Job ID = 8696820 sra ファイルのダウンロード中... Completed: 941699K bytes transferred in 43 seconds (178592K 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 0 987 0 --:--:-- 0:00:07 --:--:-- 6057 100 29611 0 29611 0 0 3431 0 --:--:-- 0:00:08 --:--:-- 13856 100 31482 0 31482 0 0 3647 0 --:--:-- 0:00:08 --:--:-- 14724 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 36336395 spots for /home/okishinya/chipatlas/results/dm3/SRX110758/SRR388340.sra Written 36336395 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: 00:22:05 36336395 reads; of these: 36336395 (100.00%) were unpaired; of these: 5361812 (14.76%) aligned 0 times 26557777 (73.09%) aligned exactly 1 time 4416806 (12.16%) aligned >1 times 85.24% overall alignment rate Time searching: 00:22:06 Overall time: 00:22:06 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 8 files... [bam_rmdupse_core] 11800495 / 30974583 = 0.3810 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 @ Fri, 10 Mar 2017 12:32:40: # Command line: callpeak -t SRX110758.bam -f BAM -g dm -n SRX110758.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX110758.05 # format = BAM # ChIP-seq file = ['SRX110758.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 @ Fri, 10 Mar 2017 12:32:40: # Command line: callpeak -t SRX110758.bam -f BAM -g dm -n SRX110758.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX110758.20 # format = BAM # ChIP-seq file = ['SRX110758.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 @ Fri, 10 Mar 2017 12:32:40: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:32:40: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:32:40: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:32:40: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:32:40: # Command line: callpeak -t SRX110758.bam -f BAM -g dm -n SRX110758.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX110758.10 # format = BAM # ChIP-seq file = ['SRX110758.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 @ Fri, 10 Mar 2017 12:32:40: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:32:40: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:32:47: 1000000 INFO @ Fri, 10 Mar 2017 12:32:47: 1000000 INFO @ Fri, 10 Mar 2017 12:32:52: 1000000 INFO @ Fri, 10 Mar 2017 12:32:54: 2000000 INFO @ Fri, 10 Mar 2017 12:32:55: 2000000 INFO @ Fri, 10 Mar 2017 12:33:01: 3000000 INFO @ Fri, 10 Mar 2017 12:33:03: 3000000 INFO @ Fri, 10 Mar 2017 12:33:04: 2000000 INFO @ Fri, 10 Mar 2017 12:33:07: 4000000 INFO @ Fri, 10 Mar 2017 12:33:11: 4000000 INFO @ Fri, 10 Mar 2017 12:33:14: 5000000 INFO @ Fri, 10 Mar 2017 12:33:17: 3000000 INFO @ Fri, 10 Mar 2017 12:33:19: 5000000 INFO @ Fri, 10 Mar 2017 12:33:21: 6000000 INFO @ Fri, 10 Mar 2017 12:33:26: 6000000 INFO @ Fri, 10 Mar 2017 12:33:28: 7000000 INFO @ Fri, 10 Mar 2017 12:33:30: 4000000 INFO @ Fri, 10 Mar 2017 12:33:34: 7000000 INFO @ Fri, 10 Mar 2017 12:33:35: 8000000 INFO @ Fri, 10 Mar 2017 12:33:42: 9000000 INFO @ Fri, 10 Mar 2017 12:33:42: 8000000 INFO @ Fri, 10 Mar 2017 12:33:42: 5000000 INFO @ Fri, 10 Mar 2017 12:33:48: 10000000 INFO @ Fri, 10 Mar 2017 12:33:49: 9000000 INFO @ Fri, 10 Mar 2017 12:33:54: 6000000 INFO @ Fri, 10 Mar 2017 12:33:55: 11000000 INFO @ Fri, 10 Mar 2017 12:33:57: 10000000 INFO @ Fri, 10 Mar 2017 12:34:02: 12000000 INFO @ Fri, 10 Mar 2017 12:34:05: 11000000 INFO @ Fri, 10 Mar 2017 12:34:06: 7000000 INFO @ Fri, 10 Mar 2017 12:34:09: 13000000 INFO @ Fri, 10 Mar 2017 12:34:12: 12000000 INFO @ Fri, 10 Mar 2017 12:34:15: 14000000 INFO @ Fri, 10 Mar 2017 12:34:19: 8000000 INFO @ Fri, 10 Mar 2017 12:34:20: 13000000 INFO @ Fri, 10 Mar 2017 12:34:22: 15000000 INFO @ Fri, 10 Mar 2017 12:34:27: 14000000 INFO @ Fri, 10 Mar 2017 12:34:29: 16000000 INFO @ Fri, 10 Mar 2017 12:34:32: 9000000 INFO @ Fri, 10 Mar 2017 12:34:34: 15000000 INFO @ Fri, 10 Mar 2017 12:34:36: 17000000 INFO @ Fri, 10 Mar 2017 12:34:42: 16000000 INFO @ Fri, 10 Mar 2017 12:34:42: 18000000 INFO @ Fri, 10 Mar 2017 12:34:44: 10000000 INFO @ Fri, 10 Mar 2017 12:34:49: 19000000 INFO @ Fri, 10 Mar 2017 12:34:49: 17000000 INFO @ Fri, 10 Mar 2017 12:34:51: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 12:34:51: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 12:34:51: #1 total tags in treatment: 19174088 INFO @ Fri, 10 Mar 2017 12:34:51: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:34:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:34:56: #1 tags after filtering in treatment: 19168986 INFO @ Fri, 10 Mar 2017 12:34:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:34:56: #1 finished! INFO @ Fri, 10 Mar 2017 12:34:56: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:34:57: 18000000 INFO @ Fri, 10 Mar 2017 12:34:57: 11000000 INFO @ Fri, 10 Mar 2017 12:35:01: #2 number of paired peaks: 4027 INFO @ Fri, 10 Mar 2017 12:35:01: start model_add_line... INFO @ Fri, 10 Mar 2017 12:35:04: 19000000 INFO @ Fri, 10 Mar 2017 12:35:06: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 12:35:06: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 12:35:06: #1 total tags in treatment: 19174088 INFO @ Fri, 10 Mar 2017 12:35:06: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:35:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:35:09: 12000000 INFO @ Fri, 10 Mar 2017 12:35:10: #1 tags after filtering in treatment: 19168986 INFO @ Fri, 10 Mar 2017 12:35:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:35:10: #1 finished! INFO @ Fri, 10 Mar 2017 12:35:10: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:35:15: #2 number of paired peaks: 4027 INFO @ Fri, 10 Mar 2017 12:35:15: start model_add_line... INFO @ Fri, 10 Mar 2017 12:35:23: 13000000 INFO @ Fri, 10 Mar 2017 12:35:38: 14000000 INFO @ Fri, 10 Mar 2017 12:35:52: 15000000 INFO @ Fri, 10 Mar 2017 12:35:58: start X-correlation... INFO @ Fri, 10 Mar 2017 12:35:58: end of X-cor INFO @ Fri, 10 Mar 2017 12:35:58: #2 finished! INFO @ Fri, 10 Mar 2017 12:35:58: #2 predicted fragment length is 72 bps INFO @ Fri, 10 Mar 2017 12:35:58: #2 alternative fragment length(s) may be 72 bps INFO @ Fri, 10 Mar 2017 12:35:58: #2.2 Generate R script for model : SRX110758.20_model.r WARNING @ Fri, 10 Mar 2017 12:35:59: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Mar 2017 12:35:59: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Fri, 10 Mar 2017 12:35:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Mar 2017 12:35:59: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:35:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:36:08: 16000000 INFO @ Fri, 10 Mar 2017 12:36:11: start X-correlation... INFO @ Fri, 10 Mar 2017 12:36:11: end of X-cor INFO @ Fri, 10 Mar 2017 12:36:11: #2 finished! INFO @ Fri, 10 Mar 2017 12:36:11: #2 predicted fragment length is 72 bps INFO @ Fri, 10 Mar 2017 12:36:11: #2 alternative fragment length(s) may be 72 bps INFO @ Fri, 10 Mar 2017 12:36:11: #2.2 Generate R script for model : SRX110758.10_model.r WARNING @ Fri, 10 Mar 2017 12:36:11: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Mar 2017 12:36:11: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Fri, 10 Mar 2017 12:36:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Mar 2017 12:36:11: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:36:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:36:23: 17000000 INFO @ Fri, 10 Mar 2017 12:36:37: 18000000 INFO @ Fri, 10 Mar 2017 12:36:51: 19000000 INFO @ Fri, 10 Mar 2017 12:36:54: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 12:36:54: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 12:36:54: #1 total tags in treatment: 19174088 INFO @ Fri, 10 Mar 2017 12:36:54: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:36:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:36:59: #1 tags after filtering in treatment: 19168986 INFO @ Fri, 10 Mar 2017 12:36:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:36:59: #1 finished! INFO @ Fri, 10 Mar 2017 12:36:59: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:37:04: #2 number of paired peaks: 4027 INFO @ Fri, 10 Mar 2017 12:37:04: start model_add_line... INFO @ Fri, 10 Mar 2017 12:37:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:38:02: start X-correlation... INFO @ Fri, 10 Mar 2017 12:38:02: end of X-cor INFO @ Fri, 10 Mar 2017 12:38:02: #2 finished! INFO @ Fri, 10 Mar 2017 12:38:02: #2 predicted fragment length is 72 bps INFO @ Fri, 10 Mar 2017 12:38:02: #2 alternative fragment length(s) may be 72 bps INFO @ Fri, 10 Mar 2017 12:38:02: #2.2 Generate R script for model : SRX110758.05_model.r WARNING @ Fri, 10 Mar 2017 12:38:02: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Mar 2017 12:38:02: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Fri, 10 Mar 2017 12:38:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Mar 2017 12:38:02: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:38:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:38:09: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:39:20: #4 Write output xls file... SRX110758.20_peaks.xls INFO @ Fri, 10 Mar 2017 12:39:20: #4 Write peak in narrowPeak format file... SRX110758.20_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:39:20: #4 Write summits bed file... SRX110758.20_summits.bed INFO @ Fri, 10 Mar 2017 12:39:20: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (8071 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:39:48: #4 Write output xls file... SRX110758.10_peaks.xls INFO @ Fri, 10 Mar 2017 12:39:48: #4 Write peak in narrowPeak format file... SRX110758.10_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:39:49: #4 Write summits bed file... SRX110758.10_summits.bed INFO @ Fri, 10 Mar 2017 12:39:49: Done! pass1 - making usageList (13 chroms): 5 millis pass2 - checking and writing primary data (13805 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:40:00: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:41:45: #4 Write output xls file... SRX110758.05_peaks.xls INFO @ Fri, 10 Mar 2017 12:41:45: #4 Write peak in narrowPeak format file... SRX110758.05_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:41:45: #4 Write summits bed file... SRX110758.05_summits.bed INFO @ Fri, 10 Mar 2017 12:41:45: Done! pass1 - making usageList (14 chroms): 6 millis pass2 - checking and writing primary data (19778 records, 4 fields): 33 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。