Job ID = 9029225 sra ファイルのダウンロード中... Completed: 717606K bytes transferred in 11 seconds (509814K 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 2640 0 --:--:-- 0:00:07 --:--:-- 14689 100 51278 0 51278 0 0 5953 0 --:--:-- 0:00:08 --:--:-- 21672 100 60080 0 60080 0 0 6843 0 --:--:-- 0:00:08 --:--:-- 23737 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 29780594 spots for /home/okishinya/chipatlas/results/dm3/SRX1433365/SRR2919830.sra Written 29780594 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: 00:11:31 29780594 reads; of these: 29780594 (100.00%) were unpaired; of these: 816449 (2.74%) aligned 0 times 22675455 (76.14%) aligned exactly 1 time 6288690 (21.12%) aligned >1 times 97.26% overall alignment rate Time searching: 00:11:31 Overall time: 00:11:31 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] 5446062 / 28964145 = 0.1880 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 13:12:17: # Command line: callpeak -t SRX1433365.bam -f BAM -g dm -n SRX1433365.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1433365.05 # format = BAM # ChIP-seq file = ['SRX1433365.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 13:12:17: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:12:17: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:12:17: # Command line: callpeak -t SRX1433365.bam -f BAM -g dm -n SRX1433365.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1433365.20 # format = BAM # ChIP-seq file = ['SRX1433365.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 13:12:17: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:12:17: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:12:17: # Command line: callpeak -t SRX1433365.bam -f BAM -g dm -n SRX1433365.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1433365.10 # format = BAM # ChIP-seq file = ['SRX1433365.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 13:12:17: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:12:17: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:12:22: 1000000 INFO @ Sat, 03 Jun 2017 13:12:22: 1000000 INFO @ Sat, 03 Jun 2017 13:12:22: 1000000 INFO @ Sat, 03 Jun 2017 13:12:28: 2000000 INFO @ Sat, 03 Jun 2017 13:12:28: 2000000 INFO @ Sat, 03 Jun 2017 13:12:28: 2000000 INFO @ Sat, 03 Jun 2017 13:12:33: 3000000 INFO @ Sat, 03 Jun 2017 13:12:33: 3000000 INFO @ Sat, 03 Jun 2017 13:12:34: 3000000 INFO @ Sat, 03 Jun 2017 13:12:39: 4000000 INFO @ Sat, 03 Jun 2017 13:12:39: 4000000 INFO @ Sat, 03 Jun 2017 13:12:39: 4000000 INFO @ Sat, 03 Jun 2017 13:12:45: 5000000 INFO @ Sat, 03 Jun 2017 13:12:45: 5000000 INFO @ Sat, 03 Jun 2017 13:12:45: 5000000 INFO @ Sat, 03 Jun 2017 13:12:50: 6000000 INFO @ Sat, 03 Jun 2017 13:12:51: 6000000 INFO @ Sat, 03 Jun 2017 13:12:51: 6000000 INFO @ Sat, 03 Jun 2017 13:12:56: 7000000 INFO @ Sat, 03 Jun 2017 13:12:56: 7000000 INFO @ Sat, 03 Jun 2017 13:12:57: 7000000 INFO @ Sat, 03 Jun 2017 13:13:02: 8000000 INFO @ Sat, 03 Jun 2017 13:13:03: 8000000 INFO @ Sat, 03 Jun 2017 13:13:03: 8000000 INFO @ Sat, 03 Jun 2017 13:13:08: 9000000 INFO @ Sat, 03 Jun 2017 13:13:08: 9000000 INFO @ Sat, 03 Jun 2017 13:13:09: 9000000 INFO @ Sat, 03 Jun 2017 13:13:14: 10000000 INFO @ Sat, 03 Jun 2017 13:13:14: 10000000 INFO @ Sat, 03 Jun 2017 13:13:15: 10000000 INFO @ Sat, 03 Jun 2017 13:13:20: 11000000 INFO @ Sat, 03 Jun 2017 13:13:20: 11000000 INFO @ Sat, 03 Jun 2017 13:13:21: 11000000 INFO @ Sat, 03 Jun 2017 13:13:26: 12000000 INFO @ Sat, 03 Jun 2017 13:13:26: 12000000 INFO @ Sat, 03 Jun 2017 13:13:27: 12000000 INFO @ Sat, 03 Jun 2017 13:13:31: 13000000 INFO @ Sat, 03 Jun 2017 13:13:32: 13000000 INFO @ Sat, 03 Jun 2017 13:13:33: 13000000 INFO @ Sat, 03 Jun 2017 13:13:38: 14000000 INFO @ Sat, 03 Jun 2017 13:13:38: 14000000 INFO @ Sat, 03 Jun 2017 13:13:39: 14000000 INFO @ Sat, 03 Jun 2017 13:13:44: 15000000 INFO @ Sat, 03 Jun 2017 13:13:44: 15000000 INFO @ Sat, 03 Jun 2017 13:13:46: 15000000 INFO @ Sat, 03 Jun 2017 13:13:50: 16000000 INFO @ Sat, 03 Jun 2017 13:13:50: 16000000 INFO @ Sat, 03 Jun 2017 13:13:52: 16000000 INFO @ Sat, 03 Jun 2017 13:13:57: 17000000 INFO @ Sat, 03 Jun 2017 13:13:57: 17000000 INFO @ Sat, 03 Jun 2017 13:13:58: 17000000 INFO @ Sat, 03 Jun 2017 13:14:03: 18000000 INFO @ Sat, 03 Jun 2017 13:14:03: 18000000 INFO @ Sat, 03 Jun 2017 13:14:05: 18000000 INFO @ Sat, 03 Jun 2017 13:14:09: 19000000 INFO @ Sat, 03 Jun 2017 13:14:09: 19000000 INFO @ Sat, 03 Jun 2017 13:14:11: 19000000 INFO @ Sat, 03 Jun 2017 13:14:15: 20000000 INFO @ Sat, 03 Jun 2017 13:14:15: 20000000 INFO @ Sat, 03 Jun 2017 13:14:17: 20000000 INFO @ Sat, 03 Jun 2017 13:14:21: 21000000 INFO @ Sat, 03 Jun 2017 13:14:21: 21000000 INFO @ Sat, 03 Jun 2017 13:14:23: 21000000 INFO @ Sat, 03 Jun 2017 13:14:27: 22000000 INFO @ Sat, 03 Jun 2017 13:14:27: 22000000 INFO @ Sat, 03 Jun 2017 13:14:29: 22000000 INFO @ Sat, 03 Jun 2017 13:14:33: 23000000 INFO @ Sat, 03 Jun 2017 13:14:34: 23000000 INFO @ Sat, 03 Jun 2017 13:14:35: 23000000 INFO @ Sat, 03 Jun 2017 13:14:36: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:14:36: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:14:36: #1 total tags in treatment: 23518083 INFO @ Sat, 03 Jun 2017 13:14:36: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:14:36: #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 13:14:37: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:14:37: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:14:37: #1 total tags in treatment: 23518083 INFO @ Sat, 03 Jun 2017 13:14:37: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:14:37: #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 13:14:39: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:14:39: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:14:39: #1 total tags in treatment: 23518083 INFO @ Sat, 03 Jun 2017 13:14:39: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:14:39: #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 13:14:41: #1 tags after filtering in treatment: 23512081 INFO @ Sat, 03 Jun 2017 13:14:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:14:41: #1 finished! INFO @ Sat, 03 Jun 2017 13:14:41: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:14:41: #1 tags after filtering in treatment: 23512081 INFO @ Sat, 03 Jun 2017 13:14:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:14:41: #1 finished! INFO @ Sat, 03 Jun 2017 13:14:41: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:14:43: #1 tags after filtering in treatment: 23512081 INFO @ Sat, 03 Jun 2017 13:14:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:14:43: #1 finished! INFO @ Sat, 03 Jun 2017 13:14:43: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:14:45: #2 number of paired peaks: 112 WARNING @ Sat, 03 Jun 2017 13:14:45: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Sat, 03 Jun 2017 13:14:45: start model_add_line... INFO @ Sat, 03 Jun 2017 13:14:45: #2 number of paired peaks: 112 WARNING @ Sat, 03 Jun 2017 13:14:45: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Sat, 03 Jun 2017 13:14:45: start model_add_line... INFO @ Sat, 03 Jun 2017 13:14:46: #2 number of paired peaks: 112 WARNING @ Sat, 03 Jun 2017 13:14:46: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Sat, 03 Jun 2017 13:14:46: start model_add_line... INFO @ Sat, 03 Jun 2017 13:14:47: start X-correlation... INFO @ Sat, 03 Jun 2017 13:14:47: end of X-cor INFO @ Sat, 03 Jun 2017 13:14:47: #2 finished! INFO @ Sat, 03 Jun 2017 13:14:47: #2 predicted fragment length is 55 bps INFO @ Sat, 03 Jun 2017 13:14:47: #2 alternative fragment length(s) may be 4,55,74,541,560 bps INFO @ Sat, 03 Jun 2017 13:14:47: #2.2 Generate R script for model : SRX1433365.10_model.r WARNING @ Sat, 03 Jun 2017 13:14:47: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:14:47: #2 You may need to consider one of the other alternative d(s): 4,55,74,541,560 WARNING @ Sat, 03 Jun 2017 13:14:47: #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 13:14:47: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:14:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:14:48: start X-correlation... INFO @ Sat, 03 Jun 2017 13:14:48: end of X-cor INFO @ Sat, 03 Jun 2017 13:14:48: #2 finished! INFO @ Sat, 03 Jun 2017 13:14:48: #2 predicted fragment length is 55 bps INFO @ Sat, 03 Jun 2017 13:14:48: #2 alternative fragment length(s) may be 4,55,74,541,560 bps INFO @ Sat, 03 Jun 2017 13:14:48: #2.2 Generate R script for model : SRX1433365.20_model.r WARNING @ Sat, 03 Jun 2017 13:14:48: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:14:48: #2 You may need to consider one of the other alternative d(s): 4,55,74,541,560 WARNING @ Sat, 03 Jun 2017 13:14:48: #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 13:14:48: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:14:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:14:49: start X-correlation... INFO @ Sat, 03 Jun 2017 13:14:49: end of X-cor INFO @ Sat, 03 Jun 2017 13:14:49: #2 finished! INFO @ Sat, 03 Jun 2017 13:14:49: #2 predicted fragment length is 55 bps INFO @ Sat, 03 Jun 2017 13:14:49: #2 alternative fragment length(s) may be 4,55,74,541,560 bps INFO @ Sat, 03 Jun 2017 13:14:49: #2.2 Generate R script for model : SRX1433365.05_model.r WARNING @ Sat, 03 Jun 2017 13:14:49: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:14:49: #2 You may need to consider one of the other alternative d(s): 4,55,74,541,560 WARNING @ Sat, 03 Jun 2017 13:14:49: #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 13:14:49: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:14:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:16:36: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:16:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:16:44: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:17:58: #4 Write output xls file... SRX1433365.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:17:58: #4 Write peak in narrowPeak format file... SRX1433365.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:17:58: #4 Write summits bed file... SRX1433365.10_summits.bed INFO @ Sat, 03 Jun 2017 13:17:58: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1363 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:18:01: #4 Write output xls file... SRX1433365.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:18:01: #4 Write peak in narrowPeak format file... SRX1433365.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:18:01: #4 Write summits bed file... SRX1433365.20_summits.bed INFO @ Sat, 03 Jun 2017 13:18:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (756 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:18:06: #4 Write output xls file... SRX1433365.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:18:06: #4 Write peak in narrowPeak format file... SRX1433365.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:18:06: #4 Write summits bed file... SRX1433365.05_summits.bed INFO @ Sat, 03 Jun 2017 13:18:06: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2074 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。