René's URL Explorer Experiment

{"@context":"https://schema.org","@type":"DiscussionForumPosting","headline":"problem on simulation of tumor reads ","articleBody":"Hi, first of all, thanks for the tool!\r\n\r\nI met a problem in simulating reads with CNV, where normal reads are generated nicely but no tumor reads. I tried setting the \"region file\" to include \"chr1\" to reduce memory use (the machine I use have 32G mem).  Could you suggest a way through?\r\n\r\nThe \"SIMULATION_IS_COMPLETE.txt\" file reads:\r\n/========================\r\nSIMULATION STARTED WITH THE FOLLOWING PARAMETERS\r\n\r\nSNP Rate: 0.05\r\nIndel Rate: 0.001\r\nTransition/Transversion Ratio: 2\r\nCNV Rate: 0\r\nCNV Minimum Size: 0\r\nCNV Maximum Size: 0\r\nPloidy: 2\r\nSubclones: 1\r\nNumber of Reads: 1000000\r\nRead Length: 100\r\n\r\nCopying temporary files for normal reads ..\r\nCopying temporary files for tumor reads ..\r\n\r\nGenerating normal reads ..\r\n\r\nGenerating fasta file for given regions...\r\n\r\n-------------------------------------------\r\nReference: /ref/my_sim/normal/GRCh37.fa\r\nRegion file: /ref/my_sim/normal/target.chr1.bed\r\nFragment: 200 +- 50 \u003e 120\r\nPaired-end mode? True\r\nSequencing model: /easyscnvsim_lib/Wessim/models/ill100v4_p.gzip\r\nRead length: 100 Read number: 10000\r\nOutput File: /ref/my_sim/normal/normal\r\nGzip compress? False\r\nQuality base: 33\r\nThread number: 2\r\nJob started at: 2018-07-13 04:43:37\r\n/-------------------------------------------\r\n\r\nexiting subprocess 2\r\nexiting subprocess 1\r\nDone generating 10000 reads in 18.700755 secs\r\nMerging subresults...\r\nFinished generating normal reads ..\r\n\r\nSimulating tumor variations in subclone 1 ..\r\nThis step takes some time. Be patient and don't terminate the Docker container :)\r\n\r\nWait! Wait! Simulating the variations in subclone 1 is complete. But it's still generating reads ..\r\n\r\nCleaning temporary files ..\r\n\r\nTraceback (most recent call last):\r\n  File \"cnv-sim.py\", line 103, in \u003cmodule\u003e\r\n    main()\r\n  File \"cnv-sim.py\", line 65, in main\r\n    args = parser.parse_args()\r\n  File \"/usr/lib/python2.7/argparse.py\", line 1690, in parse_args\r\n    args, argv = self.parse_known_args(args, namespace)\r\n  File \"/usr/lib/python2.7/argparse.py\", line 1722, in parse_known_args\r\n    namespace, args = self._parse_known_args(args, namespace)\r\n  File \"/usr/lib/python2.7/argparse.py\", line 1931, in _parse_known_args\r\n    stop_index = consume_positionals(start_index)\r\n  File \"/usr/lib/python2.7/argparse.py\", line 1887, in consume_positionals\r\n    take_action(action, args)\r\n  File \"/usr/lib/python2.7/argparse.py\", line 1780, in take_action\r\n    argument_values = self._get_values(action, argument_strings)\r\n  File \"/usr/lib/python2.7/argparse.py\", line 2220, in _get_values\r\n    value = self._get_value(action, arg_string)\r\n  File \"/usr/lib/python2.7/argparse.py\", line 2249, in _get_value\r\n    result = type_func(arg_string)\r\nIOError: [Errno 2] No such file or directory: '/ref/my_sim/tumor/subclone_1/allele_1.fa'\r\n/========================","author":{"url":"https://github.com/arthuryxt","@type":"Person","name":"arthuryxt"},"datePublished":"2018-07-13T04:53:45.000Z","interactionStatistic":{"@type":"InteractionCounter","interactionType":"https://schema.org/CommentAction","userInteractionCount":0},"url":"https://github.com/2/VarSimLab/issues/2"}