Job ID = 10487580 sra ファイルのダウンロード中... Completed: 4766026K bytes transferred in 192 seconds (202589K 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... Written 70652649 spots for /home/okishinya/chipatlas/results/rn6/SRX2611108/SRR5311152.sra Written 70652649 spots total 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 03:50:09 70652649 reads; of these: 70652649 (100.00%) were unpaired; of these: 16325190 (23.11%) aligned 0 times 41793534 (59.15%) aligned exactly 1 time 12533925 (17.74%) aligned >1 times 76.89% overall alignment rate Time searching: 03:50:13 Overall time: 03:50:13 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 40 files... [bam_rmdupse_core] 16448754 / 54327459 = 0.3028 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 @ Sun, 18 Mar 2018 14:00:49: # Command line: callpeak -t SRX2611108.bam -f BAM -g 2.15e9 -n SRX2611108.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2611108.05 # format = BAM # ChIP-seq file = ['SRX2611108.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 @ Sun, 18 Mar 2018 14:00:49: #1 read tag files... INFO @ Sun, 18 Mar 2018 14:00:49: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 14:00:50: # Command line: callpeak -t SRX2611108.bam -f BAM -g 2.15e9 -n SRX2611108.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2611108.20 # format = BAM # ChIP-seq file = ['SRX2611108.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 @ Sun, 18 Mar 2018 14:00:50: #1 read tag files... INFO @ Sun, 18 Mar 2018 14:00:50: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 14:00:50: # Command line: callpeak -t SRX2611108.bam -f BAM -g 2.15e9 -n SRX2611108.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2611108.10 # format = BAM # ChIP-seq file = ['SRX2611108.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 @ Sun, 18 Mar 2018 14:00:50: #1 read tag files... INFO @ Sun, 18 Mar 2018 14:00:50: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 14:01:01: 1000000 INFO @ Sun, 18 Mar 2018 14:01:02: 1000000 INFO @ Sun, 18 Mar 2018 14:01:03: 1000000 INFO @ Sun, 18 Mar 2018 14:01:12: 2000000 INFO @ Sun, 18 Mar 2018 14:01:14: 2000000 INFO @ Sun, 18 Mar 2018 14:01:14: 2000000 INFO @ Sun, 18 Mar 2018 14:01:24: 3000000 INFO @ Sun, 18 Mar 2018 14:01:24: 3000000 INFO @ Sun, 18 Mar 2018 14:01:26: 3000000 INFO @ Sun, 18 Mar 2018 14:01:35: 4000000 INFO @ Sun, 18 Mar 2018 14:01:36: 4000000 INFO @ Sun, 18 Mar 2018 14:01:38: 4000000 INFO @ Sun, 18 Mar 2018 14:01:46: 5000000 INFO @ Sun, 18 Mar 2018 14:01:48: 5000000 INFO @ Sun, 18 Mar 2018 14:01:50: 5000000 INFO @ Sun, 18 Mar 2018 14:01:57: 6000000 INFO @ Sun, 18 Mar 2018 14:02:00: 6000000 INFO @ Sun, 18 Mar 2018 14:02:02: 6000000 INFO @ Sun, 18 Mar 2018 14:02:08: 7000000 INFO @ Sun, 18 Mar 2018 14:02:12: 7000000 INFO @ Sun, 18 Mar 2018 14:02:14: 7000000 INFO @ Sun, 18 Mar 2018 14:02:19: 8000000 INFO @ Sun, 18 Mar 2018 14:02:24: 8000000 INFO @ Sun, 18 Mar 2018 14:02:26: 8000000 INFO @ Sun, 18 Mar 2018 14:02:30: 9000000 INFO @ Sun, 18 Mar 2018 14:02:35: 9000000 INFO @ Sun, 18 Mar 2018 14:02:37: 9000000 INFO @ Sun, 18 Mar 2018 14:02:41: 10000000 INFO @ Sun, 18 Mar 2018 14:02:48: 10000000 INFO @ Sun, 18 Mar 2018 14:02:50: 10000000 INFO @ Sun, 18 Mar 2018 14:02:54: 11000000 INFO @ Sun, 18 Mar 2018 14:02:59: 11000000 INFO @ Sun, 18 Mar 2018 14:03:02: 11000000 INFO @ Sun, 18 Mar 2018 14:03:05: 12000000 INFO @ Sun, 18 Mar 2018 14:03:09: 12000000 INFO @ Sun, 18 Mar 2018 14:03:13: 12000000 INFO @ Sun, 18 Mar 2018 14:03:16: 13000000 INFO @ Sun, 18 Mar 2018 14:03:21: 13000000 INFO @ Sun, 18 Mar 2018 14:03:25: 13000000 INFO @ Sun, 18 Mar 2018 14:03:26: 14000000 INFO @ Sun, 18 Mar 2018 14:03:33: 14000000 INFO @ Sun, 18 Mar 2018 14:03:37: 14000000 INFO @ Sun, 18 Mar 2018 14:03:37: 15000000 INFO @ Sun, 18 Mar 2018 14:03:45: 15000000 INFO @ Sun, 18 Mar 2018 14:03:48: 16000000 INFO @ Sun, 18 Mar 2018 14:03:49: 15000000 INFO @ Sun, 18 Mar 2018 14:03:57: 16000000 INFO @ Sun, 18 Mar 2018 14:03:59: 17000000 INFO @ Sun, 18 Mar 2018 14:04:00: 16000000 INFO @ Sun, 18 Mar 2018 14:04:08: 17000000 INFO @ Sun, 18 Mar 2018 14:04:10: 18000000 INFO @ Sun, 18 Mar 2018 14:04:12: 17000000 INFO @ Sun, 18 Mar 2018 14:04:20: 18000000 INFO @ Sun, 18 Mar 2018 14:04:21: 19000000 INFO @ Sun, 18 Mar 2018 14:04:24: 18000000 INFO @ Sun, 18 Mar 2018 14:04:31: 19000000 INFO @ Sun, 18 Mar 2018 14:04:34: 20000000 INFO @ Sun, 18 Mar 2018 14:04:38: 19000000 INFO @ Sun, 18 Mar 2018 14:04:42: 20000000 INFO @ Sun, 18 Mar 2018 14:04:44: 21000000 INFO @ Sun, 18 Mar 2018 14:04:50: 20000000 INFO @ Sun, 18 Mar 2018 14:04:53: 21000000 INFO @ Sun, 18 Mar 2018 14:04:55: 22000000 INFO @ Sun, 18 Mar 2018 14:05:02: 21000000 INFO @ Sun, 18 Mar 2018 14:05:05: 22000000 INFO @ Sun, 18 Mar 2018 14:05:06: 23000000 INFO @ Sun, 18 Mar 2018 14:05:13: 22000000 INFO @ Sun, 18 Mar 2018 14:05:17: 23000000 INFO @ Sun, 18 Mar 2018 14:05:17: 24000000 INFO @ Sun, 18 Mar 2018 14:05:25: 23000000 INFO @ Sun, 18 Mar 2018 14:05:28: 25000000 INFO @ Sun, 18 Mar 2018 14:05:29: 24000000 INFO @ Sun, 18 Mar 2018 14:05:36: 24000000 INFO @ Sun, 18 Mar 2018 14:05:40: 26000000 INFO @ Sun, 18 Mar 2018 14:05:41: 25000000 INFO @ Sun, 18 Mar 2018 14:05:48: 25000000 INFO @ Sun, 18 Mar 2018 14:05:51: 27000000 INFO @ Sun, 18 Mar 2018 14:05:53: 26000000 INFO @ Sun, 18 Mar 2018 14:06:00: 26000000 INFO @ Sun, 18 Mar 2018 14:06:02: 28000000 INFO @ Sun, 18 Mar 2018 14:06:05: 27000000 INFO @ Sun, 18 Mar 2018 14:06:12: 27000000 INFO @ Sun, 18 Mar 2018 14:06:13: 29000000 INFO @ Sun, 18 Mar 2018 14:06:16: 28000000 INFO @ Sun, 18 Mar 2018 14:06:23: 30000000 INFO @ Sun, 18 Mar 2018 14:06:24: 28000000 INFO @ Sun, 18 Mar 2018 14:06:28: 29000000 INFO @ Sun, 18 Mar 2018 14:06:34: 31000000 INFO @ Sun, 18 Mar 2018 14:06:35: 29000000 INFO @ Sun, 18 Mar 2018 14:06:40: 30000000 INFO @ Sun, 18 Mar 2018 14:06:46: 32000000 INFO @ Sun, 18 Mar 2018 14:06:47: 30000000 INFO @ Sun, 18 Mar 2018 14:06:51: 31000000 INFO @ Sun, 18 Mar 2018 14:06:58: 33000000 INFO @ Sun, 18 Mar 2018 14:06:58: 31000000 INFO @ Sun, 18 Mar 2018 14:07:03: 32000000 INFO @ Sun, 18 Mar 2018 14:07:09: 32000000 INFO @ Sun, 18 Mar 2018 14:07:10: 34000000 INFO @ Sun, 18 Mar 2018 14:07:15: 33000000 INFO @ Sun, 18 Mar 2018 14:07:21: 33000000 INFO @ Sun, 18 Mar 2018 14:07:21: 35000000 INFO @ Sun, 18 Mar 2018 14:07:26: 34000000 INFO @ Sun, 18 Mar 2018 14:07:33: 36000000 INFO @ Sun, 18 Mar 2018 14:07:33: 34000000 INFO @ Sun, 18 Mar 2018 14:07:37: 35000000 INFO @ Sun, 18 Mar 2018 14:07:45: 37000000 INFO @ Sun, 18 Mar 2018 14:07:46: 35000000 INFO @ Sun, 18 Mar 2018 14:07:48: 36000000 INFO @ Sun, 18 Mar 2018 14:07:56: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 14:07:56: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 14:07:56: #1 total tags in treatment: 37878705 INFO @ Sun, 18 Mar 2018 14:07:56: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 14:07:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 14:07:57: #1 tags after filtering in treatment: 37878631 INFO @ Sun, 18 Mar 2018 14:07:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 14:07:57: #1 finished! INFO @ Sun, 18 Mar 2018 14:07:57: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 14:07:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 14:07:59: 37000000 INFO @ Sun, 18 Mar 2018 14:07:59: 36000000 INFO @ Sun, 18 Mar 2018 14:08:00: #2 number of paired peaks: 7732 INFO @ Sun, 18 Mar 2018 14:08:00: start model_add_line... INFO @ Sun, 18 Mar 2018 14:08:01: start X-correlation... INFO @ Sun, 18 Mar 2018 14:08:01: end of X-cor INFO @ Sun, 18 Mar 2018 14:08:01: #2 finished! INFO @ Sun, 18 Mar 2018 14:08:01: #2 predicted fragment length is 150 bps INFO @ Sun, 18 Mar 2018 14:08:01: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 18 Mar 2018 14:08:01: #2.2 Generate R script for model : SRX2611108.05_model.r WARNING @ Sun, 18 Mar 2018 14:08:01: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 14:08:01: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Sun, 18 Mar 2018 14:08:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 14:08:01: #3 Call peaks... INFO @ Sun, 18 Mar 2018 14:08:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 14:08:08: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 14:08:08: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 14:08:08: #1 total tags in treatment: 37878705 INFO @ Sun, 18 Mar 2018 14:08:08: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 14:08:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 14:08:09: #1 tags after filtering in treatment: 37878631 INFO @ Sun, 18 Mar 2018 14:08:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 14:08:09: #1 finished! INFO @ Sun, 18 Mar 2018 14:08:09: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 14:08:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 14:08:09: 37000000 INFO @ Sun, 18 Mar 2018 14:08:13: #2 number of paired peaks: 7732 INFO @ Sun, 18 Mar 2018 14:08:13: start model_add_line... INFO @ Sun, 18 Mar 2018 14:08:14: start X-correlation... INFO @ Sun, 18 Mar 2018 14:08:14: end of X-cor INFO @ Sun, 18 Mar 2018 14:08:14: #2 finished! INFO @ Sun, 18 Mar 2018 14:08:14: #2 predicted fragment length is 150 bps INFO @ Sun, 18 Mar 2018 14:08:14: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 18 Mar 2018 14:08:14: #2.2 Generate R script for model : SRX2611108.20_model.r WARNING @ Sun, 18 Mar 2018 14:08:14: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 14:08:14: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Sun, 18 Mar 2018 14:08:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 14:08:14: #3 Call peaks... INFO @ Sun, 18 Mar 2018 14:08:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 14:08:19: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 14:08:19: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 14:08:19: #1 total tags in treatment: 37878705 INFO @ Sun, 18 Mar 2018 14:08:19: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 14:08:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 14:08:20: #1 tags after filtering in treatment: 37878631 INFO @ Sun, 18 Mar 2018 14:08:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 14:08:20: #1 finished! INFO @ Sun, 18 Mar 2018 14:08:20: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 14:08:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 14:08:24: #2 number of paired peaks: 7732 INFO @ Sun, 18 Mar 2018 14:08:24: start model_add_line... INFO @ Sun, 18 Mar 2018 14:08:24: start X-correlation... INFO @ Sun, 18 Mar 2018 14:08:24: end of X-cor INFO @ Sun, 18 Mar 2018 14:08:24: #2 finished! INFO @ Sun, 18 Mar 2018 14:08:24: #2 predicted fragment length is 150 bps INFO @ Sun, 18 Mar 2018 14:08:24: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 18 Mar 2018 14:08:24: #2.2 Generate R script for model : SRX2611108.10_model.r WARNING @ Sun, 18 Mar 2018 14:08:24: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 14:08:24: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Sun, 18 Mar 2018 14:08:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 14:08:24: #3 Call peaks... INFO @ Sun, 18 Mar 2018 14:08:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 14:09:42: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 14:09:46: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 14:09:52: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 14:10:35: #4 Write output xls file... SRX2611108.05_peaks.xls INFO @ Sun, 18 Mar 2018 14:10:35: #4 Write peak in narrowPeak format file... SRX2611108.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 14:10:35: #4 Write summits bed file... SRX2611108.05_summits.bed INFO @ Sun, 18 Mar 2018 14:10:35: Done! pass1 - making usageList (78 chroms): 1 millis pass2 - checking and writing primary data (4157 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 14:10:36: #4 Write output xls file... SRX2611108.20_peaks.xls INFO @ Sun, 18 Mar 2018 14:10:36: #4 Write peak in narrowPeak format file... SRX2611108.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 14:10:36: #4 Write summits bed file... SRX2611108.20_summits.bed INFO @ Sun, 18 Mar 2018 14:10:36: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (714 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 14:10:45: #4 Write output xls file... SRX2611108.10_peaks.xls INFO @ Sun, 18 Mar 2018 14:10:45: #4 Write peak in narrowPeak format file... SRX2611108.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 14:10:45: #4 Write summits bed file... SRX2611108.10_summits.bed INFO @ Sun, 18 Mar 2018 14:10:45: Done! pass1 - making usageList (51 chroms): 1 millis pass2 - checking and writing primary data (1644 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。