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From: David E. (gringer) <dav...@mp...> - 2011-07-15 10:48:42
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On 15/07/11 10:12, David Eccles (gringer) wrote: > I'll fetch the input data that failed once I get back home, and also > see what happens with real phiX data off our sequencer. So, for real phiX data, I prepared the sequence by masking out bases with quality scores less than 20, and then filtering out the 'N' bases, using the attached script (with 'proportion=1'), which produces an interleaved FASTA file. Despite all that filtering, I still have 4GB of >Q20 phiX data that came off the sequencer. Based on the presence of the sequence 'ATCCAACCTGCAGAGTTTTATCGCTT' in these data, it it looks like a circularised phiX genome was used. I put the top 100k lines from this interleaved file into Ray, and it seems to work fine: $ mpirun -np 10 ../../code/Ray -i ~/illuminadata/110517_H134_0062_A816HKABXX/Data/Intensities/BaseCalls/fastq/ignore/head100k_interleaved_noN_phiX_region1101.fasta ... Rank 0 is creating seeds [1/1072] Rank 9 is creating seeds [1/1102] Rank 7 is creating seeds [1/1094] Rank 3 is creating seeds [1/1182] Rank 5 is creating seeds [1/1102] Rank 4 is creating seeds [1/1168] Rank 2 is creating seeds [1/1090] Rank 8 is creating seeds [1/1206] Rank 1 is creating seeds [1/1124] Rank 6 is creating seeds [1/1164] Rank 0 has 0 seeds Rank 0 is creating seeds [1072/1072] (completed) Rank 0: peak number of workers: 1032, maximum: 30000 Rank 0: VirtualCommunicator: 172441 pushed messages generated 918 virtual messages (0.532356%) Rank 2 has 0 seeds Rank 2 is creating seeds [1090/1090] (completed) Rank 2: peak number of workers: 1040, maximum: 30000 Rank 2: VirtualCommunicator: 172482 pushed messages generated 876 virtual messages (0.507879%) Rank 7 has 0 seeds Rank 7 is creating seeds [1094/1094] (completed) Rank 7: peak number of workers: 1056, maximum: 30000 Rank 7: VirtualCommunicator: 172598 pushed messages generated 860 virtual messages (0.498268%) Rank 8 has 0 seeds Rank 8 is creating seeds [1206/1206] (completed) Rank 8: peak number of workers: 1128, maximum: 30000 Rank 8: VirtualCommunicator: 173161 pushed messages generated 863 virtual messages (0.498380%) Rank 3 has 0 seeds Rank 3 is creating seeds [1182/1182] (completed) Rank 3: peak number of workers: 1136, maximum: 30000 Rank 3: VirtualCommunicator: 173111 pushed messages generated 867 virtual messages (0.500835%) Rank 5 has 0 seeds Rank 5 is creating seeds [1102/1102] (completed) Rank 5: peak number of workers: 1054, maximum: 30000 Rank 5: VirtualCommunicator: 172651 pushed messages generated 936 virtual messages (0.542134%) Rank 6 has 0 seeds Rank 6 is creating seeds [1164/1164] (completed) Rank 6: peak number of workers: 1114, maximum: 30000 Rank 6: VirtualCommunicator: 173032 pushed messages generated 862 virtual messages (0.498174%) Rank 4 has 0 seeds Rank 4 is creating seeds [1168/1168] (completed) Rank 4: peak number of workers: 1116, maximum: 30000 Rank 4: VirtualCommunicator: 173056 pushed messages generated 852 virtual messages (0.492326%) Rank 1 has 0 seeds Rank 1 is creating seeds [1124/1124] (completed) Rank 1: peak number of workers: 1088, maximum: 30000 Rank 1: VirtualCommunicator: 183555 pushed messages generated 11665 virtual messages (6.355043%) Rank 9 discovered a seed with 5363 vertices Rank 9 has 1 seeds Rank 9 is creating seeds [1102/1102] (completed) Rank 9: peak number of workers: 1052, maximum: 30000 Rank 9: VirtualCommunicator: 183307 pushed messages generated 11631 virtual messages (6.345093%) ... Rank 1 is extending seeds [0/0] (completed) Rank 1 extended 0 seeds out of 0 (-nan%) Rank 6 is extending seeds [0/0] (completed) Rank 6 extended 0 seeds out of 0 (-nan%) Rank 4 is extending seeds [0/0] (completed) Rank 4 extended 0 seeds out of 0 (-nan%) Rank 5 is extending seeds [0/0] (completed) Rank 5 extended 0 seeds out of 0 (-nan%) Rank 3 is extending seeds [0/0] (completed) Rank 3 extended 0 seeds out of 0 (-nan%) Rank 0 is extending seeds [0/0] (completed) Rank 0 extended 0 seeds out of 0 (-nan%) Rank 8 is extending seeds [0/0] (completed) Rank 8 extended 0 seeds out of 0 (-nan%) Rank 2 is extending seeds [0/0] (completed) Rank 2 extended 0 seeds out of 0 (-nan%) Rank 7 is extending seeds [0/0] (completed) Rank 7 extended 0 seeds out of 0 (-nan%) Rank 9 is extending seeds [1/1] Rank 9 starts on a seed, length is 5363 [0/1] Rank 9 reached 0 vertices (GTGTTAACAGTCGGGAGAGGA) from seed 1 Rank 9 reached 5363 vertices from seed 1 (changing direction) Rank 9 reached 0 vertices (CTGGTTATATTGACCATGCCG) from seed 1 Rank 9 reached 5365 vertices (CCTCTCCCGACTGTTAACACT) from seed 1 Rank 9 (extension done) Rank 9 is extending seeds [1/1] (completed) Rank 9 extended 1 seeds out of 1 (100.00%) ... Number of contigs: 1 Total length of contigs: 5385 Number of contigs >= 500 nt: 1 Total length of contigs >= 500 nt: 5385 Number of scaffolds: 1 Total length of scaffolds: 5385 Number of scaffolds >= 500 nt: 1 Total length of scaffolds >= 500: 5385 I'll have a look at what comes out if I break the circularity of this DNA by removing sequence that includes the start and end pieces together. -- David |
