Job ID = 9029242 sra ファイルのダウンロード中... Completed: 639052K bytes transferred in 12 seconds (433954K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 20110 0 20110 0 0 2651 0 --:--:-- 0:00:07 --:--:-- 14929 100 49070 0 49070 0 0 5719 0 --:--:-- 0:00:08 --:--:-- 20943 100 62146 0 62146 0 0 7105 0 --:--:-- 0:00:08 --:--:-- 24769 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 26926875 spots for /home/okishinya/chipatlas/results/dm3/SRX1433391/SRR2919807.sra Written 26926875 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: 00:10:37 26926875 reads; of these: 26926875 (100.00%) were unpaired; of these: 921872 (3.42%) aligned 0 times 19533675 (72.54%) aligned exactly 1 time 6471328 (24.03%) aligned >1 times 96.58% overall alignment rate Time searching: 00:10:37 Overall time: 00:10:37 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] 3589794 / 26005003 = 0.1380 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 13:11:06: # Command line: callpeak -t SRX1433391.bam -f BAM -g dm -n SRX1433391.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1433391.10 # format = BAM # ChIP-seq file = ['SRX1433391.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 13:11:06: # Command line: callpeak -t SRX1433391.bam -f BAM -g dm -n SRX1433391.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1433391.05 # format = BAM # ChIP-seq file = ['SRX1433391.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 13:11:06: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:11:06: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:11:06: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:11:06: # Command line: callpeak -t SRX1433391.bam -f BAM -g dm -n SRX1433391.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1433391.20 # format = BAM # ChIP-seq file = ['SRX1433391.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 13:11:06: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:11:06: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:11:06: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:11:12: 1000000 INFO @ Sat, 03 Jun 2017 13:11:13: 1000000 INFO @ Sat, 03 Jun 2017 13:11:13: 1000000 INFO @ Sat, 03 Jun 2017 13:11:18: 2000000 INFO @ Sat, 03 Jun 2017 13:11:20: 2000000 INFO @ Sat, 03 Jun 2017 13:11:20: 2000000 INFO @ Sat, 03 Jun 2017 13:11:24: 3000000 INFO @ Sat, 03 Jun 2017 13:11:27: 3000000 INFO @ Sat, 03 Jun 2017 13:11:27: 3000000 INFO @ Sat, 03 Jun 2017 13:11:30: 4000000 INFO @ Sat, 03 Jun 2017 13:11:34: 4000000 INFO @ Sat, 03 Jun 2017 13:11:34: 4000000 INFO @ Sat, 03 Jun 2017 13:11:36: 5000000 INFO @ Sat, 03 Jun 2017 13:11:41: 5000000 INFO @ Sat, 03 Jun 2017 13:11:41: 5000000 INFO @ Sat, 03 Jun 2017 13:11:42: 6000000 INFO @ Sat, 03 Jun 2017 13:11:48: 6000000 INFO @ Sat, 03 Jun 2017 13:11:48: 6000000 INFO @ Sat, 03 Jun 2017 13:11:48: 7000000 INFO @ Sat, 03 Jun 2017 13:11:54: 8000000 INFO @ Sat, 03 Jun 2017 13:11:55: 7000000 INFO @ Sat, 03 Jun 2017 13:11:55: 7000000 INFO @ Sat, 03 Jun 2017 13:12:00: 9000000 INFO @ Sat, 03 Jun 2017 13:12:02: 8000000 INFO @ Sat, 03 Jun 2017 13:12:02: 8000000 INFO @ Sat, 03 Jun 2017 13:12:07: 10000000 INFO @ Sat, 03 Jun 2017 13:12:09: 9000000 INFO @ Sat, 03 Jun 2017 13:12:09: 9000000 INFO @ Sat, 03 Jun 2017 13:12:13: 11000000 INFO @ Sat, 03 Jun 2017 13:12:17: 10000000 INFO @ Sat, 03 Jun 2017 13:12:17: 10000000 INFO @ Sat, 03 Jun 2017 13:12:19: 12000000 INFO @ Sat, 03 Jun 2017 13:12:24: 11000000 INFO @ Sat, 03 Jun 2017 13:12:24: 11000000 INFO @ Sat, 03 Jun 2017 13:12:26: 13000000 INFO @ Sat, 03 Jun 2017 13:12:31: 12000000 INFO @ Sat, 03 Jun 2017 13:12:31: 12000000 INFO @ Sat, 03 Jun 2017 13:12:32: 14000000 INFO @ Sat, 03 Jun 2017 13:12:38: 13000000 INFO @ Sat, 03 Jun 2017 13:12:38: 13000000 INFO @ Sat, 03 Jun 2017 13:12:38: 15000000 INFO @ Sat, 03 Jun 2017 13:12:44: 16000000 INFO @ Sat, 03 Jun 2017 13:12:45: 14000000 INFO @ Sat, 03 Jun 2017 13:12:45: 14000000 INFO @ Sat, 03 Jun 2017 13:12:51: 17000000 INFO @ Sat, 03 Jun 2017 13:12:51: 15000000 INFO @ Sat, 03 Jun 2017 13:12:51: 15000000 INFO @ Sat, 03 Jun 2017 13:12:57: 18000000 INFO @ Sat, 03 Jun 2017 13:12:58: 16000000 INFO @ Sat, 03 Jun 2017 13:12:58: 16000000 INFO @ Sat, 03 Jun 2017 13:13:03: 19000000 INFO @ Sat, 03 Jun 2017 13:13:05: 17000000 INFO @ Sat, 03 Jun 2017 13:13:05: 17000000 INFO @ Sat, 03 Jun 2017 13:13:09: 20000000 INFO @ Sat, 03 Jun 2017 13:13:12: 18000000 INFO @ Sat, 03 Jun 2017 13:13:12: 18000000 INFO @ Sat, 03 Jun 2017 13:13:17: 21000000 INFO @ Sat, 03 Jun 2017 13:13:20: 19000000 INFO @ Sat, 03 Jun 2017 13:13:20: 19000000 INFO @ Sat, 03 Jun 2017 13:13:25: 22000000 INFO @ Sat, 03 Jun 2017 13:13:28: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 13:13:28: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 13:13:28: #1 total tags in treatment: 22415209 INFO @ Sat, 03 Jun 2017 13:13:28: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:13:28: #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 13:13:29: 20000000 INFO @ Sat, 03 Jun 2017 13:13:29: 20000000 INFO @ Sat, 03 Jun 2017 13:13:33: #1 tags after filtering in treatment: 22408092 INFO @ Sat, 03 Jun 2017 13:13:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:13:33: #1 finished! INFO @ Sat, 03 Jun 2017 13:13:33: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:13:37: #2 number of paired peaks: 314 WARNING @ Sat, 03 Jun 2017 13:13:37: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Sat, 03 Jun 2017 13:13:37: start model_add_line... INFO @ Sat, 03 Jun 2017 13:13:37: 21000000 INFO @ Sat, 03 Jun 2017 13:13:37: 21000000 INFO @ Sat, 03 Jun 2017 13:13:42: start X-correlation... INFO @ Sat, 03 Jun 2017 13:13:42: end of X-cor INFO @ Sat, 03 Jun 2017 13:13:42: #2 finished! INFO @ Sat, 03 Jun 2017 13:13:42: #2 predicted fragment length is 41 bps INFO @ Sat, 03 Jun 2017 13:13:42: #2 alternative fragment length(s) may be 3,41 bps INFO @ Sat, 03 Jun 2017 13:13:42: #2.2 Generate R script for model : SRX1433391.05_model.r WARNING @ Sat, 03 Jun 2017 13:13:42: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:13:42: #2 You may need to consider one of the other alternative d(s): 3,41 WARNING @ Sat, 03 Jun 2017 13:13:42: #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 13:13:42: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:13:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:13:46: 22000000 INFO @ Sat, 03 Jun 2017 13:13:46: 22000000 INFO @ Sat, 03 Jun 2017 13:13:49: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 13:13:49: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 13:13:49: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 13:13:49: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 13:13:49: #1 total tags in treatment: 22415209 INFO @ Sat, 03 Jun 2017 13:13:49: #1 total tags in treatment: 22415209 INFO @ Sat, 03 Jun 2017 13:13:49: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:13:49: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:13:49: #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 13:13:49: #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 13:13:54: #1 tags after filtering in treatment: 22408092 INFO @ Sat, 03 Jun 2017 13:13:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:13:54: #1 finished! INFO @ Sat, 03 Jun 2017 13:13:54: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:13:54: #1 tags after filtering in treatment: 22408092 INFO @ Sat, 03 Jun 2017 13:13:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:13:54: #1 finished! INFO @ Sat, 03 Jun 2017 13:13:54: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:13:57: #2 number of paired peaks: 314 WARNING @ Sat, 03 Jun 2017 13:13:57: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Sat, 03 Jun 2017 13:13:57: start model_add_line... INFO @ Sat, 03 Jun 2017 13:13:58: #2 number of paired peaks: 314 WARNING @ Sat, 03 Jun 2017 13:13:58: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Sat, 03 Jun 2017 13:13:58: start model_add_line... INFO @ Sat, 03 Jun 2017 13:14:03: start X-correlation... INFO @ Sat, 03 Jun 2017 13:14:03: end of X-cor INFO @ Sat, 03 Jun 2017 13:14:03: #2 finished! INFO @ Sat, 03 Jun 2017 13:14:03: #2 predicted fragment length is 41 bps INFO @ Sat, 03 Jun 2017 13:14:03: #2 alternative fragment length(s) may be 3,41 bps INFO @ Sat, 03 Jun 2017 13:14:03: #2.2 Generate R script for model : SRX1433391.10_model.r WARNING @ Sat, 03 Jun 2017 13:14:03: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:14:03: #2 You may need to consider one of the other alternative d(s): 3,41 WARNING @ Sat, 03 Jun 2017 13:14:03: #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 13:14:03: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:14:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:14:03: start X-correlation... INFO @ Sat, 03 Jun 2017 13:14:03: end of X-cor INFO @ Sat, 03 Jun 2017 13:14:03: #2 finished! INFO @ Sat, 03 Jun 2017 13:14:03: #2 predicted fragment length is 41 bps INFO @ Sat, 03 Jun 2017 13:14:03: #2 alternative fragment length(s) may be 3,41 bps INFO @ Sat, 03 Jun 2017 13:14:03: #2.2 Generate R script for model : SRX1433391.20_model.r WARNING @ Sat, 03 Jun 2017 13:14:03: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:14:03: #2 You may need to consider one of the other alternative d(s): 3,41 WARNING @ Sat, 03 Jun 2017 13:14:03: #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 13:14:03: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:14:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:15:35: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:15:51: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:15:57: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:16:59: #4 Write output xls file... SRX1433391.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:16:59: #4 Write peak in narrowPeak format file... SRX1433391.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:16:59: #4 Write summits bed file... SRX1433391.05_summits.bed INFO @ Sat, 03 Jun 2017 13:16:59: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3396 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:17:19: #4 Write output xls file... SRX1433391.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:17:19: #4 Write peak in narrowPeak format file... SRX1433391.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:17:19: #4 Write summits bed file... SRX1433391.20_summits.bed INFO @ Sat, 03 Jun 2017 13:17:19: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1201 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:17:19: #4 Write output xls file... SRX1433391.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:17:19: #4 Write peak in narrowPeak format file... SRX1433391.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:17:19: #4 Write summits bed file... SRX1433391.10_summits.bed INFO @ Sat, 03 Jun 2017 13:17:19: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2280 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。