Job ID = 9029815 sra ファイルのダウンロード中... Completed: 791042K bytes transferred in 9 seconds (696678K 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 22318 0 22318 0 0 2915 0 --:--:-- 0:00:07 --:--:-- 17811 100 29932 0 29932 0 0 3747 0 --:--:-- 0:00:07 --:--:-- 18884 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 34893030 spots for /home/okishinya/chipatlas/results/dm3/SRX2172427/SRR4252438.sra Written 34893030 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: 00:13:09 34893030 reads; of these: 34893030 (100.00%) were unpaired; of these: 1487411 (4.26%) aligned 0 times 25467142 (72.99%) aligned exactly 1 time 7938477 (22.75%) aligned >1 times 95.74% overall alignment rate Time searching: 00:13:09 Overall time: 00:13:09 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 16 files... [bam_rmdupse_core] 7958332 / 33405619 = 0.2382 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 15:45:50: # Command line: callpeak -t SRX2172427.bam -f BAM -g dm -n SRX2172427.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2172427.10 # format = BAM # ChIP-seq file = ['SRX2172427.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 15:45:50: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:45:50: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:45:50: # Command line: callpeak -t SRX2172427.bam -f BAM -g dm -n SRX2172427.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2172427.20 # format = BAM # ChIP-seq file = ['SRX2172427.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 15:45:50: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:45:50: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:45:50: # Command line: callpeak -t SRX2172427.bam -f BAM -g dm -n SRX2172427.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2172427.05 # format = BAM # ChIP-seq file = ['SRX2172427.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 15:45:50: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:45:50: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:45:55: 1000000 INFO @ Sat, 03 Jun 2017 15:45:55: 1000000 INFO @ Sat, 03 Jun 2017 15:45:55: 1000000 INFO @ Sat, 03 Jun 2017 15:46:00: 2000000 INFO @ Sat, 03 Jun 2017 15:46:00: 2000000 INFO @ Sat, 03 Jun 2017 15:46:00: 2000000 INFO @ Sat, 03 Jun 2017 15:46:05: 3000000 INFO @ Sat, 03 Jun 2017 15:46:06: 3000000 INFO @ Sat, 03 Jun 2017 15:46:06: 3000000 INFO @ Sat, 03 Jun 2017 15:46:10: 4000000 INFO @ Sat, 03 Jun 2017 15:46:11: 4000000 INFO @ Sat, 03 Jun 2017 15:46:11: 4000000 INFO @ Sat, 03 Jun 2017 15:46:16: 5000000 INFO @ Sat, 03 Jun 2017 15:46:16: 5000000 INFO @ Sat, 03 Jun 2017 15:46:16: 5000000 INFO @ Sat, 03 Jun 2017 15:46:21: 6000000 INFO @ Sat, 03 Jun 2017 15:46:21: 6000000 INFO @ Sat, 03 Jun 2017 15:46:21: 6000000 INFO @ Sat, 03 Jun 2017 15:46:26: 7000000 INFO @ Sat, 03 Jun 2017 15:46:27: 7000000 INFO @ Sat, 03 Jun 2017 15:46:27: 7000000 INFO @ Sat, 03 Jun 2017 15:46:31: 8000000 INFO @ Sat, 03 Jun 2017 15:46:32: 8000000 INFO @ Sat, 03 Jun 2017 15:46:32: 8000000 INFO @ Sat, 03 Jun 2017 15:46:36: 9000000 INFO @ Sat, 03 Jun 2017 15:46:37: 9000000 INFO @ Sat, 03 Jun 2017 15:46:37: 9000000 INFO @ Sat, 03 Jun 2017 15:46:41: 10000000 INFO @ Sat, 03 Jun 2017 15:46:43: 10000000 INFO @ Sat, 03 Jun 2017 15:46:43: 10000000 INFO @ Sat, 03 Jun 2017 15:46:47: 11000000 INFO @ Sat, 03 Jun 2017 15:46:48: 11000000 INFO @ Sat, 03 Jun 2017 15:46:49: 11000000 INFO @ Sat, 03 Jun 2017 15:46:53: 12000000 INFO @ Sat, 03 Jun 2017 15:46:53: 12000000 INFO @ Sat, 03 Jun 2017 15:46:55: 12000000 INFO @ Sat, 03 Jun 2017 15:46:58: 13000000 INFO @ Sat, 03 Jun 2017 15:46:58: 13000000 INFO @ Sat, 03 Jun 2017 15:47:01: 13000000 INFO @ Sat, 03 Jun 2017 15:47:03: 14000000 INFO @ Sat, 03 Jun 2017 15:47:04: 14000000 INFO @ Sat, 03 Jun 2017 15:47:08: 14000000 INFO @ Sat, 03 Jun 2017 15:47:08: 15000000 INFO @ Sat, 03 Jun 2017 15:47:10: 15000000 INFO @ Sat, 03 Jun 2017 15:47:14: 16000000 INFO @ Sat, 03 Jun 2017 15:47:14: 15000000 INFO @ Sat, 03 Jun 2017 15:47:16: 16000000 INFO @ Sat, 03 Jun 2017 15:47:21: 17000000 INFO @ Sat, 03 Jun 2017 15:47:22: 16000000 INFO @ Sat, 03 Jun 2017 15:47:22: 17000000 INFO @ Sat, 03 Jun 2017 15:47:28: 18000000 INFO @ Sat, 03 Jun 2017 15:47:28: 18000000 INFO @ Sat, 03 Jun 2017 15:47:29: 17000000 INFO @ Sat, 03 Jun 2017 15:47:34: 19000000 INFO @ Sat, 03 Jun 2017 15:47:35: 19000000 INFO @ Sat, 03 Jun 2017 15:47:37: 18000000 INFO @ Sat, 03 Jun 2017 15:47:41: 20000000 INFO @ Sat, 03 Jun 2017 15:47:42: 20000000 INFO @ Sat, 03 Jun 2017 15:47:45: 19000000 INFO @ Sat, 03 Jun 2017 15:47:48: 21000000 INFO @ Sat, 03 Jun 2017 15:47:50: 21000000 INFO @ Sat, 03 Jun 2017 15:47:53: 20000000 INFO @ Sat, 03 Jun 2017 15:47:55: 22000000 INFO @ Sat, 03 Jun 2017 15:47:57: 22000000 INFO @ Sat, 03 Jun 2017 15:48:01: 21000000 INFO @ Sat, 03 Jun 2017 15:48:03: 23000000 INFO @ Sat, 03 Jun 2017 15:48:04: 23000000 INFO @ Sat, 03 Jun 2017 15:48:09: 22000000 INFO @ Sat, 03 Jun 2017 15:48:11: 24000000 INFO @ Sat, 03 Jun 2017 15:48:11: 24000000 INFO @ Sat, 03 Jun 2017 15:48:17: 23000000 INFO @ Sat, 03 Jun 2017 15:48:18: 25000000 INFO @ Sat, 03 Jun 2017 15:48:19: 25000000 INFO @ Sat, 03 Jun 2017 15:48:22: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 15:48:22: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 15:48:22: #1 total tags in treatment: 25447287 INFO @ Sat, 03 Jun 2017 15:48:22: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:48:22: #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 15:48:22: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 15:48:22: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 15:48:22: #1 total tags in treatment: 25447287 INFO @ Sat, 03 Jun 2017 15:48:22: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:48:22: #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 15:48:25: 24000000 INFO @ Sat, 03 Jun 2017 15:48:27: #1 tags after filtering in treatment: 25437580 INFO @ Sat, 03 Jun 2017 15:48:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:48:27: #1 finished! INFO @ Sat, 03 Jun 2017 15:48:27: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:48:27: #1 tags after filtering in treatment: 25437580 INFO @ Sat, 03 Jun 2017 15:48:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:48:27: #1 finished! INFO @ Sat, 03 Jun 2017 15:48:27: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:48:31: #2 number of paired peaks: 475 WARNING @ Sat, 03 Jun 2017 15:48:31: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Sat, 03 Jun 2017 15:48:31: start model_add_line... INFO @ Sat, 03 Jun 2017 15:48:32: #2 number of paired peaks: 475 WARNING @ Sat, 03 Jun 2017 15:48:32: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Sat, 03 Jun 2017 15:48:32: start model_add_line... INFO @ Sat, 03 Jun 2017 15:48:33: 25000000 INFO @ Sat, 03 Jun 2017 15:48:38: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 15:48:38: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 15:48:38: #1 total tags in treatment: 25447287 INFO @ Sat, 03 Jun 2017 15:48:38: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:48:38: #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 15:48:40: start X-correlation... INFO @ Sat, 03 Jun 2017 15:48:40: end of X-cor INFO @ Sat, 03 Jun 2017 15:48:40: #2 finished! INFO @ Sat, 03 Jun 2017 15:48:40: #2 predicted fragment length is 95 bps INFO @ Sat, 03 Jun 2017 15:48:40: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 03 Jun 2017 15:48:40: #2.2 Generate R script for model : SRX2172427.10_model.r WARNING @ Sat, 03 Jun 2017 15:48:40: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:48:40: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sat, 03 Jun 2017 15:48:40: #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 15:48:40: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:48:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:48:40: start X-correlation... INFO @ Sat, 03 Jun 2017 15:48:40: end of X-cor INFO @ Sat, 03 Jun 2017 15:48:40: #2 finished! INFO @ Sat, 03 Jun 2017 15:48:40: #2 predicted fragment length is 95 bps INFO @ Sat, 03 Jun 2017 15:48:40: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 03 Jun 2017 15:48:40: #2.2 Generate R script for model : SRX2172427.20_model.r WARNING @ Sat, 03 Jun 2017 15:48:40: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:48:40: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sat, 03 Jun 2017 15:48:40: #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 15:48:40: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:48:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:48:42: #1 tags after filtering in treatment: 25437580 INFO @ Sat, 03 Jun 2017 15:48:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:48:42: #1 finished! INFO @ Sat, 03 Jun 2017 15:48:42: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:48:46: #2 number of paired peaks: 475 WARNING @ Sat, 03 Jun 2017 15:48:46: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Sat, 03 Jun 2017 15:48:46: start model_add_line... INFO @ Sat, 03 Jun 2017 15:48:55: start X-correlation... INFO @ Sat, 03 Jun 2017 15:48:55: end of X-cor INFO @ Sat, 03 Jun 2017 15:48:55: #2 finished! INFO @ Sat, 03 Jun 2017 15:48:55: #2 predicted fragment length is 95 bps INFO @ Sat, 03 Jun 2017 15:48:55: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 03 Jun 2017 15:48:55: #2.2 Generate R script for model : SRX2172427.05_model.r WARNING @ Sat, 03 Jun 2017 15:48:55: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:48:55: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sat, 03 Jun 2017 15:48:55: #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 15:48:55: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:48:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:50:44: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:50:51: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:51:04: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:52:13: #4 Write output xls file... SRX2172427.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:52:13: #4 Write peak in narrowPeak format file... SRX2172427.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:52:13: #4 Write summits bed file... SRX2172427.20_summits.bed INFO @ Sat, 03 Jun 2017 15:52:13: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7044 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:52:27: #4 Write output xls file... SRX2172427.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:52:27: #4 Write peak in narrowPeak format file... SRX2172427.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:52:27: #4 Write summits bed file... SRX2172427.10_summits.bed INFO @ Sat, 03 Jun 2017 15:52:27: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11409 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:52:46: #4 Write output xls file... SRX2172427.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:52:46: #4 Write peak in narrowPeak format file... SRX2172427.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:52:46: #4 Write summits bed file... SRX2172427.05_summits.bed INFO @ Sat, 03 Jun 2017 15:52:46: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (14841 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。