Job ID = 10194823 sra ファイルのダウンロード中... Completed: 1268011K bytes transferred in 25 seconds (400735K 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 64046795 spots for /home/okishinya/chipatlas/results/rn6/SRX1977113/SRR3952245.sra Written 64046795 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: 00:00:00 Multiseed full-index search: 01:41:53 64046795 reads; of these: 64046795 (100.00%) were unpaired; of these: 15601386 (24.36%) aligned 0 times 28780340 (44.94%) aligned exactly 1 time 19665069 (30.70%) aligned >1 times 75.64% overall alignment rate Time searching: 01:41:55 Overall time: 01:41:55 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 20 files... [bam_rmdupse_core] 4773275 / 48445409 = 0.0985 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, 11 Nov 2017 02:57:55: # Command line: callpeak -t SRX1977113.bam -f BAM -g 2.15e9 -n SRX1977113.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1977113.10 # format = BAM # ChIP-seq file = ['SRX1977113.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 @ Sat, 11 Nov 2017 02:57:55: # Command line: callpeak -t SRX1977113.bam -f BAM -g 2.15e9 -n SRX1977113.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1977113.20 # format = BAM # ChIP-seq file = ['SRX1977113.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 @ Sat, 11 Nov 2017 02:57:55: # Command line: callpeak -t SRX1977113.bam -f BAM -g 2.15e9 -n SRX1977113.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1977113.05 # format = BAM # ChIP-seq file = ['SRX1977113.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 @ Sat, 11 Nov 2017 02:57:55: #1 read tag files... INFO @ Sat, 11 Nov 2017 02:57:55: #1 read tag files... INFO @ Sat, 11 Nov 2017 02:57:55: #1 read tag files... INFO @ Sat, 11 Nov 2017 02:57:55: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 02:57:55: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 02:57:55: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 02:58:02: 1000000 INFO @ Sat, 11 Nov 2017 02:58:02: 1000000 INFO @ Sat, 11 Nov 2017 02:58:02: 1000000 INFO @ Sat, 11 Nov 2017 02:58:08: 2000000 INFO @ Sat, 11 Nov 2017 02:58:08: 2000000 INFO @ Sat, 11 Nov 2017 02:58:08: 2000000 INFO @ Sat, 11 Nov 2017 02:58:14: 3000000 INFO @ Sat, 11 Nov 2017 02:58:14: 3000000 INFO @ Sat, 11 Nov 2017 02:58:15: 3000000 INFO @ Sat, 11 Nov 2017 02:58:21: 4000000 INFO @ Sat, 11 Nov 2017 02:58:21: 4000000 INFO @ Sat, 11 Nov 2017 02:58:22: 4000000 INFO @ Sat, 11 Nov 2017 02:58:27: 5000000 INFO @ Sat, 11 Nov 2017 02:58:28: 5000000 INFO @ Sat, 11 Nov 2017 02:58:28: 5000000 INFO @ Sat, 11 Nov 2017 02:58:33: 6000000 INFO @ Sat, 11 Nov 2017 02:58:34: 6000000 INFO @ Sat, 11 Nov 2017 02:58:35: 6000000 INFO @ Sat, 11 Nov 2017 02:58:40: 7000000 INFO @ Sat, 11 Nov 2017 02:58:41: 7000000 INFO @ Sat, 11 Nov 2017 02:58:42: 7000000 INFO @ Sat, 11 Nov 2017 02:58:46: 8000000 INFO @ Sat, 11 Nov 2017 02:58:48: 8000000 INFO @ Sat, 11 Nov 2017 02:58:49: 8000000 INFO @ Sat, 11 Nov 2017 02:58:52: 9000000 INFO @ Sat, 11 Nov 2017 02:58:55: 9000000 INFO @ Sat, 11 Nov 2017 02:58:56: 9000000 INFO @ Sat, 11 Nov 2017 02:58:59: 10000000 INFO @ Sat, 11 Nov 2017 02:59:01: 10000000 INFO @ Sat, 11 Nov 2017 02:59:03: 10000000 INFO @ Sat, 11 Nov 2017 02:59:05: 11000000 INFO @ Sat, 11 Nov 2017 02:59:08: 11000000 INFO @ Sat, 11 Nov 2017 02:59:10: 11000000 INFO @ Sat, 11 Nov 2017 02:59:11: 12000000 INFO @ Sat, 11 Nov 2017 02:59:15: 12000000 INFO @ Sat, 11 Nov 2017 02:59:17: 12000000 INFO @ Sat, 11 Nov 2017 02:59:18: 13000000 INFO @ Sat, 11 Nov 2017 02:59:22: 13000000 INFO @ Sat, 11 Nov 2017 02:59:24: 14000000 INFO @ Sat, 11 Nov 2017 02:59:24: 13000000 INFO @ Sat, 11 Nov 2017 02:59:29: 14000000 INFO @ Sat, 11 Nov 2017 02:59:30: 15000000 INFO @ Sat, 11 Nov 2017 02:59:31: 14000000 INFO @ Sat, 11 Nov 2017 02:59:36: 15000000 INFO @ Sat, 11 Nov 2017 02:59:36: 16000000 INFO @ Sat, 11 Nov 2017 02:59:38: 15000000 INFO @ Sat, 11 Nov 2017 02:59:42: 16000000 INFO @ Sat, 11 Nov 2017 02:59:43: 17000000 INFO @ Sat, 11 Nov 2017 02:59:45: 16000000 INFO @ Sat, 11 Nov 2017 02:59:49: 17000000 INFO @ Sat, 11 Nov 2017 02:59:49: 18000000 INFO @ Sat, 11 Nov 2017 02:59:52: 17000000 INFO @ Sat, 11 Nov 2017 02:59:56: 18000000 INFO @ Sat, 11 Nov 2017 02:59:56: 19000000 INFO @ Sat, 11 Nov 2017 02:59:59: 18000000 INFO @ Sat, 11 Nov 2017 03:00:03: 19000000 INFO @ Sat, 11 Nov 2017 03:00:03: 20000000 INFO @ Sat, 11 Nov 2017 03:00:06: 19000000 INFO @ Sat, 11 Nov 2017 03:00:09: 21000000 INFO @ Sat, 11 Nov 2017 03:00:09: 20000000 INFO @ Sat, 11 Nov 2017 03:00:13: 20000000 INFO @ Sat, 11 Nov 2017 03:00:16: 22000000 INFO @ Sat, 11 Nov 2017 03:00:16: 21000000 INFO @ Sat, 11 Nov 2017 03:00:19: 21000000 INFO @ Sat, 11 Nov 2017 03:00:22: 23000000 INFO @ Sat, 11 Nov 2017 03:00:23: 22000000 INFO @ Sat, 11 Nov 2017 03:00:26: 22000000 INFO @ Sat, 11 Nov 2017 03:00:29: 24000000 INFO @ Sat, 11 Nov 2017 03:00:30: 23000000 INFO @ Sat, 11 Nov 2017 03:00:33: 23000000 INFO @ Sat, 11 Nov 2017 03:00:36: 25000000 INFO @ Sat, 11 Nov 2017 03:00:37: 24000000 INFO @ Sat, 11 Nov 2017 03:00:39: 24000000 INFO @ Sat, 11 Nov 2017 03:00:42: 26000000 INFO @ Sat, 11 Nov 2017 03:00:44: 25000000 INFO @ Sat, 11 Nov 2017 03:00:45: 25000000 INFO @ Sat, 11 Nov 2017 03:00:49: 27000000 INFO @ Sat, 11 Nov 2017 03:00:51: 26000000 INFO @ Sat, 11 Nov 2017 03:00:52: 26000000 INFO @ Sat, 11 Nov 2017 03:00:56: 28000000 INFO @ Sat, 11 Nov 2017 03:00:58: 27000000 INFO @ Sat, 11 Nov 2017 03:00:58: 27000000 INFO @ Sat, 11 Nov 2017 03:01:03: 29000000 INFO @ Sat, 11 Nov 2017 03:01:05: 28000000 INFO @ Sat, 11 Nov 2017 03:01:05: 28000000 INFO @ Sat, 11 Nov 2017 03:01:09: 30000000 INFO @ Sat, 11 Nov 2017 03:01:11: 29000000 INFO @ Sat, 11 Nov 2017 03:01:11: 29000000 INFO @ Sat, 11 Nov 2017 03:01:16: 31000000 INFO @ Sat, 11 Nov 2017 03:01:18: 30000000 INFO @ Sat, 11 Nov 2017 03:01:18: 30000000 INFO @ Sat, 11 Nov 2017 03:01:23: 32000000 INFO @ Sat, 11 Nov 2017 03:01:24: 31000000 INFO @ Sat, 11 Nov 2017 03:01:25: 31000000 INFO @ Sat, 11 Nov 2017 03:01:30: 33000000 INFO @ Sat, 11 Nov 2017 03:01:31: 32000000 INFO @ Sat, 11 Nov 2017 03:01:32: 32000000 INFO @ Sat, 11 Nov 2017 03:01:36: 34000000 INFO @ Sat, 11 Nov 2017 03:01:37: 33000000 INFO @ Sat, 11 Nov 2017 03:01:39: 33000000 INFO @ Sat, 11 Nov 2017 03:01:43: 35000000 INFO @ Sat, 11 Nov 2017 03:01:44: 34000000 INFO @ Sat, 11 Nov 2017 03:01:46: 34000000 INFO @ Sat, 11 Nov 2017 03:01:50: 36000000 INFO @ Sat, 11 Nov 2017 03:01:51: 35000000 INFO @ Sat, 11 Nov 2017 03:01:53: 35000000 INFO @ Sat, 11 Nov 2017 03:01:56: 37000000 INFO @ Sat, 11 Nov 2017 03:01:59: 36000000 INFO @ Sat, 11 Nov 2017 03:02:00: 36000000 INFO @ Sat, 11 Nov 2017 03:02:03: 38000000 INFO @ Sat, 11 Nov 2017 03:02:06: 37000000 INFO @ Sat, 11 Nov 2017 03:02:07: 37000000 INFO @ Sat, 11 Nov 2017 03:02:10: 39000000 INFO @ Sat, 11 Nov 2017 03:02:13: 38000000 INFO @ Sat, 11 Nov 2017 03:02:13: 38000000 INFO @ Sat, 11 Nov 2017 03:02:16: 40000000 INFO @ Sat, 11 Nov 2017 03:02:20: 39000000 INFO @ Sat, 11 Nov 2017 03:02:20: 39000000 INFO @ Sat, 11 Nov 2017 03:02:23: 41000000 INFO @ Sat, 11 Nov 2017 03:02:27: 40000000 INFO @ Sat, 11 Nov 2017 03:02:27: 40000000 INFO @ Sat, 11 Nov 2017 03:02:29: 42000000 INFO @ Sat, 11 Nov 2017 03:02:34: 41000000 INFO @ Sat, 11 Nov 2017 03:02:34: 41000000 INFO @ Sat, 11 Nov 2017 03:02:36: 43000000 INFO @ Sat, 11 Nov 2017 03:02:40: 42000000 INFO @ Sat, 11 Nov 2017 03:02:40: 42000000 INFO @ Sat, 11 Nov 2017 03:02:41: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:02:41: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:02:41: #1 total tags in treatment: 43672134 INFO @ Sat, 11 Nov 2017 03:02:41: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:02:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 03:02:42: #1 tags after filtering in treatment: 43672091 INFO @ Sat, 11 Nov 2017 03:02:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:02:42: #1 finished! INFO @ Sat, 11 Nov 2017 03:02:42: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:02:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:02:46: #2 number of paired peaks: 7287 INFO @ Sat, 11 Nov 2017 03:02:46: start model_add_line... INFO @ Sat, 11 Nov 2017 03:02:46: 43000000 INFO @ Sat, 11 Nov 2017 03:02:46: start X-correlation... INFO @ Sat, 11 Nov 2017 03:02:46: end of X-cor INFO @ Sat, 11 Nov 2017 03:02:46: #2 finished! INFO @ Sat, 11 Nov 2017 03:02:46: #2 predicted fragment length is 53 bps INFO @ Sat, 11 Nov 2017 03:02:46: #2 alternative fragment length(s) may be 53 bps INFO @ Sat, 11 Nov 2017 03:02:46: #2.2 Generate R script for model : SRX1977113.05_model.r WARNING @ Sat, 11 Nov 2017 03:02:46: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 03:02:46: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sat, 11 Nov 2017 03:02:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 03:02:46: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:02:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:02:47: 43000000 INFO @ Sat, 11 Nov 2017 03:02:51: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:02:51: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:02:51: #1 total tags in treatment: 43672134 INFO @ Sat, 11 Nov 2017 03:02:51: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:02:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 03:02:52: #1 tags after filtering in treatment: 43672091 INFO @ Sat, 11 Nov 2017 03:02:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:02:52: #1 finished! INFO @ Sat, 11 Nov 2017 03:02:52: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:02:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:02:52: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:02:52: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:02:52: #1 total tags in treatment: 43672134 INFO @ Sat, 11 Nov 2017 03:02:52: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:02:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 03:02:53: #1 tags after filtering in treatment: 43672091 INFO @ Sat, 11 Nov 2017 03:02:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:02:53: #1 finished! INFO @ Sat, 11 Nov 2017 03:02:53: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:02:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:02:56: #2 number of paired peaks: 7287 INFO @ Sat, 11 Nov 2017 03:02:56: start model_add_line... INFO @ Sat, 11 Nov 2017 03:02:57: start X-correlation... INFO @ Sat, 11 Nov 2017 03:02:57: end of X-cor INFO @ Sat, 11 Nov 2017 03:02:57: #2 finished! INFO @ Sat, 11 Nov 2017 03:02:57: #2 predicted fragment length is 53 bps INFO @ Sat, 11 Nov 2017 03:02:57: #2 alternative fragment length(s) may be 53 bps INFO @ Sat, 11 Nov 2017 03:02:57: #2.2 Generate R script for model : SRX1977113.20_model.r WARNING @ Sat, 11 Nov 2017 03:02:57: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 03:02:57: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sat, 11 Nov 2017 03:02:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 03:02:57: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:02:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:02:58: #2 number of paired peaks: 7287 INFO @ Sat, 11 Nov 2017 03:02:58: start model_add_line... INFO @ Sat, 11 Nov 2017 03:02:58: start X-correlation... INFO @ Sat, 11 Nov 2017 03:02:58: end of X-cor INFO @ Sat, 11 Nov 2017 03:02:58: #2 finished! INFO @ Sat, 11 Nov 2017 03:02:58: #2 predicted fragment length is 53 bps INFO @ Sat, 11 Nov 2017 03:02:58: #2 alternative fragment length(s) may be 53 bps INFO @ Sat, 11 Nov 2017 03:02:58: #2.2 Generate R script for model : SRX1977113.10_model.r WARNING @ Sat, 11 Nov 2017 03:02:58: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 03:02:58: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sat, 11 Nov 2017 03:02:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 03:02:58: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:02:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:04:33: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:04:45: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:04:45: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:05:28: #4 Write output xls file... SRX1977113.05_peaks.xls INFO @ Sat, 11 Nov 2017 03:05:28: #4 Write peak in narrowPeak format file... SRX1977113.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:05:28: #4 Write summits bed file... SRX1977113.05_summits.bed INFO @ Sat, 11 Nov 2017 03:05:28: Done! pass1 - making usageList (127 chroms): 3 millis pass2 - checking and writing primary data (12058 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 03:05:40: #4 Write output xls file... SRX1977113.10_peaks.xls INFO @ Sat, 11 Nov 2017 03:05:40: #4 Write peak in narrowPeak format file... SRX1977113.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:05:40: #4 Write summits bed file... SRX1977113.10_summits.bed INFO @ Sat, 11 Nov 2017 03:05:40: Done! pass1 - making usageList (76 chroms): 1 millis pass2 - checking and writing primary data (3525 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 03:05:48: #4 Write output xls file... SRX1977113.20_peaks.xls INFO @ Sat, 11 Nov 2017 03:05:48: #4 Write peak in narrowPeak format file... SRX1977113.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:05:48: #4 Write summits bed file... SRX1977113.20_summits.bed INFO @ Sat, 11 Nov 2017 03:05:48: Done! pass1 - making usageList (51 chroms): 1 millis pass2 - checking and writing primary data (1079 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。