Job ID = 4288907 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,130,101 reads read : 18,260,202 reads written : 9,130,101 reads 0-length : 9,130,101 spots read : 10,720,778 reads read : 21,441,556 reads written : 10,720,778 reads 0-length : 10,720,778 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: 00:17:59 19850879 reads; of these: 19850879 (100.00%) were unpaired; of these: 1539891 (7.76%) aligned 0 times 15984089 (80.52%) aligned exactly 1 time 2326899 (11.72%) aligned >1 times 92.24% overall alignment rate Time searching: 00:18:04 Overall time: 00:18:04 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 8 files... [bam_rmdupse_core] 1633642 / 18310988 = 0.0892 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:07:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460560/SRX5460560.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460560/SRX5460560.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460560/SRX5460560.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460560/SRX5460560.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 @ Tue, 10 Dec 2019 13:07:21: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:07:21: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:07:32: 1000000 INFO @ Tue, 10 Dec 2019 13:07:42: 2000000 INFO @ Tue, 10 Dec 2019 13:07:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460560/SRX5460560.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460560/SRX5460560.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460560/SRX5460560.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460560/SRX5460560.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 @ Tue, 10 Dec 2019 13:07:50: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:07:50: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:07:53: 3000000 INFO @ Tue, 10 Dec 2019 13:07:59: 1000000 INFO @ Tue, 10 Dec 2019 13:08:04: 4000000 INFO @ Tue, 10 Dec 2019 13:08:08: 2000000 INFO @ Tue, 10 Dec 2019 13:08:15: 5000000 INFO @ Tue, 10 Dec 2019 13:08:17: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:08:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460560/SRX5460560.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460560/SRX5460560.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460560/SRX5460560.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460560/SRX5460560.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 @ Tue, 10 Dec 2019 13:08:20: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:08:20: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:08:26: 4000000 INFO @ Tue, 10 Dec 2019 13:08:27: 6000000 INFO @ Tue, 10 Dec 2019 13:08:32: 1000000 INFO @ Tue, 10 Dec 2019 13:08:35: 5000000 INFO @ Tue, 10 Dec 2019 13:08:39: 7000000 INFO @ Tue, 10 Dec 2019 13:08:44: 6000000 INFO @ Tue, 10 Dec 2019 13:08:44: 2000000 INFO @ Tue, 10 Dec 2019 13:08:51: 8000000 INFO @ Tue, 10 Dec 2019 13:08:53: 7000000 INFO @ Tue, 10 Dec 2019 13:08:56: 3000000 INFO @ Tue, 10 Dec 2019 13:09:02: 8000000 INFO @ Tue, 10 Dec 2019 13:09:03: 9000000 INFO @ Tue, 10 Dec 2019 13:09:09: 4000000 INFO @ Tue, 10 Dec 2019 13:09:11: 9000000 INFO @ Tue, 10 Dec 2019 13:09:15: 10000000 INFO @ Tue, 10 Dec 2019 13:09:20: 10000000 INFO @ Tue, 10 Dec 2019 13:09:21: 5000000 INFO @ Tue, 10 Dec 2019 13:09:27: 11000000 INFO @ Tue, 10 Dec 2019 13:09:29: 11000000 INFO @ Tue, 10 Dec 2019 13:09:33: 6000000 INFO @ Tue, 10 Dec 2019 13:09:38: 12000000 INFO @ Tue, 10 Dec 2019 13:09:39: 12000000 INFO @ Tue, 10 Dec 2019 13:09:44: 7000000 INFO @ Tue, 10 Dec 2019 13:09:47: 13000000 INFO @ Tue, 10 Dec 2019 13:09:51: 13000000 INFO @ Tue, 10 Dec 2019 13:09:57: 8000000 INFO @ Tue, 10 Dec 2019 13:09:57: 14000000 INFO @ Tue, 10 Dec 2019 13:10:03: 14000000 INFO @ Tue, 10 Dec 2019 13:10:06: 15000000 INFO @ Tue, 10 Dec 2019 13:10:08: 9000000 INFO @ Tue, 10 Dec 2019 13:10:14: 16000000 INFO @ Tue, 10 Dec 2019 13:10:15: 15000000 INFO @ Tue, 10 Dec 2019 13:10:20: 10000000 INFO @ Tue, 10 Dec 2019 13:10:20: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:10:20: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:10:20: #1 total tags in treatment: 16677346 INFO @ Tue, 10 Dec 2019 13:10:20: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:10:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:10:21: #1 tags after filtering in treatment: 16677129 INFO @ Tue, 10 Dec 2019 13:10:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:10:21: #1 finished! INFO @ Tue, 10 Dec 2019 13:10:21: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:10:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:10:26: #2 number of paired peaks: 94493 INFO @ Tue, 10 Dec 2019 13:10:26: start model_add_line... INFO @ Tue, 10 Dec 2019 13:10:26: start X-correlation... INFO @ Tue, 10 Dec 2019 13:10:26: end of X-cor INFO @ Tue, 10 Dec 2019 13:10:26: #2 finished! INFO @ Tue, 10 Dec 2019 13:10:26: #2 predicted fragment length is 183 bps INFO @ Tue, 10 Dec 2019 13:10:26: #2 alternative fragment length(s) may be 183 bps INFO @ Tue, 10 Dec 2019 13:10:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460560/SRX5460560.10_model.r INFO @ Tue, 10 Dec 2019 13:10:26: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:10:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:10:27: 16000000 INFO @ Tue, 10 Dec 2019 13:10:31: 11000000 INFO @ Tue, 10 Dec 2019 13:10:36: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:10:36: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:10:36: #1 total tags in treatment: 16677346 INFO @ Tue, 10 Dec 2019 13:10:36: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:10:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:10:36: #1 tags after filtering in treatment: 16677129 INFO @ Tue, 10 Dec 2019 13:10:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:10:36: #1 finished! INFO @ Tue, 10 Dec 2019 13:10:36: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:10:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:10:41: #2 number of paired peaks: 94493 INFO @ Tue, 10 Dec 2019 13:10:41: start model_add_line... INFO @ Tue, 10 Dec 2019 13:10:41: start X-correlation... INFO @ Tue, 10 Dec 2019 13:10:41: end of X-cor INFO @ Tue, 10 Dec 2019 13:10:41: #2 finished! INFO @ Tue, 10 Dec 2019 13:10:41: #2 predicted fragment length is 183 bps INFO @ Tue, 10 Dec 2019 13:10:41: #2 alternative fragment length(s) may be 183 bps INFO @ Tue, 10 Dec 2019 13:10:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460560/SRX5460560.05_model.r INFO @ Tue, 10 Dec 2019 13:10:41: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:10:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:10:42: 12000000 INFO @ Tue, 10 Dec 2019 13:10:53: 13000000 INFO @ Tue, 10 Dec 2019 13:11:03: 14000000 INFO @ Tue, 10 Dec 2019 13:11:14: 15000000 INFO @ Tue, 10 Dec 2019 13:11:21: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:11:24: 16000000 INFO @ Tue, 10 Dec 2019 13:11:32: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:11:32: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:11:32: #1 total tags in treatment: 16677346 INFO @ Tue, 10 Dec 2019 13:11:32: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:11:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:11:32: #1 tags after filtering in treatment: 16677129 INFO @ Tue, 10 Dec 2019 13:11:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:11:32: #1 finished! INFO @ Tue, 10 Dec 2019 13:11:32: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:11:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:11:35: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:11:37: #2 number of paired peaks: 94493 INFO @ Tue, 10 Dec 2019 13:11:37: start model_add_line... INFO @ Tue, 10 Dec 2019 13:11:37: start X-correlation... INFO @ Tue, 10 Dec 2019 13:11:38: end of X-cor INFO @ Tue, 10 Dec 2019 13:11:38: #2 finished! INFO @ Tue, 10 Dec 2019 13:11:38: #2 predicted fragment length is 183 bps INFO @ Tue, 10 Dec 2019 13:11:38: #2 alternative fragment length(s) may be 183 bps INFO @ Tue, 10 Dec 2019 13:11:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460560/SRX5460560.20_model.r INFO @ Tue, 10 Dec 2019 13:11:38: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:11:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:11:51: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460560/SRX5460560.10_peaks.xls INFO @ Tue, 10 Dec 2019 13:11:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460560/SRX5460560.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:11:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460560/SRX5460560.10_summits.bed INFO @ Tue, 10 Dec 2019 13:11:52: Done! pass1 - making usageList (86 chroms): 12 millis pass2 - checking and writing primary data (43643 records, 4 fields): 57 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:12:04: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460560/SRX5460560.05_peaks.xls INFO @ Tue, 10 Dec 2019 13:12:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460560/SRX5460560.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:12:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460560/SRX5460560.05_summits.bed INFO @ Tue, 10 Dec 2019 13:12:06: Done! pass1 - making usageList (132 chroms): 18 millis pass2 - checking and writing primary data (78531 records, 4 fields): 99 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:12:31: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:12:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460560/SRX5460560.20_peaks.xls INFO @ Tue, 10 Dec 2019 13:12:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460560/SRX5460560.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:12:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460560/SRX5460560.20_summits.bed INFO @ Tue, 10 Dec 2019 13:12:59: Done! pass1 - making usageList (50 chroms): 7 millis pass2 - checking and writing primary data (18455 records, 4 fields): 26 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。