Job ID = 11632714 sra ファイルのダウンロード中... Completed: 1389835K bytes transferred in 15 seconds (719320K 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 54311311 spots for /home/okishinya/chipatlas/results/rn6/SRX3782473/SRR6826291.sra Written 54311311 spots for /home/okishinya/chipatlas/results/rn6/SRX3782473/SRR6826291.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: 00:00:02 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:23:15 54311311 reads; of these: 54311311 (100.00%) were unpaired; of these: 2114674 (3.89%) aligned 0 times 39950275 (73.56%) aligned exactly 1 time 12246362 (22.55%) aligned >1 times 96.11% overall alignment rate Time searching: 00:23:20 Overall time: 00:23:20 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 3849584 / 52196637 = 0.0738 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, 15 Feb 2019 07:08:11: # Command line: callpeak -t SRX3782473.bam -f BAM -g 2.15e9 -n SRX3782473.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3782473.20 # format = BAM # ChIP-seq file = ['SRX3782473.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 15 Feb 2019 07:08:11: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:08:11: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:08:11: # Command line: callpeak -t SRX3782473.bam -f BAM -g 2.15e9 -n SRX3782473.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3782473.05 # format = BAM # ChIP-seq file = ['SRX3782473.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 15 Feb 2019 07:08:11: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:08:11: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:08:11: # Command line: callpeak -t SRX3782473.bam -f BAM -g 2.15e9 -n SRX3782473.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3782473.10 # format = BAM # ChIP-seq file = ['SRX3782473.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 15 Feb 2019 07:08:11: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:08:11: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:08:18: 1000000 INFO @ Fri, 15 Feb 2019 07:08:18: 1000000 INFO @ Fri, 15 Feb 2019 07:08:18: 1000000 INFO @ Fri, 15 Feb 2019 07:08:24: 2000000 INFO @ Fri, 15 Feb 2019 07:08:25: 2000000 INFO @ Fri, 15 Feb 2019 07:08:25: 2000000 INFO @ Fri, 15 Feb 2019 07:08:31: 3000000 INFO @ Fri, 15 Feb 2019 07:08:32: 3000000 INFO @ Fri, 15 Feb 2019 07:08:32: 3000000 INFO @ Fri, 15 Feb 2019 07:08:37: 4000000 INFO @ Fri, 15 Feb 2019 07:08:39: 4000000 INFO @ Fri, 15 Feb 2019 07:08:39: 4000000 INFO @ Fri, 15 Feb 2019 07:08:44: 5000000 INFO @ Fri, 15 Feb 2019 07:08:46: 5000000 INFO @ Fri, 15 Feb 2019 07:08:46: 5000000 INFO @ Fri, 15 Feb 2019 07:08:50: 6000000 INFO @ Fri, 15 Feb 2019 07:08:53: 6000000 INFO @ Fri, 15 Feb 2019 07:08:53: 6000000 INFO @ Fri, 15 Feb 2019 07:08:56: 7000000 INFO @ Fri, 15 Feb 2019 07:09:00: 7000000 INFO @ Fri, 15 Feb 2019 07:09:00: 7000000 INFO @ Fri, 15 Feb 2019 07:09:03: 8000000 INFO @ Fri, 15 Feb 2019 07:09:06: 8000000 INFO @ Fri, 15 Feb 2019 07:09:06: 8000000 INFO @ Fri, 15 Feb 2019 07:09:10: 9000000 INFO @ Fri, 15 Feb 2019 07:09:13: 9000000 INFO @ Fri, 15 Feb 2019 07:09:13: 9000000 INFO @ Fri, 15 Feb 2019 07:09:16: 10000000 INFO @ Fri, 15 Feb 2019 07:09:20: 10000000 INFO @ Fri, 15 Feb 2019 07:09:20: 10000000 INFO @ Fri, 15 Feb 2019 07:09:23: 11000000 INFO @ Fri, 15 Feb 2019 07:09:28: 11000000 INFO @ Fri, 15 Feb 2019 07:09:28: 11000000 INFO @ Fri, 15 Feb 2019 07:09:29: 12000000 INFO @ Fri, 15 Feb 2019 07:09:35: 12000000 INFO @ Fri, 15 Feb 2019 07:09:35: 12000000 INFO @ Fri, 15 Feb 2019 07:09:36: 13000000 INFO @ Fri, 15 Feb 2019 07:09:42: 14000000 INFO @ Fri, 15 Feb 2019 07:09:43: 13000000 INFO @ Fri, 15 Feb 2019 07:09:43: 13000000 INFO @ Fri, 15 Feb 2019 07:09:49: 15000000 INFO @ Fri, 15 Feb 2019 07:09:50: 14000000 INFO @ Fri, 15 Feb 2019 07:09:50: 14000000 INFO @ Fri, 15 Feb 2019 07:09:55: 16000000 INFO @ Fri, 15 Feb 2019 07:09:57: 15000000 INFO @ Fri, 15 Feb 2019 07:09:57: 15000000 INFO @ Fri, 15 Feb 2019 07:10:02: 17000000 INFO @ Fri, 15 Feb 2019 07:10:04: 16000000 INFO @ Fri, 15 Feb 2019 07:10:04: 16000000 INFO @ Fri, 15 Feb 2019 07:10:08: 18000000 INFO @ Fri, 15 Feb 2019 07:10:11: 17000000 INFO @ Fri, 15 Feb 2019 07:10:11: 17000000 INFO @ Fri, 15 Feb 2019 07:10:15: 19000000 INFO @ Fri, 15 Feb 2019 07:10:17: 18000000 INFO @ Fri, 15 Feb 2019 07:10:17: 18000000 INFO @ Fri, 15 Feb 2019 07:10:21: 20000000 INFO @ Fri, 15 Feb 2019 07:10:25: 19000000 INFO @ Fri, 15 Feb 2019 07:10:25: 19000000 INFO @ Fri, 15 Feb 2019 07:10:28: 21000000 INFO @ Fri, 15 Feb 2019 07:10:31: 20000000 INFO @ Fri, 15 Feb 2019 07:10:31: 20000000 INFO @ Fri, 15 Feb 2019 07:10:34: 22000000 INFO @ Fri, 15 Feb 2019 07:10:38: 21000000 INFO @ Fri, 15 Feb 2019 07:10:38: 21000000 INFO @ Fri, 15 Feb 2019 07:10:41: 23000000 INFO @ Fri, 15 Feb 2019 07:10:45: 22000000 INFO @ Fri, 15 Feb 2019 07:10:45: 22000000 INFO @ Fri, 15 Feb 2019 07:10:47: 24000000 INFO @ Fri, 15 Feb 2019 07:10:52: 23000000 INFO @ Fri, 15 Feb 2019 07:10:52: 23000000 INFO @ Fri, 15 Feb 2019 07:10:53: 25000000 INFO @ Fri, 15 Feb 2019 07:10:59: 24000000 INFO @ Fri, 15 Feb 2019 07:11:00: 24000000 INFO @ Fri, 15 Feb 2019 07:11:00: 26000000 INFO @ Fri, 15 Feb 2019 07:11:06: 25000000 INFO @ Fri, 15 Feb 2019 07:11:06: 25000000 INFO @ Fri, 15 Feb 2019 07:11:07: 27000000 INFO @ Fri, 15 Feb 2019 07:11:13: 26000000 INFO @ Fri, 15 Feb 2019 07:11:13: 26000000 INFO @ Fri, 15 Feb 2019 07:11:14: 28000000 INFO @ Fri, 15 Feb 2019 07:11:20: 27000000 INFO @ Fri, 15 Feb 2019 07:11:20: 27000000 INFO @ Fri, 15 Feb 2019 07:11:21: 29000000 INFO @ Fri, 15 Feb 2019 07:11:26: 28000000 INFO @ Fri, 15 Feb 2019 07:11:27: 28000000 INFO @ Fri, 15 Feb 2019 07:11:27: 30000000 INFO @ Fri, 15 Feb 2019 07:11:33: 29000000 INFO @ Fri, 15 Feb 2019 07:11:33: 29000000 INFO @ Fri, 15 Feb 2019 07:11:34: 31000000 INFO @ Fri, 15 Feb 2019 07:11:40: 30000000 INFO @ Fri, 15 Feb 2019 07:11:40: 30000000 INFO @ Fri, 15 Feb 2019 07:11:40: 32000000 INFO @ Fri, 15 Feb 2019 07:11:46: 31000000 INFO @ Fri, 15 Feb 2019 07:11:47: 31000000 INFO @ Fri, 15 Feb 2019 07:11:47: 33000000 INFO @ Fri, 15 Feb 2019 07:11:53: 32000000 INFO @ Fri, 15 Feb 2019 07:11:54: 34000000 INFO @ Fri, 15 Feb 2019 07:11:54: 32000000 INFO @ Fri, 15 Feb 2019 07:12:00: 33000000 INFO @ Fri, 15 Feb 2019 07:12:00: 35000000 INFO @ Fri, 15 Feb 2019 07:12:00: 33000000 INFO @ Fri, 15 Feb 2019 07:12:07: 36000000 INFO @ Fri, 15 Feb 2019 07:12:07: 34000000 INFO @ Fri, 15 Feb 2019 07:12:07: 34000000 INFO @ Fri, 15 Feb 2019 07:12:13: 37000000 INFO @ Fri, 15 Feb 2019 07:12:14: 35000000 INFO @ Fri, 15 Feb 2019 07:12:14: 35000000 INFO @ Fri, 15 Feb 2019 07:12:20: 38000000 INFO @ Fri, 15 Feb 2019 07:12:20: 36000000 INFO @ Fri, 15 Feb 2019 07:12:21: 36000000 INFO @ Fri, 15 Feb 2019 07:12:26: 39000000 INFO @ Fri, 15 Feb 2019 07:12:27: 37000000 INFO @ Fri, 15 Feb 2019 07:12:28: 37000000 INFO @ Fri, 15 Feb 2019 07:12:33: 40000000 INFO @ Fri, 15 Feb 2019 07:12:35: 38000000 INFO @ Fri, 15 Feb 2019 07:12:35: 38000000 INFO @ Fri, 15 Feb 2019 07:12:39: 41000000 INFO @ Fri, 15 Feb 2019 07:12:42: 39000000 INFO @ Fri, 15 Feb 2019 07:12:43: 39000000 INFO @ Fri, 15 Feb 2019 07:12:46: 42000000 INFO @ Fri, 15 Feb 2019 07:12:50: 40000000 INFO @ Fri, 15 Feb 2019 07:12:51: 40000000 INFO @ Fri, 15 Feb 2019 07:12:52: 43000000 INFO @ Fri, 15 Feb 2019 07:12:58: 41000000 INFO @ Fri, 15 Feb 2019 07:12:58: 41000000 INFO @ Fri, 15 Feb 2019 07:12:59: 44000000 INFO @ Fri, 15 Feb 2019 07:13:05: 42000000 INFO @ Fri, 15 Feb 2019 07:13:05: 45000000 INFO @ Fri, 15 Feb 2019 07:13:06: 42000000 INFO @ Fri, 15 Feb 2019 07:13:12: 43000000 INFO @ Fri, 15 Feb 2019 07:13:12: 46000000 INFO @ Fri, 15 Feb 2019 07:13:13: 43000000 INFO @ Fri, 15 Feb 2019 07:13:19: 47000000 INFO @ Fri, 15 Feb 2019 07:13:19: 44000000 INFO @ Fri, 15 Feb 2019 07:13:20: 44000000 INFO @ Fri, 15 Feb 2019 07:13:25: 48000000 INFO @ Fri, 15 Feb 2019 07:13:26: 45000000 INFO @ Fri, 15 Feb 2019 07:13:27: 45000000 INFO @ Fri, 15 Feb 2019 07:13:28: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:13:28: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:13:28: #1 total tags in treatment: 48347053 INFO @ Fri, 15 Feb 2019 07:13:28: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:13:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:13:29: #1 tags after filtering in treatment: 48346970 INFO @ Fri, 15 Feb 2019 07:13:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:13:29: #1 finished! INFO @ Fri, 15 Feb 2019 07:13:29: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:13:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:13:34: 46000000 INFO @ Fri, 15 Feb 2019 07:13:34: #2 number of paired peaks: 3879 INFO @ Fri, 15 Feb 2019 07:13:34: start model_add_line... INFO @ Fri, 15 Feb 2019 07:13:34: start X-correlation... INFO @ Fri, 15 Feb 2019 07:13:35: end of X-cor INFO @ Fri, 15 Feb 2019 07:13:35: #2 finished! INFO @ Fri, 15 Feb 2019 07:13:35: #2 predicted fragment length is 39 bps INFO @ Fri, 15 Feb 2019 07:13:35: #2 alternative fragment length(s) may be 39,574 bps INFO @ Fri, 15 Feb 2019 07:13:35: #2.2 Generate R script for model : SRX3782473.10_model.r WARNING @ Fri, 15 Feb 2019 07:13:35: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 07:13:35: #2 You may need to consider one of the other alternative d(s): 39,574 WARNING @ Fri, 15 Feb 2019 07:13:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 07:13:35: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:13:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:13:35: 46000000 INFO @ Fri, 15 Feb 2019 07:13:41: 47000000 INFO @ Fri, 15 Feb 2019 07:13:42: 47000000 INFO @ Fri, 15 Feb 2019 07:13:48: 48000000 INFO @ Fri, 15 Feb 2019 07:13:49: 48000000 INFO @ Fri, 15 Feb 2019 07:13:51: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:13:51: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:13:51: #1 total tags in treatment: 48347053 INFO @ Fri, 15 Feb 2019 07:13:51: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:13:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:13:52: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:13:52: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:13:52: #1 total tags in treatment: 48347053 INFO @ Fri, 15 Feb 2019 07:13:52: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:13:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:13:52: #1 tags after filtering in treatment: 48346970 INFO @ Fri, 15 Feb 2019 07:13:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:13:52: #1 finished! INFO @ Fri, 15 Feb 2019 07:13:52: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:13:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:13:53: #1 tags after filtering in treatment: 48346970 INFO @ Fri, 15 Feb 2019 07:13:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:13:53: #1 finished! INFO @ Fri, 15 Feb 2019 07:13:53: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:13:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:13:56: #2 number of paired peaks: 3879 INFO @ Fri, 15 Feb 2019 07:13:56: start model_add_line... INFO @ Fri, 15 Feb 2019 07:13:57: start X-correlation... INFO @ Fri, 15 Feb 2019 07:13:57: end of X-cor INFO @ Fri, 15 Feb 2019 07:13:57: #2 finished! INFO @ Fri, 15 Feb 2019 07:13:57: #2 predicted fragment length is 39 bps INFO @ Fri, 15 Feb 2019 07:13:57: #2 alternative fragment length(s) may be 39,574 bps INFO @ Fri, 15 Feb 2019 07:13:57: #2.2 Generate R script for model : SRX3782473.05_model.r WARNING @ Fri, 15 Feb 2019 07:13:57: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 07:13:57: #2 You may need to consider one of the other alternative d(s): 39,574 WARNING @ Fri, 15 Feb 2019 07:13:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 07:13:57: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:13:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:13:58: #2 number of paired peaks: 3879 INFO @ Fri, 15 Feb 2019 07:13:58: start model_add_line... INFO @ Fri, 15 Feb 2019 07:13:58: start X-correlation... INFO @ Fri, 15 Feb 2019 07:13:58: end of X-cor INFO @ Fri, 15 Feb 2019 07:13:58: #2 finished! INFO @ Fri, 15 Feb 2019 07:13:58: #2 predicted fragment length is 39 bps INFO @ Fri, 15 Feb 2019 07:13:58: #2 alternative fragment length(s) may be 39,574 bps INFO @ Fri, 15 Feb 2019 07:13:58: #2.2 Generate R script for model : SRX3782473.20_model.r WARNING @ Fri, 15 Feb 2019 07:13:58: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 07:13:58: #2 You may need to consider one of the other alternative d(s): 39,574 WARNING @ Fri, 15 Feb 2019 07:13:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 07:13:58: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:13:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:15:29: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:15:50: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:16:02: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:16:32: #4 Write output xls file... SRX3782473.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:16:32: #4 Write peak in narrowPeak format file... SRX3782473.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:16:32: #4 Write summits bed file... SRX3782473.10_summits.bed INFO @ Fri, 15 Feb 2019 07:16:32: Done! pass1 - making usageList (36 chroms): 4 millis pass2 - checking and writing primary data (1100 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:16:55: #4 Write output xls file... SRX3782473.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:16:55: #4 Write peak in narrowPeak format file... SRX3782473.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:16:55: #4 Write summits bed file... SRX3782473.20_summits.bed INFO @ Fri, 15 Feb 2019 07:16:55: Done! pass1 - making usageList (31 chroms): 4 millis pass2 - checking and writing primary data (479 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:17:07: #4 Write output xls file... SRX3782473.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:17:07: #4 Write peak in narrowPeak format file... SRX3782473.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:17:07: #4 Write summits bed file... SRX3782473.05_summits.bed INFO @ Fri, 15 Feb 2019 07:17:07: Done! pass1 - making usageList (46 chroms): 2 millis pass2 - checking and writing primary data (1802 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。