Job ID = 9029227 sra ファイルのダウンロード中... Completed: 752728K bytes transferred in 13 seconds (473112K 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 1040 0 --:--:-- 0:00:07 --:--:-- 6805 100 22317 0 22317 0 0 2779 0 --:--:-- 0:00:08 --:--:-- 12453 100 41829 0 41829 0 0 4633 0 --:--:-- 0:00:09 --:--:-- 14992 100 51965 0 51965 0 0 5182 0 --:--:-- 0:00:10 --:--:-- 13711 100 63549 0 63549 0 0 4745 0 --:--:-- 0:00:13 --:--:-- 8883 100 69341 0 69341 0 0 4697 0 --:--:-- 0:00:14 --:--:-- 8339 100 73685 0 73685 0 0 4881 0 --:--:-- 0:00:15 --:--:-- 7271 100 79477 0 79477 0 0 4989 0 --:--:-- 0:00:15 --:--:-- 5455 100 86717 0 86717 0 0 5014 0 --:--:-- 0:00:17 --:--:-- 4782 100 100k 0 100k 0 0 5615 0 --:--:-- 0:00:18 --:--:-- 7996 100 115k 0 115k 0 0 6250 0 --:--:-- 0:00:18 --:--:-- 11664 100 118k 0 118k 0 0 6356 0 --:--:-- 0:00:19 --:--:-- 11887 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 29973874 spots for /home/okishinya/chipatlas/results/dm3/SRX1433367/SRR2919832.sra Written 29973874 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: 00:12:46 29973874 reads; of these: 29973874 (100.00%) were unpaired; of these: 4914532 (16.40%) aligned 0 times 17658682 (58.91%) aligned exactly 1 time 7400660 (24.69%) aligned >1 times 83.60% overall alignment rate Time searching: 00:12:46 Overall time: 00:12:46 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 12 files... [bam_rmdupse_core] 8739074 / 25059342 = 0.3487 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 @ Sat, 03 Jun 2017 13:12:52: # Command line: callpeak -t SRX1433367.bam -f BAM -g dm -n SRX1433367.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1433367.10 # format = BAM # ChIP-seq file = ['SRX1433367.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 @ Sat, 03 Jun 2017 13:12:52: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:12:52: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:12:52: # Command line: callpeak -t SRX1433367.bam -f BAM -g dm -n SRX1433367.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1433367.05 # format = BAM # ChIP-seq file = ['SRX1433367.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 @ Sat, 03 Jun 2017 13:12:52: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:12:52: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:12:52: # Command line: callpeak -t SRX1433367.bam -f BAM -g dm -n SRX1433367.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1433367.20 # format = BAM # ChIP-seq file = ['SRX1433367.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 @ Sat, 03 Jun 2017 13:12:52: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:12:52: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:12:59: 1000000 INFO @ Sat, 03 Jun 2017 13:12:59: 1000000 INFO @ Sat, 03 Jun 2017 13:12:59: 1000000 INFO @ Sat, 03 Jun 2017 13:13:05: 2000000 INFO @ Sat, 03 Jun 2017 13:13:07: 2000000 INFO @ Sat, 03 Jun 2017 13:13:07: 2000000 INFO @ Sat, 03 Jun 2017 13:13:12: 3000000 INFO @ Sat, 03 Jun 2017 13:13:14: 3000000 INFO @ Sat, 03 Jun 2017 13:13:14: 3000000 INFO @ Sat, 03 Jun 2017 13:13:19: 4000000 INFO @ Sat, 03 Jun 2017 13:13:21: 4000000 INFO @ Sat, 03 Jun 2017 13:13:21: 4000000 INFO @ Sat, 03 Jun 2017 13:13:25: 5000000 INFO @ Sat, 03 Jun 2017 13:13:28: 5000000 INFO @ Sat, 03 Jun 2017 13:13:28: 5000000 INFO @ Sat, 03 Jun 2017 13:13:32: 6000000 INFO @ Sat, 03 Jun 2017 13:13:35: 6000000 INFO @ Sat, 03 Jun 2017 13:13:35: 6000000 INFO @ Sat, 03 Jun 2017 13:13:39: 7000000 INFO @ Sat, 03 Jun 2017 13:13:43: 7000000 INFO @ Sat, 03 Jun 2017 13:13:43: 7000000 INFO @ Sat, 03 Jun 2017 13:13:45: 8000000 INFO @ Sat, 03 Jun 2017 13:13:50: 8000000 INFO @ Sat, 03 Jun 2017 13:13:50: 8000000 INFO @ Sat, 03 Jun 2017 13:13:54: 9000000 INFO @ Sat, 03 Jun 2017 13:13:59: 9000000 INFO @ Sat, 03 Jun 2017 13:13:59: 9000000 INFO @ Sat, 03 Jun 2017 13:14:02: 10000000 INFO @ Sat, 03 Jun 2017 13:14:07: 10000000 INFO @ Sat, 03 Jun 2017 13:14:07: 10000000 INFO @ Sat, 03 Jun 2017 13:14:10: 11000000 INFO @ Sat, 03 Jun 2017 13:14:16: 11000000 INFO @ Sat, 03 Jun 2017 13:14:16: 11000000 INFO @ Sat, 03 Jun 2017 13:14:19: 12000000 INFO @ Sat, 03 Jun 2017 13:14:24: 12000000 INFO @ Sat, 03 Jun 2017 13:14:24: 12000000 INFO @ Sat, 03 Jun 2017 13:14:27: 13000000 INFO @ Sat, 03 Jun 2017 13:14:33: 13000000 INFO @ Sat, 03 Jun 2017 13:14:33: 13000000 INFO @ Sat, 03 Jun 2017 13:14:36: 14000000 INFO @ Sat, 03 Jun 2017 13:14:41: 14000000 INFO @ Sat, 03 Jun 2017 13:14:41: 14000000 INFO @ Sat, 03 Jun 2017 13:14:44: 15000000 INFO @ Sat, 03 Jun 2017 13:14:50: 15000000 INFO @ Sat, 03 Jun 2017 13:14:50: 15000000 INFO @ Sat, 03 Jun 2017 13:14:52: 16000000 INFO @ Sat, 03 Jun 2017 13:14:55: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:14:55: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:14:55: #1 total tags in treatment: 16320268 INFO @ Sat, 03 Jun 2017 13:14:55: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:14:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:14:58: #1 tags after filtering in treatment: 16315277 INFO @ Sat, 03 Jun 2017 13:14:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:14:58: #1 finished! INFO @ Sat, 03 Jun 2017 13:14:58: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:14:58: 16000000 INFO @ Sat, 03 Jun 2017 13:14:58: 16000000 INFO @ Sat, 03 Jun 2017 13:15:01: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:15:01: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:15:01: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:15:01: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:15:01: #1 total tags in treatment: 16320268 INFO @ Sat, 03 Jun 2017 13:15:01: #1 total tags in treatment: 16320268 INFO @ Sat, 03 Jun 2017 13:15:01: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:15:01: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:15:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:15:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:15:01: #2 number of paired peaks: 598 WARNING @ Sat, 03 Jun 2017 13:15:01: Fewer paired peaks (598) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 598 pairs to build model! INFO @ Sat, 03 Jun 2017 13:15:01: start model_add_line... INFO @ Sat, 03 Jun 2017 13:15:04: #1 tags after filtering in treatment: 16315277 INFO @ Sat, 03 Jun 2017 13:15:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:15:04: #1 finished! INFO @ Sat, 03 Jun 2017 13:15:04: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:15:04: #1 tags after filtering in treatment: 16315277 INFO @ Sat, 03 Jun 2017 13:15:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:15:04: #1 finished! INFO @ Sat, 03 Jun 2017 13:15:04: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:15:07: #2 number of paired peaks: 598 WARNING @ Sat, 03 Jun 2017 13:15:07: Fewer paired peaks (598) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 598 pairs to build model! INFO @ Sat, 03 Jun 2017 13:15:07: start model_add_line... INFO @ Sat, 03 Jun 2017 13:15:07: #2 number of paired peaks: 598 WARNING @ Sat, 03 Jun 2017 13:15:07: Fewer paired peaks (598) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 598 pairs to build model! INFO @ Sat, 03 Jun 2017 13:15:07: start model_add_line... INFO @ Sat, 03 Jun 2017 13:15:08: start X-correlation... INFO @ Sat, 03 Jun 2017 13:15:08: end of X-cor INFO @ Sat, 03 Jun 2017 13:15:08: #2 finished! INFO @ Sat, 03 Jun 2017 13:15:08: #2 predicted fragment length is 52 bps INFO @ Sat, 03 Jun 2017 13:15:08: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 03 Jun 2017 13:15:08: #2.2 Generate R script for model : SRX1433367.10_model.r WARNING @ Sat, 03 Jun 2017 13:15:08: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:15:08: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 03 Jun 2017 13:15:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 13:15:08: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:15:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:15:13: start X-correlation... INFO @ Sat, 03 Jun 2017 13:15:13: end of X-cor INFO @ Sat, 03 Jun 2017 13:15:13: #2 finished! INFO @ Sat, 03 Jun 2017 13:15:13: #2 predicted fragment length is 52 bps INFO @ Sat, 03 Jun 2017 13:15:13: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 03 Jun 2017 13:15:13: #2.2 Generate R script for model : SRX1433367.05_model.r WARNING @ Sat, 03 Jun 2017 13:15:13: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:15:13: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 03 Jun 2017 13:15:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 13:15:13: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:15:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:15:13: start X-correlation... INFO @ Sat, 03 Jun 2017 13:15:13: end of X-cor INFO @ Sat, 03 Jun 2017 13:15:13: #2 finished! INFO @ Sat, 03 Jun 2017 13:15:13: #2 predicted fragment length is 52 bps INFO @ Sat, 03 Jun 2017 13:15:13: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 03 Jun 2017 13:15:13: #2.2 Generate R script for model : SRX1433367.20_model.r WARNING @ Sat, 03 Jun 2017 13:15:13: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:15:13: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 03 Jun 2017 13:15:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 13:15:13: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:15:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:16:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:16:34: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:16:39: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:17:34: #4 Write output xls file... SRX1433367.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:17:34: #4 Write peak in narrowPeak format file... SRX1433367.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:17:34: #4 Write summits bed file... SRX1433367.10_summits.bed INFO @ Sat, 03 Jun 2017 13:17:34: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1761 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:17:37: #4 Write output xls file... SRX1433367.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:17:37: #4 Write peak in narrowPeak format file... SRX1433367.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:17:37: #4 Write summits bed file... SRX1433367.05_summits.bed INFO @ Sat, 03 Jun 2017 13:17:37: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2627 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:17:42: #4 Write output xls file... SRX1433367.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:17:42: #4 Write peak in narrowPeak format file... SRX1433367.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:17:42: #4 Write summits bed file... SRX1433367.20_summits.bed INFO @ Sat, 03 Jun 2017 13:17:43: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (1104 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。