Job ID = 9371943 sra ファイルのダウンロード中... Completed: 2171767K bytes transferred in 95 seconds (187109K bits/sec), in 1 file, 2 directories. 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 72549462 spots for /home/okishinya/chipatlas/results/dm3/SRX2692977/SRR5398176.sra Written 72549462 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: 03:10:04 72549462 reads; of these: 72549462 (100.00%) were unpaired; of these: 12755528 (17.58%) aligned 0 times 15409706 (21.24%) aligned exactly 1 time 44384228 (61.18%) aligned >1 times 82.42% overall alignment rate Time searching: 03:10:04 Overall time: 03:10:04 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 28 files... [bam_rmdupse_core] 32691008 / 59793934 = 0.5467 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, 04 Aug 2017 18:34:20: # Command line: callpeak -t SRX2692977.bam -f BAM -g dm -n SRX2692977.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2692977.20 # format = BAM # ChIP-seq file = ['SRX2692977.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 # Paired-End mode is off INFO @ Fri, 04 Aug 2017 18:34:20: # Command line: callpeak -t SRX2692977.bam -f BAM -g dm -n SRX2692977.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2692977.10 # format = BAM # ChIP-seq file = ['SRX2692977.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 # Paired-End mode is off INFO @ Fri, 04 Aug 2017 18:34:20: # Command line: callpeak -t SRX2692977.bam -f BAM -g dm -n SRX2692977.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2692977.05 # format = BAM # ChIP-seq file = ['SRX2692977.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 # Paired-End mode is off INFO @ Fri, 04 Aug 2017 18:34:20: #1 read tag files... INFO @ Fri, 04 Aug 2017 18:34:20: #1 read tag files... INFO @ Fri, 04 Aug 2017 18:34:20: #1 read tag files... INFO @ Fri, 04 Aug 2017 18:34:20: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 18:34:20: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 18:34:20: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 18:34:49: 1000000 INFO @ Fri, 04 Aug 2017 18:34:50: 1000000 INFO @ Fri, 04 Aug 2017 18:34:51: 1000000 INFO @ Fri, 04 Aug 2017 18:35:08: 2000000 INFO @ Fri, 04 Aug 2017 18:35:12: 2000000 INFO @ Fri, 04 Aug 2017 18:35:14: 2000000 INFO @ Fri, 04 Aug 2017 18:35:26: 3000000 INFO @ Fri, 04 Aug 2017 18:35:33: 3000000 INFO @ Fri, 04 Aug 2017 18:35:39: 4000000 INFO @ Fri, 04 Aug 2017 18:35:41: 3000000 INFO @ Fri, 04 Aug 2017 18:35:54: 4000000 INFO @ Fri, 04 Aug 2017 18:35:56: 5000000 INFO @ Fri, 04 Aug 2017 18:36:09: 4000000 INFO @ Fri, 04 Aug 2017 18:36:11: 5000000 INFO @ Fri, 04 Aug 2017 18:36:15: 6000000 INFO @ Fri, 04 Aug 2017 18:36:34: 6000000 INFO @ Fri, 04 Aug 2017 18:36:36: 5000000 INFO @ Fri, 04 Aug 2017 18:36:38: 7000000 INFO @ Fri, 04 Aug 2017 18:36:57: 7000000 INFO @ Fri, 04 Aug 2017 18:37:01: 8000000 INFO @ Fri, 04 Aug 2017 18:37:04: 6000000 INFO @ Fri, 04 Aug 2017 18:37:17: 8000000 INFO @ Fri, 04 Aug 2017 18:37:22: 9000000 INFO @ Fri, 04 Aug 2017 18:37:29: 7000000 INFO @ Fri, 04 Aug 2017 18:37:40: 9000000 INFO @ Fri, 04 Aug 2017 18:37:44: 10000000 INFO @ Fri, 04 Aug 2017 18:37:54: 8000000 INFO @ Fri, 04 Aug 2017 18:38:00: 10000000 INFO @ Fri, 04 Aug 2017 18:38:04: 11000000 INFO @ Fri, 04 Aug 2017 18:38:19: 9000000 INFO @ Fri, 04 Aug 2017 18:38:20: 11000000 INFO @ Fri, 04 Aug 2017 18:38:23: 12000000 INFO @ Fri, 04 Aug 2017 18:38:41: 13000000 INFO @ Fri, 04 Aug 2017 18:38:43: 12000000 INFO @ Fri, 04 Aug 2017 18:38:45: 10000000 INFO @ Fri, 04 Aug 2017 18:39:03: 14000000 INFO @ Fri, 04 Aug 2017 18:39:05: 13000000 INFO @ Fri, 04 Aug 2017 18:39:13: 11000000 INFO @ Fri, 04 Aug 2017 18:39:24: 14000000 INFO @ Fri, 04 Aug 2017 18:39:24: 15000000 INFO @ Fri, 04 Aug 2017 18:39:34: 12000000 INFO @ Fri, 04 Aug 2017 18:39:41: 16000000 INFO @ Fri, 04 Aug 2017 18:39:41: 15000000 INFO @ Fri, 04 Aug 2017 18:39:54: 13000000 INFO @ Fri, 04 Aug 2017 18:39:55: 17000000 INFO @ Fri, 04 Aug 2017 18:40:00: 16000000 INFO @ Fri, 04 Aug 2017 18:40:11: 14000000 INFO @ Fri, 04 Aug 2017 18:40:15: 18000000 INFO @ Fri, 04 Aug 2017 18:40:19: 17000000 INFO @ Fri, 04 Aug 2017 18:40:29: 15000000 INFO @ Fri, 04 Aug 2017 18:40:34: 18000000 INFO @ Fri, 04 Aug 2017 18:40:35: 19000000 INFO @ Fri, 04 Aug 2017 18:40:50: 16000000 INFO @ Fri, 04 Aug 2017 18:40:51: 19000000 INFO @ Fri, 04 Aug 2017 18:40:54: 20000000 INFO @ Fri, 04 Aug 2017 18:41:10: 17000000 INFO @ Fri, 04 Aug 2017 18:41:11: 20000000 INFO @ Fri, 04 Aug 2017 18:41:14: 21000000 INFO @ Fri, 04 Aug 2017 18:41:29: 18000000 INFO @ Fri, 04 Aug 2017 18:41:30: 21000000 INFO @ Fri, 04 Aug 2017 18:41:33: 22000000 INFO @ Fri, 04 Aug 2017 18:41:49: 22000000 INFO @ Fri, 04 Aug 2017 18:41:50: 19000000 INFO @ Fri, 04 Aug 2017 18:41:54: 23000000 INFO @ Fri, 04 Aug 2017 18:42:07: 23000000 INFO @ Fri, 04 Aug 2017 18:42:09: 20000000 INFO @ Fri, 04 Aug 2017 18:42:13: 24000000 INFO @ Fri, 04 Aug 2017 18:42:21: 24000000 INFO @ Fri, 04 Aug 2017 18:42:30: 25000000 INFO @ Fri, 04 Aug 2017 18:42:32: 21000000 INFO @ Fri, 04 Aug 2017 18:42:39: 25000000 INFO @ Fri, 04 Aug 2017 18:42:47: 26000000 INFO @ Fri, 04 Aug 2017 18:42:51: 22000000 INFO @ Fri, 04 Aug 2017 18:42:52: 26000000 INFO @ Fri, 04 Aug 2017 18:43:03: 27000000 INFO @ Fri, 04 Aug 2017 18:43:06: #1 tag size is determined as 75 bps INFO @ Fri, 04 Aug 2017 18:43:06: #1 tag size = 75 INFO @ Fri, 04 Aug 2017 18:43:06: #1 total tags in treatment: 27102926 INFO @ Fri, 04 Aug 2017 18:43:06: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 18:43:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 18:43:07: #1 tags after filtering in treatment: 27102926 INFO @ Fri, 04 Aug 2017 18:43:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 18:43:07: #1 finished! INFO @ Fri, 04 Aug 2017 18:43:07: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 18:43:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 18:43:09: 23000000 INFO @ Fri, 04 Aug 2017 18:43:13: #2 number of paired peaks: 2006 INFO @ Fri, 04 Aug 2017 18:43:13: start model_add_line... INFO @ Fri, 04 Aug 2017 18:43:13: 27000000 INFO @ Fri, 04 Aug 2017 18:43:13: start X-correlation... INFO @ Fri, 04 Aug 2017 18:43:13: end of X-cor INFO @ Fri, 04 Aug 2017 18:43:13: #2 finished! INFO @ Fri, 04 Aug 2017 18:43:13: #2 predicted fragment length is 47 bps INFO @ Fri, 04 Aug 2017 18:43:13: #2 alternative fragment length(s) may be 47 bps INFO @ Fri, 04 Aug 2017 18:43:13: #2.2 Generate R script for model : SRX2692977.10_model.r WARNING @ Fri, 04 Aug 2017 18:43:13: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 18:43:13: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Fri, 04 Aug 2017 18:43:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 18:43:13: #3 Call peaks... INFO @ Fri, 04 Aug 2017 18:43:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 18:43:16: #1 tag size is determined as 75 bps INFO @ Fri, 04 Aug 2017 18:43:16: #1 tag size = 75 INFO @ Fri, 04 Aug 2017 18:43:16: #1 total tags in treatment: 27102926 INFO @ Fri, 04 Aug 2017 18:43:16: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 18:43:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 18:43:17: #1 tags after filtering in treatment: 27102926 INFO @ Fri, 04 Aug 2017 18:43:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 18:43:17: #1 finished! INFO @ Fri, 04 Aug 2017 18:43:17: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 18:43:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 18:43:22: #2 number of paired peaks: 2006 INFO @ Fri, 04 Aug 2017 18:43:22: start model_add_line... INFO @ Fri, 04 Aug 2017 18:43:23: start X-correlation... INFO @ Fri, 04 Aug 2017 18:43:23: end of X-cor INFO @ Fri, 04 Aug 2017 18:43:23: #2 finished! INFO @ Fri, 04 Aug 2017 18:43:23: #2 predicted fragment length is 47 bps INFO @ Fri, 04 Aug 2017 18:43:23: #2 alternative fragment length(s) may be 47 bps INFO @ Fri, 04 Aug 2017 18:43:23: #2.2 Generate R script for model : SRX2692977.05_model.r WARNING @ Fri, 04 Aug 2017 18:43:23: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 18:43:23: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Fri, 04 Aug 2017 18:43:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 18:43:23: #3 Call peaks... INFO @ Fri, 04 Aug 2017 18:43:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 18:43:29: 24000000 INFO @ Fri, 04 Aug 2017 18:43:47: 25000000 INFO @ Fri, 04 Aug 2017 18:44:05: 26000000 INFO @ Fri, 04 Aug 2017 18:44:24: 27000000 INFO @ Fri, 04 Aug 2017 18:44:27: #1 tag size is determined as 75 bps INFO @ Fri, 04 Aug 2017 18:44:27: #1 tag size = 75 INFO @ Fri, 04 Aug 2017 18:44:27: #1 total tags in treatment: 27102926 INFO @ Fri, 04 Aug 2017 18:44:27: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 18:44:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 18:44:28: #1 tags after filtering in treatment: 27102926 INFO @ Fri, 04 Aug 2017 18:44:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 18:44:28: #1 finished! INFO @ Fri, 04 Aug 2017 18:44:28: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 18:44:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 18:44:33: #2 number of paired peaks: 2006 INFO @ Fri, 04 Aug 2017 18:44:33: start model_add_line... INFO @ Fri, 04 Aug 2017 18:44:33: start X-correlation... INFO @ Fri, 04 Aug 2017 18:44:33: end of X-cor INFO @ Fri, 04 Aug 2017 18:44:33: #2 finished! INFO @ Fri, 04 Aug 2017 18:44:33: #2 predicted fragment length is 47 bps INFO @ Fri, 04 Aug 2017 18:44:33: #2 alternative fragment length(s) may be 47 bps INFO @ Fri, 04 Aug 2017 18:44:33: #2.2 Generate R script for model : SRX2692977.20_model.r WARNING @ Fri, 04 Aug 2017 18:44:33: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 18:44:33: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Fri, 04 Aug 2017 18:44:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 18:44:33: #3 Call peaks... INFO @ Fri, 04 Aug 2017 18:44:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 18:45:13: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 18:45:15: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 18:46:23: #4 Write output xls file... SRX2692977.05_peaks.xls INFO @ Fri, 04 Aug 2017 18:46:23: #4 Write output xls file... SRX2692977.10_peaks.xls INFO @ Fri, 04 Aug 2017 18:46:23: #4 Write peak in narrowPeak format file... SRX2692977.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 18:46:23: #4 Write peak in narrowPeak format file... SRX2692977.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 18:46:23: #4 Write summits bed file... SRX2692977.10_summits.bed INFO @ Fri, 04 Aug 2017 18:46:23: Done! INFO @ Fri, 04 Aug 2017 18:46:23: #4 Write summits bed file... SRX2692977.05_summits.bed INFO @ Fri, 04 Aug 2017 18:46:24: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (14380 records, 4 fields): 35 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 7 millis pass2 - checking and writing primary data (22913 records, 4 fields): 76 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 18:46:27: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 18:47:18: #4 Write output xls file... SRX2692977.20_peaks.xls INFO @ Fri, 04 Aug 2017 18:47:18: #4 Write peak in narrowPeak format file... SRX2692977.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 18:47:18: #4 Write summits bed file... SRX2692977.20_summits.bed INFO @ Fri, 04 Aug 2017 18:47:18: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (5442 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。