Job ID = 2640444 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 45,706,554 reads read : 91,413,108 reads written : 45,706,554 reads 0-length : 45,706,554 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: 00:50:14 45706554 reads; of these: 45706554 (100.00%) were unpaired; of these: 3051090 (6.68%) aligned 0 times 33580782 (73.47%) aligned exactly 1 time 9074682 (19.85%) aligned >1 times 93.32% overall alignment rate Time searching: 00:50:17 Overall time: 00:50:17 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] 19110300 / 42655464 = 0.4480 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:06:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4320110/SRX4320110.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4320110/SRX4320110.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4320110/SRX4320110.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4320110/SRX4320110.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 18:06:45: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:06:45: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:06:56: 1000000 INFO @ Sat, 24 Aug 2019 18:07:06: 2000000 INFO @ Sat, 24 Aug 2019 18:07:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4320110/SRX4320110.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4320110/SRX4320110.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4320110/SRX4320110.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4320110/SRX4320110.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 18:07:15: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:07:15: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:07:15: 3000000 INFO @ Sat, 24 Aug 2019 18:07:26: 4000000 INFO @ Sat, 24 Aug 2019 18:07:26: 1000000 INFO @ Sat, 24 Aug 2019 18:07:36: 5000000 INFO @ Sat, 24 Aug 2019 18:07:36: 2000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:07:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4320110/SRX4320110.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4320110/SRX4320110.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4320110/SRX4320110.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4320110/SRX4320110.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 18:07:45: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:07:45: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:07:47: 6000000 INFO @ Sat, 24 Aug 2019 18:07:47: 3000000 INFO @ Sat, 24 Aug 2019 18:07:55: 1000000 INFO @ Sat, 24 Aug 2019 18:07:57: 7000000 INFO @ Sat, 24 Aug 2019 18:07:58: 4000000 INFO @ Sat, 24 Aug 2019 18:08:05: 2000000 INFO @ Sat, 24 Aug 2019 18:08:07: 8000000 INFO @ Sat, 24 Aug 2019 18:08:08: 5000000 INFO @ Sat, 24 Aug 2019 18:08:15: 3000000 INFO @ Sat, 24 Aug 2019 18:08:18: 9000000 INFO @ Sat, 24 Aug 2019 18:08:19: 6000000 INFO @ Sat, 24 Aug 2019 18:08:24: 4000000 INFO @ Sat, 24 Aug 2019 18:08:28: 10000000 INFO @ Sat, 24 Aug 2019 18:08:30: 7000000 INFO @ Sat, 24 Aug 2019 18:08:34: 5000000 INFO @ Sat, 24 Aug 2019 18:08:39: 11000000 INFO @ Sat, 24 Aug 2019 18:08:40: 8000000 INFO @ Sat, 24 Aug 2019 18:08:44: 6000000 INFO @ Sat, 24 Aug 2019 18:08:50: 12000000 INFO @ Sat, 24 Aug 2019 18:08:51: 9000000 INFO @ Sat, 24 Aug 2019 18:08:53: 7000000 INFO @ Sat, 24 Aug 2019 18:09:00: 13000000 INFO @ Sat, 24 Aug 2019 18:09:01: 10000000 INFO @ Sat, 24 Aug 2019 18:09:03: 8000000 INFO @ Sat, 24 Aug 2019 18:09:10: 14000000 INFO @ Sat, 24 Aug 2019 18:09:12: 11000000 INFO @ Sat, 24 Aug 2019 18:09:12: 9000000 INFO @ Sat, 24 Aug 2019 18:09:21: 15000000 INFO @ Sat, 24 Aug 2019 18:09:22: 10000000 INFO @ Sat, 24 Aug 2019 18:09:23: 12000000 INFO @ Sat, 24 Aug 2019 18:09:31: 16000000 INFO @ Sat, 24 Aug 2019 18:09:31: 11000000 INFO @ Sat, 24 Aug 2019 18:09:33: 13000000 INFO @ Sat, 24 Aug 2019 18:09:41: 12000000 INFO @ Sat, 24 Aug 2019 18:09:41: 17000000 INFO @ Sat, 24 Aug 2019 18:09:44: 14000000 INFO @ Sat, 24 Aug 2019 18:09:50: 13000000 INFO @ Sat, 24 Aug 2019 18:09:52: 18000000 INFO @ Sat, 24 Aug 2019 18:09:54: 15000000 INFO @ Sat, 24 Aug 2019 18:10:00: 14000000 INFO @ Sat, 24 Aug 2019 18:10:02: 19000000 INFO @ Sat, 24 Aug 2019 18:10:05: 16000000 INFO @ Sat, 24 Aug 2019 18:10:10: 15000000 INFO @ Sat, 24 Aug 2019 18:10:13: 20000000 INFO @ Sat, 24 Aug 2019 18:10:15: 17000000 INFO @ Sat, 24 Aug 2019 18:10:19: 16000000 INFO @ Sat, 24 Aug 2019 18:10:23: 21000000 INFO @ Sat, 24 Aug 2019 18:10:26: 18000000 INFO @ Sat, 24 Aug 2019 18:10:29: 17000000 INFO @ Sat, 24 Aug 2019 18:10:34: 22000000 INFO @ Sat, 24 Aug 2019 18:10:36: 19000000 INFO @ Sat, 24 Aug 2019 18:10:39: 18000000 INFO @ Sat, 24 Aug 2019 18:10:44: 23000000 INFO @ Sat, 24 Aug 2019 18:10:47: 20000000 INFO @ Sat, 24 Aug 2019 18:10:48: 19000000 INFO @ Sat, 24 Aug 2019 18:10:50: #1 tag size is determined as 74 bps INFO @ Sat, 24 Aug 2019 18:10:50: #1 tag size = 74 INFO @ Sat, 24 Aug 2019 18:10:50: #1 total tags in treatment: 23545164 INFO @ Sat, 24 Aug 2019 18:10:50: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:10:50: #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 18:10:51: #1 tags after filtering in treatment: 23545050 INFO @ Sat, 24 Aug 2019 18:10:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:10:51: #1 finished! INFO @ Sat, 24 Aug 2019 18:10:51: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:10:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:10:54: #2 number of paired peaks: 23892 INFO @ Sat, 24 Aug 2019 18:10:54: start model_add_line... INFO @ Sat, 24 Aug 2019 18:10:55: start X-correlation... INFO @ Sat, 24 Aug 2019 18:10:55: end of X-cor INFO @ Sat, 24 Aug 2019 18:10:55: #2 finished! INFO @ Sat, 24 Aug 2019 18:10:55: #2 predicted fragment length is 212 bps INFO @ Sat, 24 Aug 2019 18:10:55: #2 alternative fragment length(s) may be 212 bps INFO @ Sat, 24 Aug 2019 18:10:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4320110/SRX4320110.05_model.r INFO @ Sat, 24 Aug 2019 18:10:55: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:10:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:10:57: 21000000 INFO @ Sat, 24 Aug 2019 18:10:58: 20000000 INFO @ Sat, 24 Aug 2019 18:11:07: 22000000 INFO @ Sat, 24 Aug 2019 18:11:07: 21000000 INFO @ Sat, 24 Aug 2019 18:11:17: 22000000 INFO @ Sat, 24 Aug 2019 18:11:17: 23000000 INFO @ Sat, 24 Aug 2019 18:11:23: #1 tag size is determined as 74 bps INFO @ Sat, 24 Aug 2019 18:11:23: #1 tag size = 74 INFO @ Sat, 24 Aug 2019 18:11:23: #1 total tags in treatment: 23545164 INFO @ Sat, 24 Aug 2019 18:11:23: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:11:23: #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 18:11:23: #1 tags after filtering in treatment: 23545050 INFO @ Sat, 24 Aug 2019 18:11:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:11:23: #1 finished! INFO @ Sat, 24 Aug 2019 18:11:23: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:11:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:11:26: 23000000 INFO @ Sat, 24 Aug 2019 18:11:27: #2 number of paired peaks: 23892 INFO @ Sat, 24 Aug 2019 18:11:27: start model_add_line... INFO @ Sat, 24 Aug 2019 18:11:27: start X-correlation... INFO @ Sat, 24 Aug 2019 18:11:27: end of X-cor INFO @ Sat, 24 Aug 2019 18:11:27: #2 finished! INFO @ Sat, 24 Aug 2019 18:11:27: #2 predicted fragment length is 212 bps INFO @ Sat, 24 Aug 2019 18:11:27: #2 alternative fragment length(s) may be 212 bps INFO @ Sat, 24 Aug 2019 18:11:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4320110/SRX4320110.10_model.r INFO @ Sat, 24 Aug 2019 18:11:27: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:11:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:11:32: #1 tag size is determined as 74 bps INFO @ Sat, 24 Aug 2019 18:11:32: #1 tag size = 74 INFO @ Sat, 24 Aug 2019 18:11:32: #1 total tags in treatment: 23545164 INFO @ Sat, 24 Aug 2019 18:11:32: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:11:32: #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 18:11:32: #1 tags after filtering in treatment: 23545050 INFO @ Sat, 24 Aug 2019 18:11:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:11:32: #1 finished! INFO @ Sat, 24 Aug 2019 18:11:32: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:11:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:11:36: #2 number of paired peaks: 23892 INFO @ Sat, 24 Aug 2019 18:11:36: start model_add_line... INFO @ Sat, 24 Aug 2019 18:11:36: start X-correlation... INFO @ Sat, 24 Aug 2019 18:11:36: end of X-cor INFO @ Sat, 24 Aug 2019 18:11:36: #2 finished! INFO @ Sat, 24 Aug 2019 18:11:36: #2 predicted fragment length is 212 bps INFO @ Sat, 24 Aug 2019 18:11:36: #2 alternative fragment length(s) may be 212 bps INFO @ Sat, 24 Aug 2019 18:11:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4320110/SRX4320110.20_model.r INFO @ Sat, 24 Aug 2019 18:11:36: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:11:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:12:11: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:12:44: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:12:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4320110/SRX4320110.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:12:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4320110/SRX4320110.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:12:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4320110/SRX4320110.05_summits.bed INFO @ Sat, 24 Aug 2019 18:12:49: Done! pass1 - making usageList (87 chroms): 5 millis pass2 - checking and writing primary data (11455 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:12:52: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:13:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4320110/SRX4320110.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:13:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4320110/SRX4320110.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:13:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4320110/SRX4320110.10_summits.bed INFO @ Sat, 24 Aug 2019 18:13:22: Done! pass1 - making usageList (63 chroms): 2 millis pass2 - checking and writing primary data (4266 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:13:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4320110/SRX4320110.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:13:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4320110/SRX4320110.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:13:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4320110/SRX4320110.20_summits.bed INFO @ Sat, 24 Aug 2019 18:13:29: Done! pass1 - making usageList (41 chroms): 2 millis pass2 - checking and writing primary data (1444 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。