Job ID = 9029243 sra ファイルのダウンロード中... Completed: 656321K bytes transferred in 11 seconds (464752K 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 --:--:-- 0:00:07 --:--:-- 0 100 7663 0 7663 0 0 929 0 --:--:-- 0:00:08 --:--:-- 4215 100 22318 0 22318 0 0 2415 0 --:--:-- 0:00:09 --:--:-- 7925 100 38318 0 38318 0 0 3804 0 --:--:-- 0:00:10 --:--:-- 10506 100 52726 0 52726 0 0 4817 0 --:--:-- 0:00:10 --:--:-- 11665 100 57193 0 57193 0 0 3832 0 --:--:-- 0:00:14 --:--:-- 7446 100 59064 0 59064 0 0 3957 0 --:--:-- 0:00:14 --:--:-- 7693 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 28468981 spots for /home/okishinya/chipatlas/results/dm3/SRX1433392/SRR2919808.sra Written 28468981 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:18 28468981 reads; of these: 28468981 (100.00%) were unpaired; of these: 790968 (2.78%) aligned 0 times 19611096 (68.89%) aligned exactly 1 time 8066917 (28.34%) aligned >1 times 97.22% overall alignment rate Time searching: 00:12:19 Overall time: 00:12:19 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] 4072569 / 27678013 = 0.1471 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 13:13:09: # Command line: callpeak -t SRX1433392.bam -f BAM -g dm -n SRX1433392.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1433392.05 # format = BAM # ChIP-seq file = ['SRX1433392.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 13:13:09: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:13:09: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:13:09: # Command line: callpeak -t SRX1433392.bam -f BAM -g dm -n SRX1433392.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1433392.20 # format = BAM # ChIP-seq file = ['SRX1433392.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 13:13:09: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:13:09: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:13:09: # Command line: callpeak -t SRX1433392.bam -f BAM -g dm -n SRX1433392.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1433392.10 # format = BAM # ChIP-seq file = ['SRX1433392.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 13:13:09: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:13:09: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:13:16: 1000000 INFO @ Sat, 03 Jun 2017 13:13:16: 1000000 INFO @ Sat, 03 Jun 2017 13:13:16: 1000000 INFO @ Sat, 03 Jun 2017 13:13:23: 2000000 INFO @ Sat, 03 Jun 2017 13:13:23: 2000000 INFO @ Sat, 03 Jun 2017 13:13:23: 2000000 INFO @ Sat, 03 Jun 2017 13:13:30: 3000000 INFO @ Sat, 03 Jun 2017 13:13:30: 3000000 INFO @ Sat, 03 Jun 2017 13:13:31: 3000000 INFO @ Sat, 03 Jun 2017 13:13:36: 4000000 INFO @ Sat, 03 Jun 2017 13:13:37: 4000000 INFO @ Sat, 03 Jun 2017 13:13:38: 4000000 INFO @ Sat, 03 Jun 2017 13:13:42: 5000000 INFO @ Sat, 03 Jun 2017 13:13:45: 5000000 INFO @ Sat, 03 Jun 2017 13:13:45: 5000000 INFO @ Sat, 03 Jun 2017 13:13:48: 6000000 INFO @ Sat, 03 Jun 2017 13:13:52: 6000000 INFO @ Sat, 03 Jun 2017 13:13:52: 6000000 INFO @ Sat, 03 Jun 2017 13:13:55: 7000000 INFO @ Sat, 03 Jun 2017 13:13:57: 7000000 INFO @ Sat, 03 Jun 2017 13:13:58: 7000000 INFO @ Sat, 03 Jun 2017 13:14:01: 8000000 INFO @ Sat, 03 Jun 2017 13:14:04: 8000000 INFO @ Sat, 03 Jun 2017 13:14:04: 8000000 INFO @ Sat, 03 Jun 2017 13:14:08: 9000000 INFO @ Sat, 03 Jun 2017 13:14:11: 9000000 INFO @ Sat, 03 Jun 2017 13:14:12: 9000000 INFO @ Sat, 03 Jun 2017 13:14:16: 10000000 INFO @ Sat, 03 Jun 2017 13:14:17: 10000000 INFO @ Sat, 03 Jun 2017 13:14:20: 10000000 INFO @ Sat, 03 Jun 2017 13:14:24: 11000000 INFO @ Sat, 03 Jun 2017 13:14:25: 11000000 INFO @ Sat, 03 Jun 2017 13:14:27: 11000000 INFO @ Sat, 03 Jun 2017 13:14:31: 12000000 INFO @ Sat, 03 Jun 2017 13:14:32: 12000000 INFO @ Sat, 03 Jun 2017 13:14:35: 12000000 INFO @ Sat, 03 Jun 2017 13:14:39: 13000000 INFO @ Sat, 03 Jun 2017 13:14:39: 13000000 INFO @ Sat, 03 Jun 2017 13:14:43: 13000000 INFO @ Sat, 03 Jun 2017 13:14:45: 14000000 INFO @ Sat, 03 Jun 2017 13:14:47: 14000000 INFO @ Sat, 03 Jun 2017 13:14:51: 14000000 INFO @ Sat, 03 Jun 2017 13:14:52: 15000000 INFO @ Sat, 03 Jun 2017 13:14:54: 15000000 INFO @ Sat, 03 Jun 2017 13:14:59: 15000000 INFO @ Sat, 03 Jun 2017 13:14:59: 16000000 INFO @ Sat, 03 Jun 2017 13:15:02: 16000000 INFO @ Sat, 03 Jun 2017 13:15:06: 17000000 INFO @ Sat, 03 Jun 2017 13:15:06: 16000000 INFO @ Sat, 03 Jun 2017 13:15:10: 17000000 INFO @ Sat, 03 Jun 2017 13:15:13: 18000000 INFO @ Sat, 03 Jun 2017 13:15:14: 17000000 INFO @ Sat, 03 Jun 2017 13:15:18: 18000000 INFO @ Sat, 03 Jun 2017 13:15:20: 19000000 INFO @ Sat, 03 Jun 2017 13:15:22: 18000000 INFO @ Sat, 03 Jun 2017 13:15:25: 19000000 INFO @ Sat, 03 Jun 2017 13:15:27: 20000000 INFO @ Sat, 03 Jun 2017 13:15:30: 19000000 INFO @ Sat, 03 Jun 2017 13:15:33: 20000000 INFO @ Sat, 03 Jun 2017 13:15:34: 21000000 INFO @ Sat, 03 Jun 2017 13:15:38: 20000000 INFO @ Sat, 03 Jun 2017 13:15:41: 22000000 INFO @ Sat, 03 Jun 2017 13:15:41: 21000000 INFO @ Sat, 03 Jun 2017 13:15:46: 21000000 INFO @ Sat, 03 Jun 2017 13:15:48: 23000000 INFO @ Sat, 03 Jun 2017 13:15:49: 22000000 INFO @ Sat, 03 Jun 2017 13:15:52: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 13:15:52: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 13:15:52: #1 total tags in treatment: 23605444 INFO @ Sat, 03 Jun 2017 13:15:52: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:15:52: #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 13:15:53: 22000000 INFO @ Sat, 03 Jun 2017 13:15:56: 23000000 INFO @ Sat, 03 Jun 2017 13:15:57: #1 tags after filtering in treatment: 23598736 INFO @ Sat, 03 Jun 2017 13:15:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:15:57: #1 finished! INFO @ Sat, 03 Jun 2017 13:15:57: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:16:00: 23000000 INFO @ Sat, 03 Jun 2017 13:16:00: #2 number of paired peaks: 301 WARNING @ Sat, 03 Jun 2017 13:16:00: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Sat, 03 Jun 2017 13:16:00: start model_add_line... INFO @ Sat, 03 Jun 2017 13:16:01: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 13:16:01: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 13:16:01: #1 total tags in treatment: 23605444 INFO @ Sat, 03 Jun 2017 13:16:01: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:16:01: #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 13:16:04: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 13:16:04: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 13:16:04: #1 total tags in treatment: 23605444 INFO @ Sat, 03 Jun 2017 13:16:04: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:16:04: #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 13:16:06: start X-correlation... INFO @ Sat, 03 Jun 2017 13:16:06: end of X-cor INFO @ Sat, 03 Jun 2017 13:16:06: #2 finished! INFO @ Sat, 03 Jun 2017 13:16:06: #2 predicted fragment length is 41 bps INFO @ Sat, 03 Jun 2017 13:16:06: #2 alternative fragment length(s) may be 3,41 bps INFO @ Sat, 03 Jun 2017 13:16:06: #2.2 Generate R script for model : SRX1433392.10_model.r WARNING @ Sat, 03 Jun 2017 13:16:06: #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 13:16:06: #2 You may need to consider one of the other alternative d(s): 3,41 WARNING @ Sat, 03 Jun 2017 13:16:06: #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 13:16:06: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:16:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:16:06: #1 tags after filtering in treatment: 23598736 INFO @ Sat, 03 Jun 2017 13:16:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:16:06: #1 finished! INFO @ Sat, 03 Jun 2017 13:16:06: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:16:08: #1 tags after filtering in treatment: 23598736 INFO @ Sat, 03 Jun 2017 13:16:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:16:08: #1 finished! INFO @ Sat, 03 Jun 2017 13:16:08: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:16:10: #2 number of paired peaks: 301 WARNING @ Sat, 03 Jun 2017 13:16:10: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Sat, 03 Jun 2017 13:16:10: start model_add_line... INFO @ Sat, 03 Jun 2017 13:16:13: #2 number of paired peaks: 301 WARNING @ Sat, 03 Jun 2017 13:16:13: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Sat, 03 Jun 2017 13:16:13: start model_add_line... INFO @ Sat, 03 Jun 2017 13:16:16: start X-correlation... INFO @ Sat, 03 Jun 2017 13:16:16: end of X-cor INFO @ Sat, 03 Jun 2017 13:16:16: #2 finished! INFO @ Sat, 03 Jun 2017 13:16:16: #2 predicted fragment length is 41 bps INFO @ Sat, 03 Jun 2017 13:16:16: #2 alternative fragment length(s) may be 3,41 bps INFO @ Sat, 03 Jun 2017 13:16:16: #2.2 Generate R script for model : SRX1433392.20_model.r WARNING @ Sat, 03 Jun 2017 13:16:16: #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 13:16:16: #2 You may need to consider one of the other alternative d(s): 3,41 WARNING @ Sat, 03 Jun 2017 13:16:16: #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 13:16:16: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:16:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:16:18: start X-correlation... INFO @ Sat, 03 Jun 2017 13:16:18: end of X-cor INFO @ Sat, 03 Jun 2017 13:16:18: #2 finished! INFO @ Sat, 03 Jun 2017 13:16:18: #2 predicted fragment length is 41 bps INFO @ Sat, 03 Jun 2017 13:16:18: #2 alternative fragment length(s) may be 3,41 bps INFO @ Sat, 03 Jun 2017 13:16:18: #2.2 Generate R script for model : SRX1433392.05_model.r WARNING @ Sat, 03 Jun 2017 13:16:18: #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 13:16:18: #2 You may need to consider one of the other alternative d(s): 3,41 WARNING @ Sat, 03 Jun 2017 13:16:18: #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 13:16:18: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:16:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:18:04: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:18:12: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:18:20: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:19:28: #4 Write output xls file... SRX1433392.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:19:28: #4 Write peak in narrowPeak format file... SRX1433392.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:19:28: #4 Write summits bed file... SRX1433392.10_summits.bed INFO @ Sat, 03 Jun 2017 13:19:28: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2392 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:19:42: #4 Write output xls file... SRX1433392.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:19:42: #4 Write peak in narrowPeak format file... SRX1433392.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:19:42: #4 Write summits bed file... SRX1433392.20_summits.bed INFO @ Sat, 03 Jun 2017 13:19:42: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1267 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:19:50: #4 Write output xls file... SRX1433392.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:19:50: #4 Write peak in narrowPeak format file... SRX1433392.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:19:50: #4 Write summits bed file... SRX1433392.05_summits.bed INFO @ Sat, 03 Jun 2017 13:19:50: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3499 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。