Job ID = 11632725 sra ファイルのダウンロード中... Completed: 542101K bytes transferred in 8 seconds (525355K 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 29104493 spots for /home/okishinya/chipatlas/results/rn6/SRX4497195/SRR7633465.sra Written 29104493 spots for /home/okishinya/chipatlas/results/rn6/SRX4497195/SRR7633465.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:22:29 29104493 reads; of these: 29104493 (100.00%) were unpaired; of these: 907608 (3.12%) aligned 0 times 20233154 (69.52%) aligned exactly 1 time 7963731 (27.36%) aligned >1 times 96.88% overall alignment rate Time searching: 00:22:32 Overall time: 00:22:32 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 12 files... [bam_rmdupse_core] 4795643 / 28196885 = 0.1701 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 07:09:22: # Command line: callpeak -t SRX4497195.bam -f BAM -g 2.15e9 -n SRX4497195.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4497195.20 # format = BAM # ChIP-seq file = ['SRX4497195.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 07:09:22: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:09:22: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:09:22: # Command line: callpeak -t SRX4497195.bam -f BAM -g 2.15e9 -n SRX4497195.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4497195.05 # format = BAM # ChIP-seq file = ['SRX4497195.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 07:09:22: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:09:22: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:09:22: # Command line: callpeak -t SRX4497195.bam -f BAM -g 2.15e9 -n SRX4497195.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4497195.10 # format = BAM # ChIP-seq file = ['SRX4497195.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 07:09:22: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:09:22: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:09:29: 1000000 INFO @ Fri, 15 Feb 2019 07:09:29: 1000000 INFO @ Fri, 15 Feb 2019 07:09:29: 1000000 INFO @ Fri, 15 Feb 2019 07:09:35: 2000000 INFO @ Fri, 15 Feb 2019 07:09:36: 2000000 INFO @ Fri, 15 Feb 2019 07:09:36: 2000000 INFO @ Fri, 15 Feb 2019 07:09:42: 3000000 INFO @ Fri, 15 Feb 2019 07:09:42: 3000000 INFO @ Fri, 15 Feb 2019 07:09:42: 3000000 INFO @ Fri, 15 Feb 2019 07:09:49: 4000000 INFO @ Fri, 15 Feb 2019 07:09:49: 4000000 INFO @ Fri, 15 Feb 2019 07:09:49: 4000000 INFO @ Fri, 15 Feb 2019 07:09:55: 5000000 INFO @ Fri, 15 Feb 2019 07:09:56: 5000000 INFO @ Fri, 15 Feb 2019 07:09:56: 5000000 INFO @ Fri, 15 Feb 2019 07:10:02: 6000000 INFO @ Fri, 15 Feb 2019 07:10:02: 6000000 INFO @ Fri, 15 Feb 2019 07:10:03: 6000000 INFO @ Fri, 15 Feb 2019 07:10:08: 7000000 INFO @ Fri, 15 Feb 2019 07:10:09: 7000000 INFO @ Fri, 15 Feb 2019 07:10:09: 7000000 INFO @ Fri, 15 Feb 2019 07:10:15: 8000000 INFO @ Fri, 15 Feb 2019 07:10:16: 8000000 INFO @ Fri, 15 Feb 2019 07:10:17: 8000000 INFO @ Fri, 15 Feb 2019 07:10:22: 9000000 INFO @ Fri, 15 Feb 2019 07:10:22: 9000000 INFO @ Fri, 15 Feb 2019 07:10:24: 9000000 INFO @ Fri, 15 Feb 2019 07:10:29: 10000000 INFO @ Fri, 15 Feb 2019 07:10:29: 10000000 INFO @ Fri, 15 Feb 2019 07:10:31: 10000000 INFO @ Fri, 15 Feb 2019 07:10:35: 11000000 INFO @ Fri, 15 Feb 2019 07:10:35: 11000000 INFO @ Fri, 15 Feb 2019 07:10:38: 11000000 INFO @ Fri, 15 Feb 2019 07:10:42: 12000000 INFO @ Fri, 15 Feb 2019 07:10:42: 12000000 INFO @ Fri, 15 Feb 2019 07:10:45: 12000000 INFO @ Fri, 15 Feb 2019 07:10:48: 13000000 INFO @ Fri, 15 Feb 2019 07:10:49: 13000000 INFO @ Fri, 15 Feb 2019 07:10:52: 13000000 INFO @ Fri, 15 Feb 2019 07:10:55: 14000000 INFO @ Fri, 15 Feb 2019 07:10:56: 14000000 INFO @ Fri, 15 Feb 2019 07:10:58: 14000000 INFO @ Fri, 15 Feb 2019 07:11:01: 15000000 INFO @ Fri, 15 Feb 2019 07:11:03: 15000000 INFO @ Fri, 15 Feb 2019 07:11:05: 15000000 INFO @ Fri, 15 Feb 2019 07:11:08: 16000000 INFO @ Fri, 15 Feb 2019 07:11:10: 16000000 INFO @ Fri, 15 Feb 2019 07:11:12: 16000000 INFO @ Fri, 15 Feb 2019 07:11:14: 17000000 INFO @ Fri, 15 Feb 2019 07:11:16: 17000000 INFO @ Fri, 15 Feb 2019 07:11:19: 17000000 INFO @ Fri, 15 Feb 2019 07:11:21: 18000000 INFO @ Fri, 15 Feb 2019 07:11:23: 18000000 INFO @ Fri, 15 Feb 2019 07:11:26: 18000000 INFO @ Fri, 15 Feb 2019 07:11:28: 19000000 INFO @ Fri, 15 Feb 2019 07:11:30: 19000000 INFO @ Fri, 15 Feb 2019 07:11:33: 19000000 INFO @ Fri, 15 Feb 2019 07:11:34: 20000000 INFO @ Fri, 15 Feb 2019 07:11:36: 20000000 INFO @ Fri, 15 Feb 2019 07:11:40: 20000000 INFO @ Fri, 15 Feb 2019 07:11:41: 21000000 INFO @ Fri, 15 Feb 2019 07:11:43: 21000000 INFO @ Fri, 15 Feb 2019 07:11:47: 21000000 INFO @ Fri, 15 Feb 2019 07:11:48: 22000000 INFO @ Fri, 15 Feb 2019 07:11:50: 22000000 INFO @ Fri, 15 Feb 2019 07:11:54: 22000000 INFO @ Fri, 15 Feb 2019 07:11:55: 23000000 INFO @ Fri, 15 Feb 2019 07:11:56: 23000000 INFO @ Fri, 15 Feb 2019 07:11:58: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:11:58: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:11:58: #1 total tags in treatment: 23401242 INFO @ Fri, 15 Feb 2019 07:11:58: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:11:58: #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 07:11:59: #1 tags after filtering in treatment: 23401126 INFO @ Fri, 15 Feb 2019 07:11:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:11:59: #1 finished! INFO @ Fri, 15 Feb 2019 07:11:59: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:11:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:11:59: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:11:59: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:11:59: #1 total tags in treatment: 23401242 INFO @ Fri, 15 Feb 2019 07:11:59: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:11:59: #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 07:12:00: #1 tags after filtering in treatment: 23401126 INFO @ Fri, 15 Feb 2019 07:12:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:12:00: #1 finished! INFO @ Fri, 15 Feb 2019 07:12:00: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:12:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:12:01: 23000000 INFO @ Fri, 15 Feb 2019 07:12:02: #2 number of paired peaks: 22896 INFO @ Fri, 15 Feb 2019 07:12:02: start model_add_line... INFO @ Fri, 15 Feb 2019 07:12:02: start X-correlation... INFO @ Fri, 15 Feb 2019 07:12:02: end of X-cor INFO @ Fri, 15 Feb 2019 07:12:02: #2 finished! INFO @ Fri, 15 Feb 2019 07:12:02: #2 predicted fragment length is 164 bps INFO @ Fri, 15 Feb 2019 07:12:02: #2 alternative fragment length(s) may be 58,164,213 bps INFO @ Fri, 15 Feb 2019 07:12:02: #2.2 Generate R script for model : SRX4497195.20_model.r INFO @ Fri, 15 Feb 2019 07:12:02: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:12:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:12:03: #2 number of paired peaks: 22896 INFO @ Fri, 15 Feb 2019 07:12:03: start model_add_line... INFO @ Fri, 15 Feb 2019 07:12:03: start X-correlation... INFO @ Fri, 15 Feb 2019 07:12:03: end of X-cor INFO @ Fri, 15 Feb 2019 07:12:03: #2 finished! INFO @ Fri, 15 Feb 2019 07:12:03: #2 predicted fragment length is 164 bps INFO @ Fri, 15 Feb 2019 07:12:03: #2 alternative fragment length(s) may be 58,164,213 bps INFO @ Fri, 15 Feb 2019 07:12:03: #2.2 Generate R script for model : SRX4497195.10_model.r INFO @ Fri, 15 Feb 2019 07:12:03: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:12:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:12:04: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:12:04: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:12:04: #1 total tags in treatment: 23401242 INFO @ Fri, 15 Feb 2019 07:12:04: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:12:04: #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 07:12:05: #1 tags after filtering in treatment: 23401126 INFO @ Fri, 15 Feb 2019 07:12:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:12:05: #1 finished! INFO @ Fri, 15 Feb 2019 07:12:05: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:12:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:12:08: #2 number of paired peaks: 22896 INFO @ Fri, 15 Feb 2019 07:12:08: start model_add_line... INFO @ Fri, 15 Feb 2019 07:12:08: start X-correlation... INFO @ Fri, 15 Feb 2019 07:12:08: end of X-cor INFO @ Fri, 15 Feb 2019 07:12:08: #2 finished! INFO @ Fri, 15 Feb 2019 07:12:08: #2 predicted fragment length is 164 bps INFO @ Fri, 15 Feb 2019 07:12:08: #2 alternative fragment length(s) may be 58,164,213 bps INFO @ Fri, 15 Feb 2019 07:12:08: #2.2 Generate R script for model : SRX4497195.05_model.r INFO @ Fri, 15 Feb 2019 07:12:08: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:12:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:13:00: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:13:02: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:13:09: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:13:36: #4 Write output xls file... SRX4497195.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:13:36: #4 Write peak in narrowPeak format file... SRX4497195.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:13:36: #4 Write summits bed file... SRX4497195.10_summits.bed INFO @ Fri, 15 Feb 2019 07:13:36: Done! pass1 - making usageList (40 chroms): 4 millis pass2 - checking and writing primary data (559 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:13:41: #4 Write output xls file... SRX4497195.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:13:41: #4 Write peak in narrowPeak format file... SRX4497195.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:13:41: #4 Write summits bed file... SRX4497195.20_summits.bed INFO @ Fri, 15 Feb 2019 07:13:41: Done! pass1 - making usageList (29 chroms): 4 millis pass2 - checking and writing primary data (275 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:13:45: #4 Write output xls file... SRX4497195.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:13:45: #4 Write peak in narrowPeak format file... SRX4497195.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:13:45: #4 Write summits bed file... SRX4497195.05_summits.bed INFO @ Fri, 15 Feb 2019 07:13:45: Done! pass1 - making usageList (46 chroms): 3 millis pass2 - checking and writing primary data (1118 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。