Job ID = 11388792 sra ファイルのダウンロード中... Completed: 928950K bytes transferred in 23 seconds (317589K 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 36740927 spots for /home/okishinya/chipatlas/results/rn6/SRX2867570/SRR5627023.sra Written 36740927 spots for /home/okishinya/chipatlas/results/rn6/SRX2867570/SRR5627023.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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:55:59 36740927 reads; of these: 36740927 (100.00%) were unpaired; of these: 1525744 (4.15%) aligned 0 times 25452537 (69.28%) aligned exactly 1 time 9762646 (26.57%) aligned >1 times 95.85% overall alignment rate Time searching: 01:56:03 Overall time: 01:56:03 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] 1234780 / 35215183 = 0.0351 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 @ Thu, 13 Dec 2018 00:57:41: # Command line: callpeak -t SRX2867570.bam -f BAM -g 2.15e9 -n SRX2867570.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2867570.10 # format = BAM # ChIP-seq file = ['SRX2867570.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 @ Thu, 13 Dec 2018 00:57:41: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:57:41: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:57:41: # Command line: callpeak -t SRX2867570.bam -f BAM -g 2.15e9 -n SRX2867570.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2867570.20 # format = BAM # ChIP-seq file = ['SRX2867570.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 @ Thu, 13 Dec 2018 00:57:41: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:57:41: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:57:41: # Command line: callpeak -t SRX2867570.bam -f BAM -g 2.15e9 -n SRX2867570.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2867570.05 # format = BAM # ChIP-seq file = ['SRX2867570.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 @ Thu, 13 Dec 2018 00:57:41: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:57:41: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:57:54: 1000000 INFO @ Thu, 13 Dec 2018 00:57:55: 1000000 INFO @ Thu, 13 Dec 2018 00:57:56: 1000000 INFO @ Thu, 13 Dec 2018 00:58:07: 2000000 INFO @ Thu, 13 Dec 2018 00:58:10: 2000000 INFO @ Thu, 13 Dec 2018 00:58:12: 2000000 INFO @ Thu, 13 Dec 2018 00:58:19: 3000000 INFO @ Thu, 13 Dec 2018 00:58:24: 3000000 INFO @ Thu, 13 Dec 2018 00:58:28: 3000000 INFO @ Thu, 13 Dec 2018 00:58:31: 4000000 INFO @ Thu, 13 Dec 2018 00:58:38: 4000000 INFO @ Thu, 13 Dec 2018 00:58:40: 5000000 INFO @ Thu, 13 Dec 2018 00:58:43: 4000000 INFO @ Thu, 13 Dec 2018 00:58:50: 6000000 INFO @ Thu, 13 Dec 2018 00:58:54: 5000000 INFO @ Thu, 13 Dec 2018 00:58:59: 7000000 INFO @ Thu, 13 Dec 2018 00:59:01: 5000000 INFO @ Thu, 13 Dec 2018 00:59:09: 6000000 INFO @ Thu, 13 Dec 2018 00:59:10: 8000000 INFO @ Thu, 13 Dec 2018 00:59:20: 9000000 INFO @ Thu, 13 Dec 2018 00:59:25: 6000000 INFO @ Thu, 13 Dec 2018 00:59:27: 7000000 INFO @ Thu, 13 Dec 2018 00:59:31: 10000000 INFO @ Thu, 13 Dec 2018 00:59:41: 11000000 INFO @ Thu, 13 Dec 2018 00:59:45: 8000000 INFO @ Thu, 13 Dec 2018 00:59:48: 7000000 INFO @ Thu, 13 Dec 2018 00:59:52: 12000000 INFO @ Thu, 13 Dec 2018 01:00:03: 9000000 INFO @ Thu, 13 Dec 2018 01:00:04: 13000000 INFO @ Thu, 13 Dec 2018 01:00:11: 8000000 INFO @ Thu, 13 Dec 2018 01:00:14: 14000000 INFO @ Thu, 13 Dec 2018 01:00:22: 10000000 INFO @ Thu, 13 Dec 2018 01:00:25: 15000000 INFO @ Thu, 13 Dec 2018 01:00:32: 9000000 INFO @ Thu, 13 Dec 2018 01:00:35: 16000000 INFO @ Thu, 13 Dec 2018 01:00:40: 11000000 INFO @ Thu, 13 Dec 2018 01:00:46: 17000000 INFO @ Thu, 13 Dec 2018 01:00:53: 10000000 INFO @ Thu, 13 Dec 2018 01:00:56: 18000000 INFO @ Thu, 13 Dec 2018 01:00:59: 12000000 INFO @ Thu, 13 Dec 2018 01:01:07: 19000000 INFO @ Thu, 13 Dec 2018 01:01:14: 11000000 INFO @ Thu, 13 Dec 2018 01:01:17: 13000000 INFO @ Thu, 13 Dec 2018 01:01:18: 20000000 INFO @ Thu, 13 Dec 2018 01:01:29: 21000000 INFO @ Thu, 13 Dec 2018 01:01:36: 14000000 INFO @ Thu, 13 Dec 2018 01:01:37: 12000000 INFO @ Thu, 13 Dec 2018 01:01:39: 22000000 INFO @ Thu, 13 Dec 2018 01:01:49: 23000000 INFO @ Thu, 13 Dec 2018 01:01:55: 15000000 INFO @ Thu, 13 Dec 2018 01:01:59: 13000000 INFO @ Thu, 13 Dec 2018 01:01:59: 24000000 INFO @ Thu, 13 Dec 2018 01:02:09: 25000000 INFO @ Thu, 13 Dec 2018 01:02:18: 16000000 INFO @ Thu, 13 Dec 2018 01:02:19: 26000000 INFO @ Thu, 13 Dec 2018 01:02:22: 14000000 INFO @ Thu, 13 Dec 2018 01:02:28: 27000000 INFO @ Thu, 13 Dec 2018 01:02:38: 28000000 INFO @ Thu, 13 Dec 2018 01:02:39: 17000000 INFO @ Thu, 13 Dec 2018 01:02:43: 15000000 INFO @ Thu, 13 Dec 2018 01:02:47: 29000000 INFO @ Thu, 13 Dec 2018 01:02:57: 30000000 INFO @ Thu, 13 Dec 2018 01:03:01: 18000000 INFO @ Thu, 13 Dec 2018 01:03:04: 16000000 INFO @ Thu, 13 Dec 2018 01:03:07: 31000000 INFO @ Thu, 13 Dec 2018 01:03:16: 32000000 INFO @ Thu, 13 Dec 2018 01:03:22: 19000000 INFO @ Thu, 13 Dec 2018 01:03:26: 33000000 INFO @ Thu, 13 Dec 2018 01:03:26: 17000000 INFO @ Thu, 13 Dec 2018 01:03:36: #1 tag size is determined as 76 bps INFO @ Thu, 13 Dec 2018 01:03:36: #1 tag size = 76 INFO @ Thu, 13 Dec 2018 01:03:36: #1 total tags in treatment: 33980403 INFO @ Thu, 13 Dec 2018 01:03:36: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 01:03:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 01:03:37: #1 tags after filtering in treatment: 33980325 INFO @ Thu, 13 Dec 2018 01:03:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 13 Dec 2018 01:03:37: #1 finished! INFO @ Thu, 13 Dec 2018 01:03:37: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 01:03:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 01:03:41: #2 number of paired peaks: 6266 INFO @ Thu, 13 Dec 2018 01:03:41: start model_add_line... INFO @ Thu, 13 Dec 2018 01:03:42: start X-correlation... INFO @ Thu, 13 Dec 2018 01:03:42: end of X-cor INFO @ Thu, 13 Dec 2018 01:03:42: #2 finished! INFO @ Thu, 13 Dec 2018 01:03:42: #2 predicted fragment length is 78 bps INFO @ Thu, 13 Dec 2018 01:03:42: #2 alternative fragment length(s) may be 78 bps INFO @ Thu, 13 Dec 2018 01:03:42: #2.2 Generate R script for model : SRX2867570.05_model.r WARNING @ Thu, 13 Dec 2018 01:03:42: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 13 Dec 2018 01:03:42: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Thu, 13 Dec 2018 01:03:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 13 Dec 2018 01:03:42: #3 Call peaks... INFO @ Thu, 13 Dec 2018 01:03:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 01:03:43: 20000000 INFO @ Thu, 13 Dec 2018 01:03:47: 18000000 INFO @ Thu, 13 Dec 2018 01:04:02: 21000000 INFO @ Thu, 13 Dec 2018 01:04:08: 19000000 INFO @ Thu, 13 Dec 2018 01:04:24: 22000000 INFO @ Thu, 13 Dec 2018 01:04:28: 20000000 INFO @ Thu, 13 Dec 2018 01:04:45: 23000000 INFO @ Thu, 13 Dec 2018 01:04:48: 21000000 INFO @ Thu, 13 Dec 2018 01:05:06: 24000000 INFO @ Thu, 13 Dec 2018 01:05:08: 22000000 INFO @ Thu, 13 Dec 2018 01:05:26: 25000000 INFO @ Thu, 13 Dec 2018 01:05:27: 23000000 INFO @ Thu, 13 Dec 2018 01:05:28: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 01:05:47: 26000000 INFO @ Thu, 13 Dec 2018 01:05:49: 24000000 INFO @ Thu, 13 Dec 2018 01:06:09: 27000000 INFO @ Thu, 13 Dec 2018 01:06:11: 25000000 INFO @ Thu, 13 Dec 2018 01:06:29: #4 Write output xls file... SRX2867570.05_peaks.xls INFO @ Thu, 13 Dec 2018 01:06:29: #4 Write peak in narrowPeak format file... SRX2867570.05_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 01:06:29: #4 Write summits bed file... SRX2867570.05_summits.bed INFO @ Thu, 13 Dec 2018 01:06:29: Done! pass1 - making usageList (63 chroms): 6 millis pass2 - checking and writing primary data (2816 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Thu, 13 Dec 2018 01:06:30: 28000000 INFO @ Thu, 13 Dec 2018 01:06:30: 26000000 INFO @ Thu, 13 Dec 2018 01:06:50: 27000000 INFO @ Thu, 13 Dec 2018 01:06:51: 29000000 INFO @ Thu, 13 Dec 2018 01:07:09: 28000000 INFO @ Thu, 13 Dec 2018 01:07:12: 30000000 INFO @ Thu, 13 Dec 2018 01:07:27: 29000000 INFO @ Thu, 13 Dec 2018 01:07:31: 31000000 INFO @ Thu, 13 Dec 2018 01:07:47: 30000000 INFO @ Thu, 13 Dec 2018 01:07:53: 32000000 INFO @ Thu, 13 Dec 2018 01:08:07: 31000000 INFO @ Thu, 13 Dec 2018 01:08:14: 33000000 INFO @ Thu, 13 Dec 2018 01:08:28: 32000000 INFO @ Thu, 13 Dec 2018 01:08:36: #1 tag size is determined as 76 bps INFO @ Thu, 13 Dec 2018 01:08:36: #1 tag size = 76 INFO @ Thu, 13 Dec 2018 01:08:36: #1 total tags in treatment: 33980403 INFO @ Thu, 13 Dec 2018 01:08:36: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 01:08:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 01:08:37: #1 tags after filtering in treatment: 33980325 INFO @ Thu, 13 Dec 2018 01:08:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 13 Dec 2018 01:08:37: #1 finished! INFO @ Thu, 13 Dec 2018 01:08:37: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 01:08:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 01:08:41: #2 number of paired peaks: 6266 INFO @ Thu, 13 Dec 2018 01:08:41: start model_add_line... INFO @ Thu, 13 Dec 2018 01:08:42: start X-correlation... INFO @ Thu, 13 Dec 2018 01:08:42: end of X-cor INFO @ Thu, 13 Dec 2018 01:08:42: #2 finished! INFO @ Thu, 13 Dec 2018 01:08:42: #2 predicted fragment length is 78 bps INFO @ Thu, 13 Dec 2018 01:08:42: #2 alternative fragment length(s) may be 78 bps INFO @ Thu, 13 Dec 2018 01:08:42: #2.2 Generate R script for model : SRX2867570.20_model.r WARNING @ Thu, 13 Dec 2018 01:08:42: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 13 Dec 2018 01:08:42: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Thu, 13 Dec 2018 01:08:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 13 Dec 2018 01:08:42: #3 Call peaks... INFO @ Thu, 13 Dec 2018 01:08:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 01:08:44: 33000000 INFO @ Thu, 13 Dec 2018 01:09:05: #1 tag size is determined as 76 bps INFO @ Thu, 13 Dec 2018 01:09:05: #1 tag size = 76 INFO @ Thu, 13 Dec 2018 01:09:05: #1 total tags in treatment: 33980403 INFO @ Thu, 13 Dec 2018 01:09:05: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 01:09:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 01:09:07: #1 tags after filtering in treatment: 33980325 INFO @ Thu, 13 Dec 2018 01:09:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 13 Dec 2018 01:09:07: #1 finished! INFO @ Thu, 13 Dec 2018 01:09:07: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 01:09:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 01:09:11: #2 number of paired peaks: 6266 INFO @ Thu, 13 Dec 2018 01:09:11: start model_add_line... INFO @ Thu, 13 Dec 2018 01:09:11: start X-correlation... INFO @ Thu, 13 Dec 2018 01:09:11: end of X-cor INFO @ Thu, 13 Dec 2018 01:09:11: #2 finished! INFO @ Thu, 13 Dec 2018 01:09:11: #2 predicted fragment length is 78 bps INFO @ Thu, 13 Dec 2018 01:09:11: #2 alternative fragment length(s) may be 78 bps INFO @ Thu, 13 Dec 2018 01:09:11: #2.2 Generate R script for model : SRX2867570.10_model.r WARNING @ Thu, 13 Dec 2018 01:09:11: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 13 Dec 2018 01:09:11: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Thu, 13 Dec 2018 01:09:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 13 Dec 2018 01:09:11: #3 Call peaks... INFO @ Thu, 13 Dec 2018 01:09:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 01:10:36: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 01:10:54: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 01:11:44: #4 Write output xls file... SRX2867570.20_peaks.xls INFO @ Thu, 13 Dec 2018 01:11:44: #4 Write peak in narrowPeak format file... SRX2867570.20_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 01:11:44: #4 Write summits bed file... SRX2867570.20_summits.bed INFO @ Thu, 13 Dec 2018 01:11:44: Done! pass1 - making usageList (39 chroms): 6 millis pass2 - checking and writing primary data (631 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 13 Dec 2018 01:11:55: #4 Write output xls file... SRX2867570.10_peaks.xls INFO @ Thu, 13 Dec 2018 01:11:55: #4 Write peak in narrowPeak format file... SRX2867570.10_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 01:11:55: #4 Write summits bed file... SRX2867570.10_summits.bed INFO @ Thu, 13 Dec 2018 01:11:55: Done! pass1 - making usageList (52 chroms): 4 millis pass2 - checking and writing primary data (1325 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。