiplot --b1 $B1 --b2 $B2 \\\r\n  -c chrX:+:44873511:45112602:Homo_sapiens.GRCh38.84.clean.gff3 \\\r\n  --l1 WT --l2 E4 \\\r\n  --exon_s 1 --intron_s 5 -o test_coordinate_output\r\n\r\nwhere $B1 and $B2 are variables containing the comma-delimited bam files. When I run the script I get the following error:\r\n\r\nIndexing GFF...\r\n  - GFF: .../rmats.out/test_coordinate_output/Sashimi_index/tmp.gff3\r\n  - Outputting to: .../rmats.out/test_coordinate_output/Sashimi_index\r\nWARNING: No entries found for gene chrX:44873511:45112603:+ in GFF .../rmats.out/test_coordinate_output/Sashimi_index/tmp.gff3\r\nSkipping gene chrX:44873511:45112603:+...\r\nLoaded 0 genes\r\n  - Loading of genes from GFF took 0.02 seconds\r\nOutputting gene records in GFF format...\r\n  - Output file: .../rmats.out/test_coordinate_output/Sashimi_index/genes.gff\r\n  - Serialization of genes from GFF took 0.02 seconds\r\nIndexing of GFF took 0.04 seconds.\r\nTraceback (most recent call last):\r\n  File \"/apps/gcc/5.2.0/python/apps/2.7.10/rmats2sashimiplot/2.0.3/lib/python2.7/site-packages/rmats2sashimiplot-2.0.2-py2.7.egg/MISO/misopy/sashimi_plot/sashimi_plot.py\", line 293, in <module>\r\n    main()\r\n  File \"/apps/gcc/5.2.0/python/apps/2.7.10/rmats2sashimiplot/2.0.3/lib/python2.7/site-packages/rmats2sashimiplot-2.0.2-py2.7.egg/MISO/misopy/sashimi_plot/sashimi_plot.py\", line 289, in main\r\n    plot_label=plot_label)\r\n  File \"/apps/gcc/5.2.0/python/apps/2.7.10/rmats2sashimiplot/2.0.3/lib/python2.7/site-packages/rmats2sashimiplot-2.0.2-py2.7.egg/MISO/misopy/sashimi_plot/sashimi_plot.py\", line 148, in plot_event\r\n    %(event_name, pickle_dir)\r\nException: Event chrX:44873511:45112603:+ not found in pickled directory .../rmats.out/test_coordinate_output/Sashimi_index. Are you sure this is the right directory for the event?\r\n\r\n[Note that for simplicity I replaced the initial part of all pathnames with \"...\"]. What am I doing wrong?\r\n\r\nThanks!\r\n"},"comment":{"url":"https://api.github.com/repos/Xinglab/rmats2sashimiplot/issues/comments/401100306","html_url":"https://github.com/Xinglab/rmats2sashimiplot/issues/24#issuecomment-401100306","issue_url":"https://api.github.com/repos/Xinglab/rmats2sashimiplot/issues/24","id":401100306,"node_id":"MDEyOklzc3VlQ29tbWVudDQwMTEwMDMwNg==","user":{"login":"OwenDonohoe","id":39618568,"node_id":"MDQ6VXNlcjM5NjE4NTY4","avatar_url":"https://avatars3.githubusercontent.com/u/39618568?v=4","gravatar_id":"","url":"https://api.github.com/users/OwenDonohoe","html_url":"https://github.com/OwenDonohoe","followers_url":"https://api.github.com/users/OwenDonohoe/followers","following_url":"https://api.github.com/users/OwenDonohoe/following{/other_user}","gists_url":"https://api.github.com/users/OwenDonohoe/gists{/gist_id}","starred_url":"https://api.github.com/users/OwenDonohoe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/OwenDonohoe/subscriptions","organizations_url":"https://api.github.com/users/OwenDonohoe/orgs","repos_url":"https://api.github.com/users/OwenDonohoe/repos","events_url":"https://api.github.com/users/OwenDonohoe/events{/privacy}","received_events_url":"https://api.github.com/users/OwenDonohoe/received_events","type":"User","site_admin":false},"created_at":"2018-06-28T16:47:33Z","updated_at":"2018-06-28T16:47:33Z","author_association":"NONE","body":"Just to elabourate:\r\n\r\nhere is the gene entry in gtt3 file (it was generated via StringTie)\r\n\r\n\r\n\r\nchrX | StringTie | gene | 132369315 | 132490100 | . | - | . | ID=MSTRG.896;Name=MSTRG.896\r\n-- | -- | -- | -- | -- | -- | -- | -- | --\r\n\r\nand here is the error output\r\n\r\nowen@owen-VirtualBox:/media/sf_Ubuntu_Shared/RNA_Seq_Training/chrx/mapping$ rmats2sashimiplot --b1 ERR188234_chrX.bam,ERR188245_chrX.bam,ERR188273_chrX.bam,ERR188337_chrX.bam,ERR188428_chrX.bam,ERR204916_chrX.bam --b2 ERR188044_chrX.bam,ERR188104_chrX.bam,ERR188257_chrX.bam,ERR188383_chrX.bam,ERR188401_chrX.bam,ERR188454_chrX.bam -c chrX:-:132369315:132490100:./bam_test/ensGene.gff3 --l1 Female --l2 Male --exon_s 1 --intron_s 5 -o test_coordinate_output\r\n\r\n'ERR188234_chrX.bam' seems to be indexed already. Please Check out this index file 'ERR188234_chrX.bam.bai'\r\n'ERR188245_chrX.bam' seems to be indexed already. Please Check out this index file 'ERR188245_chrX.bam.bai'\r\n'ERR188273_chrX.bam' seems to be indexed already. Please Check out this index file 'ERR188273_chrX.bam.bai'\r\n'ERR188337_chrX.bam' seems to be indexed already. Please Check out this index file 'ERR188337_chrX.bam.bai'\r\n'ERR188428_chrX.bam' seems to be indexed already. Please Check out this index file 'ERR188428_chrX.bam.bai'\r\n'ERR204916_chrX.bam' seems to be indexed already. Please Check out this index file 'ERR204916_chrX.bam.bai'\r\n'ERR188044_chrX.bam' seems to be indexed already. Please Check out this index file 'ERR188044_chrX.bam.bai'\r\n'ERR188104_chrX.bam' seems to be indexed already. Please Check out this index file 'ERR188104_chrX.bam.bai'\r\n'ERR188257_chrX.bam' seems to be indexed already. Please Check out this index file 'ERR188257_chrX.bam.bai'\r\n'ERR188383_chrX.bam' seems to be indexed already. Please Check out this index file 'ERR188383_chrX.bam.bai'\r\n'ERR188401_chrX.bam' seems to be indexed already. Please Check out this index file 'ERR188401_chrX.bam.bai'\r\n'ERR188454_chrX.bam' seems to be indexed already. Please Check out this index file 'ERR188454_chrX.bam.bai'\r\n\r\n<module 'misopy' from '/usr/local/lib/python2.7/dist-packages/rmats2sashimiplot-2.0.2-py2.7.egg/MISO/misopy/__init__.pyc'>\r\nIndexing GFF...\r\n  - GFF: /media/sf_Ubuntu_Shared/RNA_Seq_Training/chrx/mapping/test_coordinate_output/Sashimi_index/tmp.gff3\r\n  - Outputting to: /media/sf_Ubuntu_Shared/RNA_Seq_Training/chrx/mapping/test_coordinate_output/Sashimi_index\r\nWARNING: No entries found for gene chrX:132369315:132490101:- in GFF /media/sf_Ubuntu_Shared/RNA_Seq_Training/chrx/mapping/test_coordinate_output/Sashimi_index/tmp.gff3\r\nSkipping gene chrX:132369315:132490101:-...\r\nLoaded 0 genes\r\n  - Loading of genes from GFF took 0.01 seconds\r\nOutputting gene records in GFF format...\r\n  - Output file: /media/sf_Ubuntu_Shared/RNA_Seq_Training/chrx/mapping/test_coordinate_output/Sashimi_index/genes.gff\r\nTraceback (most recent call last):\r\n  File \"/usr/local/lib/python2.7/dist-packages/rmats2sashimiplot-2.0.2-py2.7.egg/MISO/misopy/index_gff.py\", line 204, in <module>\r\n    main()\r\n  File \"/usr/local/lib/python2.7/dist-packages/rmats2sashimiplot-2.0.2-py2.7.egg/MISO/misopy/index_gff.py\", line 196, in main\r\n    compress_id=options.compress_id)\r\n  File \"/usr/local/lib/python2.7/dist-packages/rmats2sashimiplot-2.0.2-py2.7.egg/MISO/misopy/index_gff.py\", line 167, in index_gff\r\n    compress_id=compress_id)\r\n  File \"/usr/local/lib/python2.7/dist-packages/rmats2sashimiplot-2.0.2-py2.7.egg/MISO/misopy/index_gff.py\", line 131, in serialize_genes\r\n    with open(genes_filename, \"w\") as gff_out:\r\nIOError: [Errno 26] Text file busy: '/media/sf_Ubuntu_Shared/RNA_Seq_Training/chrx/mapping/test_coordinate_output/Sashimi_index/genes.gff'\r\nTraceback (most recent call last):\r\n  File \"/usr/local/lib/python2.7/dist-packages/rmats2sashimiplot-2.0.2-py2.7.egg/MISO/misopy/sashimi_plot/sashimi_plot.py\", line 293, in <module>\r\n    main()\r\n  File \"/usr/local/lib/python2.7/dist-packages/rmats2sashimiplot-2.0.2-py2.7.egg/MISO/misopy/sashimi_plot/sashimi_plot.py\", line 289, in main\r\n    plot_label=plot_label)\r\n  File \"/usr/local/lib/python2.7/dist-packages/rmats2sashimiplot-2.0.2-py2.7.egg/MISO/misopy/sashimi_plot/sashimi_plot.py\", line 148, in plot_event\r\n    %(event_name, pickle_dir)\r\nException: Event chrX:132369315:132490101:- not found in pickled directory /media/sf_Ubuntu_Shared/RNA_Seq_Training/chrx/mapping/test_coordinate_output/Sashimi_index. Are you sure this is the right directory for the event?\r\n"}}
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