Job ID = 2640606 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,226,034 reads read : 60,452,068 reads written : 30,226,034 reads 0-length : 30,226,034 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:00:01 Multiseed full-index search: 00:19:59 30226034 reads; of these: 30226034 (100.00%) were unpaired; of these: 782353 (2.59%) aligned 0 times 24463206 (80.93%) aligned exactly 1 time 4980475 (16.48%) aligned >1 times 97.41% overall alignment rate Time searching: 00:20:02 Overall time: 00:20:02 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] 8974730 / 29443681 = 0.3048 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:36:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375034/SRX5375034.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375034/SRX5375034.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375034/SRX5375034.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375034/SRX5375034.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, 24 Aug 2019 18:36:08: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:36:08: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:36:15: 1000000 INFO @ Sat, 24 Aug 2019 18:36:23: 2000000 INFO @ Sat, 24 Aug 2019 18:36:30: 3000000 INFO @ Sat, 24 Aug 2019 18:36:37: 4000000 INFO @ Sat, 24 Aug 2019 18:36:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375034/SRX5375034.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375034/SRX5375034.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375034/SRX5375034.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375034/SRX5375034.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, 24 Aug 2019 18:36:37: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:36:37: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:36:44: 5000000 INFO @ Sat, 24 Aug 2019 18:36:45: 1000000 INFO @ Sat, 24 Aug 2019 18:36:51: 6000000 INFO @ Sat, 24 Aug 2019 18:36:53: 2000000 INFO @ Sat, 24 Aug 2019 18:36:59: 7000000 INFO @ Sat, 24 Aug 2019 18:37:00: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:37:06: 8000000 INFO @ Sat, 24 Aug 2019 18:37:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375034/SRX5375034.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375034/SRX5375034.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375034/SRX5375034.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375034/SRX5375034.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, 24 Aug 2019 18:37:07: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:37:07: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:37:08: 4000000 INFO @ Sat, 24 Aug 2019 18:37:14: 9000000 INFO @ Sat, 24 Aug 2019 18:37:15: 1000000 INFO @ Sat, 24 Aug 2019 18:37:16: 5000000 INFO @ Sat, 24 Aug 2019 18:37:22: 10000000 INFO @ Sat, 24 Aug 2019 18:37:23: 2000000 INFO @ Sat, 24 Aug 2019 18:37:23: 6000000 INFO @ Sat, 24 Aug 2019 18:37:29: 11000000 INFO @ Sat, 24 Aug 2019 18:37:31: 3000000 INFO @ Sat, 24 Aug 2019 18:37:31: 7000000 INFO @ Sat, 24 Aug 2019 18:37:37: 12000000 INFO @ Sat, 24 Aug 2019 18:37:38: 4000000 INFO @ Sat, 24 Aug 2019 18:37:39: 8000000 INFO @ Sat, 24 Aug 2019 18:37:44: 13000000 INFO @ Sat, 24 Aug 2019 18:37:46: 5000000 INFO @ Sat, 24 Aug 2019 18:37:47: 9000000 INFO @ Sat, 24 Aug 2019 18:37:52: 14000000 INFO @ Sat, 24 Aug 2019 18:37:54: 6000000 INFO @ Sat, 24 Aug 2019 18:37:55: 10000000 INFO @ Sat, 24 Aug 2019 18:37:59: 15000000 INFO @ Sat, 24 Aug 2019 18:38:02: 7000000 INFO @ Sat, 24 Aug 2019 18:38:02: 11000000 INFO @ Sat, 24 Aug 2019 18:38:07: 16000000 INFO @ Sat, 24 Aug 2019 18:38:09: 12000000 INFO @ Sat, 24 Aug 2019 18:38:10: 8000000 INFO @ Sat, 24 Aug 2019 18:38:14: 17000000 INFO @ Sat, 24 Aug 2019 18:38:17: 13000000 INFO @ Sat, 24 Aug 2019 18:38:18: 9000000 INFO @ Sat, 24 Aug 2019 18:38:22: 18000000 INFO @ Sat, 24 Aug 2019 18:38:25: 14000000 INFO @ Sat, 24 Aug 2019 18:38:26: 10000000 INFO @ Sat, 24 Aug 2019 18:38:30: 19000000 INFO @ Sat, 24 Aug 2019 18:38:32: 15000000 INFO @ Sat, 24 Aug 2019 18:38:34: 11000000 INFO @ Sat, 24 Aug 2019 18:38:37: 20000000 INFO @ Sat, 24 Aug 2019 18:38:40: 16000000 INFO @ Sat, 24 Aug 2019 18:38:41: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:38:41: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:38:41: #1 total tags in treatment: 20468951 INFO @ Sat, 24 Aug 2019 18:38:41: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:38:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:38:41: 12000000 INFO @ Sat, 24 Aug 2019 18:38:42: #1 tags after filtering in treatment: 20468748 INFO @ Sat, 24 Aug 2019 18:38:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:38:42: #1 finished! INFO @ Sat, 24 Aug 2019 18:38:42: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:38:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:38:47: #2 number of paired peaks: 75124 INFO @ Sat, 24 Aug 2019 18:38:47: start model_add_line... INFO @ Sat, 24 Aug 2019 18:38:47: start X-correlation... INFO @ Sat, 24 Aug 2019 18:38:47: 17000000 INFO @ Sat, 24 Aug 2019 18:38:47: end of X-cor INFO @ Sat, 24 Aug 2019 18:38:47: #2 finished! INFO @ Sat, 24 Aug 2019 18:38:47: #2 predicted fragment length is 164 bps INFO @ Sat, 24 Aug 2019 18:38:47: #2 alternative fragment length(s) may be 164 bps INFO @ Sat, 24 Aug 2019 18:38:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375034/SRX5375034.05_model.r INFO @ Sat, 24 Aug 2019 18:38:47: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:38:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:38:49: 13000000 INFO @ Sat, 24 Aug 2019 18:38:55: 18000000 INFO @ Sat, 24 Aug 2019 18:38:57: 14000000 INFO @ Sat, 24 Aug 2019 18:39:03: 19000000 INFO @ Sat, 24 Aug 2019 18:39:05: 15000000 INFO @ Sat, 24 Aug 2019 18:39:10: 20000000 INFO @ Sat, 24 Aug 2019 18:39:13: 16000000 INFO @ Sat, 24 Aug 2019 18:39:14: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:39:14: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:39:14: #1 total tags in treatment: 20468951 INFO @ Sat, 24 Aug 2019 18:39:14: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:39:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:39:15: #1 tags after filtering in treatment: 20468748 INFO @ Sat, 24 Aug 2019 18:39:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:39:15: #1 finished! INFO @ Sat, 24 Aug 2019 18:39:15: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:39:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:39:20: #2 number of paired peaks: 75124 INFO @ Sat, 24 Aug 2019 18:39:20: start model_add_line... INFO @ Sat, 24 Aug 2019 18:39:21: start X-correlation... INFO @ Sat, 24 Aug 2019 18:39:21: end of X-cor INFO @ Sat, 24 Aug 2019 18:39:21: #2 finished! INFO @ Sat, 24 Aug 2019 18:39:21: #2 predicted fragment length is 164 bps INFO @ Sat, 24 Aug 2019 18:39:21: #2 alternative fragment length(s) may be 164 bps INFO @ Sat, 24 Aug 2019 18:39:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375034/SRX5375034.10_model.r INFO @ Sat, 24 Aug 2019 18:39:21: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:39:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:39:23: 17000000 INFO @ Sat, 24 Aug 2019 18:39:31: 18000000 INFO @ Sat, 24 Aug 2019 18:39:39: 19000000 INFO @ Sat, 24 Aug 2019 18:39:47: 20000000 INFO @ Sat, 24 Aug 2019 18:39:51: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:39:51: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:39:51: #1 total tags in treatment: 20468951 INFO @ Sat, 24 Aug 2019 18:39:51: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:39:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:39:51: #1 tags after filtering in treatment: 20468748 INFO @ Sat, 24 Aug 2019 18:39:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:39:51: #1 finished! INFO @ Sat, 24 Aug 2019 18:39:51: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:39:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:39:54: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:39:57: #2 number of paired peaks: 75124 INFO @ Sat, 24 Aug 2019 18:39:57: start model_add_line... INFO @ Sat, 24 Aug 2019 18:39:57: start X-correlation... INFO @ Sat, 24 Aug 2019 18:39:57: end of X-cor INFO @ Sat, 24 Aug 2019 18:39:57: #2 finished! INFO @ Sat, 24 Aug 2019 18:39:57: #2 predicted fragment length is 164 bps INFO @ Sat, 24 Aug 2019 18:39:57: #2 alternative fragment length(s) may be 164 bps INFO @ Sat, 24 Aug 2019 18:39:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375034/SRX5375034.20_model.r INFO @ Sat, 24 Aug 2019 18:39:57: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:39:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:40:26: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:40:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375034/SRX5375034.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:40:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375034/SRX5375034.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:40:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375034/SRX5375034.05_summits.bed INFO @ Sat, 24 Aug 2019 18:40:31: Done! pass1 - making usageList (128 chroms): 12 millis pass2 - checking and writing primary data (35520 records, 4 fields): 57 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:41:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375034/SRX5375034.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:41:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375034/SRX5375034.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:41:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375034/SRX5375034.10_summits.bed INFO @ Sat, 24 Aug 2019 18:41:01: Done! pass1 - making usageList (107 chroms): 8 millis pass2 - checking and writing primary data (25135 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:41:05: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:41:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375034/SRX5375034.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:41:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375034/SRX5375034.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:41:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375034/SRX5375034.20_summits.bed INFO @ Sat, 24 Aug 2019 18:41:42: Done! pass1 - making usageList (80 chroms): 6 millis pass2 - checking and writing primary data (14115 records, 4 fields): 23 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。