Job ID = 9041712 sra ファイルのダウンロード中... Completed: 1841430K bytes transferred in 14 seconds (1045800K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 7663 0 7663 0 0 1013 0 --:--:-- 0:00:07 --:--:-- 6417 100 31005 0 31005 0 0 3693 0 --:--:-- 0:00:08 --:--:-- 15318 100 82373 0 82373 0 0 8772 0 --:--:-- 0:00:09 --:--:-- 27275 100 103k 0 103k 0 0 11086 0 --:--:-- 0:00:09 --:--:-- 33255 sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 55092790 spots for /home/okishinya/chipatlas/results/dm3/SRX1361360/SRR2749798.sra Written 55092790 spots total rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:28 55092790 reads; of these: 55092790 (100.00%) were unpaired; of these: 2435165 (4.42%) aligned 0 times 39481296 (71.66%) aligned exactly 1 time 13176329 (23.92%) aligned >1 times 95.58% overall alignment rate Time searching: 00:09:28 Overall time: 00:09:28 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 24 files... [bam_rmdupse_core] 24518727 / 52657625 = 0.4656 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 05 Jun 2017 01:57:01: # Command line: callpeak -t SRX1361360.bam -f BAM -g dm -n SRX1361360.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1361360.20 # format = BAM # ChIP-seq file = ['SRX1361360.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off INFO @ Mon, 05 Jun 2017 01:57:01: #1 read tag files... INFO @ Mon, 05 Jun 2017 01:57:01: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 01:57:01: # Command line: callpeak -t SRX1361360.bam -f BAM -g dm -n SRX1361360.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1361360.10 # format = BAM # ChIP-seq file = ['SRX1361360.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off INFO @ Mon, 05 Jun 2017 01:57:01: #1 read tag files... INFO @ Mon, 05 Jun 2017 01:57:01: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 01:57:01: # Command line: callpeak -t SRX1361360.bam -f BAM -g dm -n SRX1361360.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1361360.05 # format = BAM # ChIP-seq file = ['SRX1361360.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off INFO @ Mon, 05 Jun 2017 01:57:01: #1 read tag files... INFO @ Mon, 05 Jun 2017 01:57:01: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 01:57:09: 1000000 INFO @ Mon, 05 Jun 2017 01:57:09: 1000000 INFO @ Mon, 05 Jun 2017 01:57:09: 1000000 INFO @ Mon, 05 Jun 2017 01:57:16: 2000000 INFO @ Mon, 05 Jun 2017 01:57:16: 2000000 INFO @ Mon, 05 Jun 2017 01:57:16: 2000000 INFO @ Mon, 05 Jun 2017 01:57:22: 3000000 INFO @ Mon, 05 Jun 2017 01:57:22: 3000000 INFO @ Mon, 05 Jun 2017 01:57:22: 3000000 INFO @ Mon, 05 Jun 2017 01:57:29: 4000000 INFO @ Mon, 05 Jun 2017 01:57:29: 4000000 INFO @ Mon, 05 Jun 2017 01:57:29: 4000000 INFO @ Mon, 05 Jun 2017 01:57:35: 5000000 INFO @ Mon, 05 Jun 2017 01:57:36: 5000000 INFO @ Mon, 05 Jun 2017 01:57:36: 5000000 INFO @ Mon, 05 Jun 2017 01:57:42: 6000000 INFO @ Mon, 05 Jun 2017 01:57:42: 6000000 INFO @ Mon, 05 Jun 2017 01:57:42: 6000000 INFO @ Mon, 05 Jun 2017 01:57:50: 7000000 INFO @ Mon, 05 Jun 2017 01:57:50: 7000000 INFO @ Mon, 05 Jun 2017 01:57:50: 7000000 INFO @ Mon, 05 Jun 2017 01:57:57: 8000000 INFO @ Mon, 05 Jun 2017 01:57:57: 8000000 INFO @ Mon, 05 Jun 2017 01:57:57: 8000000 INFO @ Mon, 05 Jun 2017 01:58:03: 9000000 INFO @ Mon, 05 Jun 2017 01:58:04: 9000000 INFO @ Mon, 05 Jun 2017 01:58:04: 9000000 INFO @ Mon, 05 Jun 2017 01:58:09: 10000000 INFO @ Mon, 05 Jun 2017 01:58:10: 10000000 INFO @ Mon, 05 Jun 2017 01:58:10: 10000000 INFO @ Mon, 05 Jun 2017 01:58:16: 11000000 INFO @ Mon, 05 Jun 2017 01:58:16: 11000000 INFO @ Mon, 05 Jun 2017 01:58:17: 11000000 INFO @ Mon, 05 Jun 2017 01:58:22: 12000000 INFO @ Mon, 05 Jun 2017 01:58:23: 12000000 INFO @ Mon, 05 Jun 2017 01:58:24: 12000000 INFO @ Mon, 05 Jun 2017 01:58:30: 13000000 INFO @ Mon, 05 Jun 2017 01:58:31: 13000000 INFO @ Mon, 05 Jun 2017 01:58:32: 13000000 INFO @ Mon, 05 Jun 2017 01:58:37: 14000000 INFO @ Mon, 05 Jun 2017 01:58:38: 14000000 INFO @ Mon, 05 Jun 2017 01:58:39: 14000000 INFO @ Mon, 05 Jun 2017 01:58:44: 15000000 INFO @ Mon, 05 Jun 2017 01:58:45: 15000000 INFO @ Mon, 05 Jun 2017 01:58:46: 15000000 INFO @ Mon, 05 Jun 2017 01:58:50: 16000000 INFO @ Mon, 05 Jun 2017 01:58:52: 16000000 INFO @ Mon, 05 Jun 2017 01:58:52: 16000000 INFO @ Mon, 05 Jun 2017 01:58:57: 17000000 INFO @ Mon, 05 Jun 2017 01:58:58: 17000000 INFO @ Mon, 05 Jun 2017 01:58:59: 17000000 INFO @ Mon, 05 Jun 2017 01:59:03: 18000000 INFO @ Mon, 05 Jun 2017 01:59:05: 18000000 INFO @ Mon, 05 Jun 2017 01:59:06: 18000000 INFO @ Mon, 05 Jun 2017 01:59:11: 19000000 INFO @ Mon, 05 Jun 2017 01:59:14: 19000000 INFO @ Mon, 05 Jun 2017 01:59:14: 19000000 INFO @ Mon, 05 Jun 2017 01:59:17: 20000000 INFO @ Mon, 05 Jun 2017 01:59:21: 20000000 INFO @ Mon, 05 Jun 2017 01:59:22: 20000000 INFO @ Mon, 05 Jun 2017 01:59:25: 21000000 INFO @ Mon, 05 Jun 2017 01:59:29: 21000000 INFO @ Mon, 05 Jun 2017 01:59:30: 21000000 INFO @ Mon, 05 Jun 2017 01:59:33: 22000000 INFO @ Mon, 05 Jun 2017 01:59:36: 22000000 INFO @ Mon, 05 Jun 2017 01:59:38: 22000000 INFO @ Mon, 05 Jun 2017 01:59:40: 23000000 INFO @ Mon, 05 Jun 2017 01:59:44: 23000000 INFO @ Mon, 05 Jun 2017 01:59:46: 23000000 INFO @ Mon, 05 Jun 2017 01:59:48: 24000000 INFO @ Mon, 05 Jun 2017 01:59:50: 24000000 INFO @ Mon, 05 Jun 2017 01:59:52: 24000000 INFO @ Mon, 05 Jun 2017 01:59:54: 25000000 INFO @ Mon, 05 Jun 2017 01:59:57: 25000000 INFO @ Mon, 05 Jun 2017 01:59:59: 25000000 INFO @ Mon, 05 Jun 2017 02:00:01: 26000000 INFO @ Mon, 05 Jun 2017 02:00:04: 26000000 INFO @ Mon, 05 Jun 2017 02:00:05: 26000000 INFO @ Mon, 05 Jun 2017 02:00:07: 27000000 INFO @ Mon, 05 Jun 2017 02:00:11: 27000000 INFO @ Mon, 05 Jun 2017 02:00:11: 27000000 INFO @ Mon, 05 Jun 2017 02:00:13: 28000000 INFO @ Mon, 05 Jun 2017 02:00:15: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 02:00:15: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 02:00:15: #1 total tags in treatment: 28138898 INFO @ Mon, 05 Jun 2017 02:00:15: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 02:00:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 02:00:17: 28000000 INFO @ Mon, 05 Jun 2017 02:00:18: 28000000 INFO @ Mon, 05 Jun 2017 02:00:18: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 02:00:18: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 02:00:18: #1 total tags in treatment: 28138898 INFO @ Mon, 05 Jun 2017 02:00:18: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 02:00:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 02:00:19: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 02:00:19: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 02:00:19: #1 total tags in treatment: 28138898 INFO @ Mon, 05 Jun 2017 02:00:19: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 02:00:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 02:00:20: #1 tags after filtering in treatment: 28124781 INFO @ Mon, 05 Jun 2017 02:00:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 02:00:20: #1 finished! INFO @ Mon, 05 Jun 2017 02:00:20: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 02:00:24: #1 tags after filtering in treatment: 28124781 INFO @ Mon, 05 Jun 2017 02:00:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 02:00:24: #1 finished! INFO @ Mon, 05 Jun 2017 02:00:24: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 02:00:25: #1 tags after filtering in treatment: 28124781 INFO @ Mon, 05 Jun 2017 02:00:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 02:00:25: #1 finished! INFO @ Mon, 05 Jun 2017 02:00:25: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 02:00:25: #2 number of paired peaks: 918 WARNING @ Mon, 05 Jun 2017 02:00:25: Fewer paired peaks (918) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 918 pairs to build model! INFO @ Mon, 05 Jun 2017 02:00:25: start model_add_line... INFO @ Mon, 05 Jun 2017 02:00:29: #2 number of paired peaks: 918 WARNING @ Mon, 05 Jun 2017 02:00:29: Fewer paired peaks (918) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 918 pairs to build model! INFO @ Mon, 05 Jun 2017 02:00:29: start model_add_line... INFO @ Mon, 05 Jun 2017 02:00:30: #2 number of paired peaks: 918 WARNING @ Mon, 05 Jun 2017 02:00:30: Fewer paired peaks (918) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 918 pairs to build model! INFO @ Mon, 05 Jun 2017 02:00:30: start model_add_line... INFO @ Mon, 05 Jun 2017 02:00:41: start X-correlation... INFO @ Mon, 05 Jun 2017 02:00:41: end of X-cor INFO @ Mon, 05 Jun 2017 02:00:41: #2 finished! INFO @ Mon, 05 Jun 2017 02:00:41: #2 predicted fragment length is 227 bps INFO @ Mon, 05 Jun 2017 02:00:41: #2 alternative fragment length(s) may be 227 bps INFO @ Mon, 05 Jun 2017 02:00:41: #2.2 Generate R script for model : SRX1361360.20_model.r INFO @ Mon, 05 Jun 2017 02:00:41: #3 Call peaks... INFO @ Mon, 05 Jun 2017 02:00:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 02:00:45: start X-correlation... INFO @ Mon, 05 Jun 2017 02:00:45: end of X-cor INFO @ Mon, 05 Jun 2017 02:00:45: #2 finished! INFO @ Mon, 05 Jun 2017 02:00:45: #2 predicted fragment length is 227 bps INFO @ Mon, 05 Jun 2017 02:00:45: #2 alternative fragment length(s) may be 227 bps INFO @ Mon, 05 Jun 2017 02:00:45: #2.2 Generate R script for model : SRX1361360.10_model.r INFO @ Mon, 05 Jun 2017 02:00:45: #3 Call peaks... INFO @ Mon, 05 Jun 2017 02:00:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 02:00:46: start X-correlation... INFO @ Mon, 05 Jun 2017 02:00:46: end of X-cor INFO @ Mon, 05 Jun 2017 02:00:46: #2 finished! INFO @ Mon, 05 Jun 2017 02:00:46: #2 predicted fragment length is 227 bps INFO @ Mon, 05 Jun 2017 02:00:46: #2 alternative fragment length(s) may be 227 bps INFO @ Mon, 05 Jun 2017 02:00:46: #2.2 Generate R script for model : SRX1361360.05_model.r INFO @ Mon, 05 Jun 2017 02:00:46: #3 Call peaks... INFO @ Mon, 05 Jun 2017 02:00:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 02:03:09: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 02:03:16: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 02:03:18: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 02:05:01: #4 Write output xls file... SRX1361360.10_peaks.xls INFO @ Mon, 05 Jun 2017 02:05:01: #4 Write peak in narrowPeak format file... SRX1361360.10_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 02:05:01: #4 Write summits bed file... SRX1361360.10_summits.bed INFO @ Mon, 05 Jun 2017 02:05:02: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7414 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 02:05:08: #4 Write output xls file... SRX1361360.20_peaks.xls INFO @ Mon, 05 Jun 2017 02:05:08: #4 Write peak in narrowPeak format file... SRX1361360.20_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 02:05:08: #4 Write summits bed file... SRX1361360.20_summits.bed INFO @ Mon, 05 Jun 2017 02:05:08: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (5767 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 02:05:14: #4 Write output xls file... SRX1361360.05_peaks.xls INFO @ Mon, 05 Jun 2017 02:05:14: #4 Write peak in narrowPeak format file... SRX1361360.05_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 02:05:14: #4 Write summits bed file... SRX1361360.05_summits.bed INFO @ Mon, 05 Jun 2017 02:05:14: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (8909 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。