Job ID = 11171415 sra ファイルのダウンロード中... Completed: 606464K bytes transferred in 7 seconds (692868K bits/sec), in 1 file. 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... Read 45923038 spots for /home/okishinya/chipatlas/results/dm3/SRX4315048/SRR7444509.sra Written 45923038 spots for /home/okishinya/chipatlas/results/dm3/SRX4315048/SRR7444509.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:13:50 45923038 reads; of these: 45923038 (100.00%) were unpaired; of these: 5663 (0.01%) aligned 0 times 41767323 (90.95%) aligned exactly 1 time 4150052 (9.04%) aligned >1 times 99.99% overall alignment rate Time searching: 00:13:50 Overall time: 00:13:50 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 20 files... [bam_rmdupse_core] 10147107 / 45917375 = 0.2210 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, 08 Sep 2018 14:48:02: # Command line: callpeak -t SRX4315048.bam -f BAM -g dm -n SRX4315048.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4315048.10 # format = BAM # ChIP-seq file = ['SRX4315048.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 @ Sat, 08 Sep 2018 14:48:02: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:48:02: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:48:02: # Command line: callpeak -t SRX4315048.bam -f BAM -g dm -n SRX4315048.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4315048.05 # format = BAM # ChIP-seq file = ['SRX4315048.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 @ Sat, 08 Sep 2018 14:48:02: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:48:02: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:48:02: # Command line: callpeak -t SRX4315048.bam -f BAM -g dm -n SRX4315048.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4315048.20 # format = BAM # ChIP-seq file = ['SRX4315048.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 @ Sat, 08 Sep 2018 14:48:02: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:48:02: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:48:10: 1000000 INFO @ Sat, 08 Sep 2018 14:48:11: 1000000 INFO @ Sat, 08 Sep 2018 14:48:11: 1000000 INFO @ Sat, 08 Sep 2018 14:48:19: 2000000 INFO @ Sat, 08 Sep 2018 14:48:19: 2000000 INFO @ Sat, 08 Sep 2018 14:48:20: 2000000 INFO @ Sat, 08 Sep 2018 14:48:27: 3000000 INFO @ Sat, 08 Sep 2018 14:48:28: 3000000 INFO @ Sat, 08 Sep 2018 14:48:29: 3000000 INFO @ Sat, 08 Sep 2018 14:48:35: 4000000 INFO @ Sat, 08 Sep 2018 14:48:36: 4000000 INFO @ Sat, 08 Sep 2018 14:48:38: 4000000 INFO @ Sat, 08 Sep 2018 14:48:43: 5000000 INFO @ Sat, 08 Sep 2018 14:48:45: 5000000 INFO @ Sat, 08 Sep 2018 14:48:47: 5000000 INFO @ Sat, 08 Sep 2018 14:48:51: 6000000 INFO @ Sat, 08 Sep 2018 14:48:53: 6000000 INFO @ Sat, 08 Sep 2018 14:48:56: 6000000 INFO @ Sat, 08 Sep 2018 14:49:00: 7000000 INFO @ Sat, 08 Sep 2018 14:49:02: 7000000 INFO @ Sat, 08 Sep 2018 14:49:05: 7000000 INFO @ Sat, 08 Sep 2018 14:49:08: 8000000 INFO @ Sat, 08 Sep 2018 14:49:10: 8000000 INFO @ Sat, 08 Sep 2018 14:49:13: 8000000 INFO @ Sat, 08 Sep 2018 14:49:16: 9000000 INFO @ Sat, 08 Sep 2018 14:49:19: 9000000 INFO @ Sat, 08 Sep 2018 14:49:22: 9000000 INFO @ Sat, 08 Sep 2018 14:49:24: 10000000 INFO @ Sat, 08 Sep 2018 14:49:27: 10000000 INFO @ Sat, 08 Sep 2018 14:49:31: 10000000 INFO @ Sat, 08 Sep 2018 14:49:32: 11000000 INFO @ Sat, 08 Sep 2018 14:49:36: 11000000 INFO @ Sat, 08 Sep 2018 14:49:40: 11000000 INFO @ Sat, 08 Sep 2018 14:49:40: 12000000 INFO @ Sat, 08 Sep 2018 14:49:44: 12000000 INFO @ Sat, 08 Sep 2018 14:49:49: 13000000 INFO @ Sat, 08 Sep 2018 14:49:49: 12000000 INFO @ Sat, 08 Sep 2018 14:49:52: 13000000 INFO @ Sat, 08 Sep 2018 14:49:57: 14000000 INFO @ Sat, 08 Sep 2018 14:49:58: 13000000 INFO @ Sat, 08 Sep 2018 14:50:01: 14000000 INFO @ Sat, 08 Sep 2018 14:50:05: 15000000 INFO @ Sat, 08 Sep 2018 14:50:06: 14000000 INFO @ Sat, 08 Sep 2018 14:50:09: 15000000 INFO @ Sat, 08 Sep 2018 14:50:13: 16000000 INFO @ Sat, 08 Sep 2018 14:50:15: 15000000 INFO @ Sat, 08 Sep 2018 14:50:18: 16000000 INFO @ Sat, 08 Sep 2018 14:50:21: 17000000 INFO @ Sat, 08 Sep 2018 14:50:24: 16000000 INFO @ Sat, 08 Sep 2018 14:50:26: 17000000 INFO @ Sat, 08 Sep 2018 14:50:29: 18000000 INFO @ Sat, 08 Sep 2018 14:50:33: 17000000 INFO @ Sat, 08 Sep 2018 14:50:34: 18000000 INFO @ Sat, 08 Sep 2018 14:50:37: 19000000 INFO @ Sat, 08 Sep 2018 14:50:42: 18000000 INFO @ Sat, 08 Sep 2018 14:50:43: 19000000 INFO @ Sat, 08 Sep 2018 14:50:45: 20000000 INFO @ Sat, 08 Sep 2018 14:50:50: 19000000 INFO @ Sat, 08 Sep 2018 14:50:51: 20000000 INFO @ Sat, 08 Sep 2018 14:50:53: 21000000 INFO @ Sat, 08 Sep 2018 14:50:59: 20000000 INFO @ Sat, 08 Sep 2018 14:50:59: 21000000 INFO @ Sat, 08 Sep 2018 14:51:01: 22000000 INFO @ Sat, 08 Sep 2018 14:51:08: 22000000 INFO @ Sat, 08 Sep 2018 14:51:08: 21000000 INFO @ Sat, 08 Sep 2018 14:51:10: 23000000 INFO @ Sat, 08 Sep 2018 14:51:16: 23000000 INFO @ Sat, 08 Sep 2018 14:51:17: 22000000 INFO @ Sat, 08 Sep 2018 14:51:18: 24000000 INFO @ Sat, 08 Sep 2018 14:51:25: 24000000 INFO @ Sat, 08 Sep 2018 14:51:25: 23000000 INFO @ Sat, 08 Sep 2018 14:51:26: 25000000 INFO @ Sat, 08 Sep 2018 14:51:33: 25000000 INFO @ Sat, 08 Sep 2018 14:51:34: 26000000 INFO @ Sat, 08 Sep 2018 14:51:34: 24000000 INFO @ Sat, 08 Sep 2018 14:51:41: 26000000 INFO @ Sat, 08 Sep 2018 14:51:42: 27000000 INFO @ Sat, 08 Sep 2018 14:51:43: 25000000 INFO @ Sat, 08 Sep 2018 14:51:50: 27000000 INFO @ Sat, 08 Sep 2018 14:51:50: 28000000 INFO @ Sat, 08 Sep 2018 14:51:52: 26000000 INFO @ Sat, 08 Sep 2018 14:51:58: 28000000 INFO @ Sat, 08 Sep 2018 14:51:58: 29000000 INFO @ Sat, 08 Sep 2018 14:52:00: 27000000 INFO @ Sat, 08 Sep 2018 14:52:07: 30000000 INFO @ Sat, 08 Sep 2018 14:52:07: 29000000 INFO @ Sat, 08 Sep 2018 14:52:09: 28000000 INFO @ Sat, 08 Sep 2018 14:52:15: 31000000 INFO @ Sat, 08 Sep 2018 14:52:16: 30000000 INFO @ Sat, 08 Sep 2018 14:52:18: 29000000 INFO @ Sat, 08 Sep 2018 14:52:23: 32000000 INFO @ Sat, 08 Sep 2018 14:52:24: 31000000 INFO @ Sat, 08 Sep 2018 14:52:27: 30000000 INFO @ Sat, 08 Sep 2018 14:52:31: 33000000 INFO @ Sat, 08 Sep 2018 14:52:32: 32000000 INFO @ Sat, 08 Sep 2018 14:52:36: 31000000 INFO @ Sat, 08 Sep 2018 14:52:39: 34000000 INFO @ Sat, 08 Sep 2018 14:52:41: 33000000 INFO @ Sat, 08 Sep 2018 14:52:45: 32000000 INFO @ Sat, 08 Sep 2018 14:52:47: 35000000 INFO @ Sat, 08 Sep 2018 14:52:49: 34000000 INFO @ Sat, 08 Sep 2018 14:52:53: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 14:52:53: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 14:52:53: #1 total tags in treatment: 35770268 INFO @ Sat, 08 Sep 2018 14:52:53: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:52:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:52:54: 33000000 INFO @ Sat, 08 Sep 2018 14:52:54: #1 tags after filtering in treatment: 35770268 INFO @ Sat, 08 Sep 2018 14:52:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 14:52:54: #1 finished! INFO @ Sat, 08 Sep 2018 14:52:54: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:52:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:52:57: #2 number of paired peaks: 3136 INFO @ Sat, 08 Sep 2018 14:52:57: start model_add_line... INFO @ Sat, 08 Sep 2018 14:52:58: start X-correlation... INFO @ Sat, 08 Sep 2018 14:52:58: end of X-cor INFO @ Sat, 08 Sep 2018 14:52:58: #2 finished! INFO @ Sat, 08 Sep 2018 14:52:58: #2 predicted fragment length is 114 bps INFO @ Sat, 08 Sep 2018 14:52:58: #2 alternative fragment length(s) may be 114 bps INFO @ Sat, 08 Sep 2018 14:52:58: #2.2 Generate R script for model : SRX4315048.05_model.r WARNING @ Sat, 08 Sep 2018 14:52:58: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:52:58: #2 You may need to consider one of the other alternative d(s): 114 WARNING @ Sat, 08 Sep 2018 14:52:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 14:52:58: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:52:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:52:58: 35000000 INFO @ Sat, 08 Sep 2018 14:53:01: 34000000 INFO @ Sat, 08 Sep 2018 14:53:04: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 14:53:04: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 14:53:04: #1 total tags in treatment: 35770268 INFO @ Sat, 08 Sep 2018 14:53:04: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:53:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:53:05: #1 tags after filtering in treatment: 35770268 INFO @ Sat, 08 Sep 2018 14:53:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 14:53:05: #1 finished! INFO @ Sat, 08 Sep 2018 14:53:05: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:53:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:53:08: #2 number of paired peaks: 3136 INFO @ Sat, 08 Sep 2018 14:53:08: start model_add_line... INFO @ Sat, 08 Sep 2018 14:53:08: start X-correlation... INFO @ Sat, 08 Sep 2018 14:53:08: end of X-cor INFO @ Sat, 08 Sep 2018 14:53:08: #2 finished! INFO @ Sat, 08 Sep 2018 14:53:08: #2 predicted fragment length is 114 bps INFO @ Sat, 08 Sep 2018 14:53:08: #2 alternative fragment length(s) may be 114 bps INFO @ Sat, 08 Sep 2018 14:53:08: #2.2 Generate R script for model : SRX4315048.20_model.r WARNING @ Sat, 08 Sep 2018 14:53:08: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:53:08: #2 You may need to consider one of the other alternative d(s): 114 WARNING @ Sat, 08 Sep 2018 14:53:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 14:53:08: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:53:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:53:09: 35000000 INFO @ Sat, 08 Sep 2018 14:53:15: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 14:53:15: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 14:53:15: #1 total tags in treatment: 35770268 INFO @ Sat, 08 Sep 2018 14:53:15: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:53:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:53:15: #1 tags after filtering in treatment: 35770268 INFO @ Sat, 08 Sep 2018 14:53:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 14:53:15: #1 finished! INFO @ Sat, 08 Sep 2018 14:53:15: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:53:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:53:18: #2 number of paired peaks: 3136 INFO @ Sat, 08 Sep 2018 14:53:18: start model_add_line... INFO @ Sat, 08 Sep 2018 14:53:19: start X-correlation... INFO @ Sat, 08 Sep 2018 14:53:19: end of X-cor INFO @ Sat, 08 Sep 2018 14:53:19: #2 finished! INFO @ Sat, 08 Sep 2018 14:53:19: #2 predicted fragment length is 114 bps INFO @ Sat, 08 Sep 2018 14:53:19: #2 alternative fragment length(s) may be 114 bps INFO @ Sat, 08 Sep 2018 14:53:19: #2.2 Generate R script for model : SRX4315048.10_model.r WARNING @ Sat, 08 Sep 2018 14:53:19: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:53:19: #2 You may need to consider one of the other alternative d(s): 114 WARNING @ Sat, 08 Sep 2018 14:53:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 14:53:19: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:53:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:54:16: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:54:23: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:54:35: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:54:55: #4 Write output xls file... SRX4315048.05_peaks.xls INFO @ Sat, 08 Sep 2018 14:54:55: #4 Write peak in narrowPeak format file... SRX4315048.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:54:56: #4 Write summits bed file... SRX4315048.05_summits.bed INFO @ Sat, 08 Sep 2018 14:54:56: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11045 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 14:54:59: #4 Write output xls file... SRX4315048.20_peaks.xls INFO @ Sat, 08 Sep 2018 14:54:59: #4 Write peak in narrowPeak format file... SRX4315048.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:54:59: #4 Write summits bed file... SRX4315048.20_summits.bed INFO @ Sat, 08 Sep 2018 14:54:59: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6614 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 14:55:10: #4 Write output xls file... SRX4315048.10_peaks.xls INFO @ Sat, 08 Sep 2018 14:55:10: #4 Write peak in narrowPeak format file... SRX4315048.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:55:10: #4 Write summits bed file... SRX4315048.10_summits.bed INFO @ Sat, 08 Sep 2018 14:55:10: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9054 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。