Job ID = 2590606 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 64,180,475 reads read : 128,360,950 reads written : 64,180,475 reads 0-length : 64,180,475 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:17:33 64180475 reads; of these: 64180475 (100.00%) were unpaired; of these: 1585211 (2.47%) aligned 0 times 50955236 (79.39%) aligned exactly 1 time 11640028 (18.14%) aligned >1 times 97.53% overall alignment rate Time searching: 00:17:33 Overall time: 00:17:33 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 28 files... [bam_rmdupse_core] 36585771 / 62595264 = 0.5845 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 @ Mon, 12 Aug 2019 23:19:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923190/SRX4923190.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923190/SRX4923190.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923190/SRX4923190.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923190/SRX4923190.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 12 Aug 2019 23:19:15: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:19:15: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:19:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923190/SRX4923190.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923190/SRX4923190.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923190/SRX4923190.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923190/SRX4923190.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 12 Aug 2019 23:19:16: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:19:16: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:19:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923190/SRX4923190.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923190/SRX4923190.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923190/SRX4923190.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923190/SRX4923190.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 12 Aug 2019 23:19:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:19:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:19:22: 1000000 INFO @ Mon, 12 Aug 2019 23:19:23: 1000000 INFO @ Mon, 12 Aug 2019 23:19:24: 1000000 INFO @ Mon, 12 Aug 2019 23:19:29: 2000000 INFO @ Mon, 12 Aug 2019 23:19:30: 2000000 INFO @ Mon, 12 Aug 2019 23:19:31: 2000000 INFO @ Mon, 12 Aug 2019 23:19:36: 3000000 INFO @ Mon, 12 Aug 2019 23:19:37: 3000000 INFO @ Mon, 12 Aug 2019 23:19:37: 3000000 INFO @ Mon, 12 Aug 2019 23:19:42: 4000000 INFO @ Mon, 12 Aug 2019 23:19:43: 4000000 INFO @ Mon, 12 Aug 2019 23:19:44: 4000000 INFO @ Mon, 12 Aug 2019 23:19:49: 5000000 INFO @ Mon, 12 Aug 2019 23:19:50: 5000000 INFO @ Mon, 12 Aug 2019 23:19:52: 5000000 INFO @ Mon, 12 Aug 2019 23:19:56: 6000000 INFO @ Mon, 12 Aug 2019 23:19:57: 6000000 INFO @ Mon, 12 Aug 2019 23:19:59: 6000000 INFO @ Mon, 12 Aug 2019 23:20:02: 7000000 INFO @ Mon, 12 Aug 2019 23:20:04: 7000000 INFO @ Mon, 12 Aug 2019 23:20:06: 7000000 INFO @ Mon, 12 Aug 2019 23:20:09: 8000000 INFO @ Mon, 12 Aug 2019 23:20:10: 8000000 INFO @ Mon, 12 Aug 2019 23:20:13: 8000000 INFO @ Mon, 12 Aug 2019 23:20:15: 9000000 INFO @ Mon, 12 Aug 2019 23:20:17: 9000000 INFO @ Mon, 12 Aug 2019 23:20:20: 9000000 INFO @ Mon, 12 Aug 2019 23:20:21: 10000000 INFO @ Mon, 12 Aug 2019 23:20:23: 10000000 INFO @ Mon, 12 Aug 2019 23:20:27: 10000000 INFO @ Mon, 12 Aug 2019 23:20:28: 11000000 INFO @ Mon, 12 Aug 2019 23:20:30: 11000000 INFO @ Mon, 12 Aug 2019 23:20:34: 11000000 INFO @ Mon, 12 Aug 2019 23:20:35: 12000000 INFO @ Mon, 12 Aug 2019 23:20:37: 12000000 INFO @ Mon, 12 Aug 2019 23:20:41: 12000000 INFO @ Mon, 12 Aug 2019 23:20:42: 13000000 INFO @ Mon, 12 Aug 2019 23:20:44: 13000000 INFO @ Mon, 12 Aug 2019 23:20:48: 13000000 INFO @ Mon, 12 Aug 2019 23:20:49: 14000000 INFO @ Mon, 12 Aug 2019 23:20:51: 14000000 INFO @ Mon, 12 Aug 2019 23:20:55: 14000000 INFO @ Mon, 12 Aug 2019 23:20:57: 15000000 INFO @ Mon, 12 Aug 2019 23:20:59: 15000000 INFO @ Mon, 12 Aug 2019 23:21:02: 15000000 INFO @ Mon, 12 Aug 2019 23:21:04: 16000000 INFO @ Mon, 12 Aug 2019 23:21:06: 16000000 INFO @ Mon, 12 Aug 2019 23:21:10: 16000000 INFO @ Mon, 12 Aug 2019 23:21:11: 17000000 INFO @ Mon, 12 Aug 2019 23:21:14: 17000000 INFO @ Mon, 12 Aug 2019 23:21:18: 17000000 INFO @ Mon, 12 Aug 2019 23:21:19: 18000000 INFO @ Mon, 12 Aug 2019 23:21:21: 18000000 INFO @ Mon, 12 Aug 2019 23:21:25: 18000000 INFO @ Mon, 12 Aug 2019 23:21:27: 19000000 INFO @ Mon, 12 Aug 2019 23:21:29: 19000000 INFO @ Mon, 12 Aug 2019 23:21:33: 19000000 INFO @ Mon, 12 Aug 2019 23:21:35: 20000000 INFO @ Mon, 12 Aug 2019 23:21:37: 20000000 INFO @ Mon, 12 Aug 2019 23:21:41: 20000000 INFO @ Mon, 12 Aug 2019 23:21:43: 21000000 INFO @ Mon, 12 Aug 2019 23:21:45: 21000000 INFO @ Mon, 12 Aug 2019 23:21:49: 21000000 INFO @ Mon, 12 Aug 2019 23:21:51: 22000000 INFO @ Mon, 12 Aug 2019 23:21:52: 22000000 INFO @ Mon, 12 Aug 2019 23:21:57: 22000000 INFO @ Mon, 12 Aug 2019 23:21:58: 23000000 INFO @ Mon, 12 Aug 2019 23:21:59: 23000000 INFO @ Mon, 12 Aug 2019 23:22:04: 24000000 INFO @ Mon, 12 Aug 2019 23:22:05: 23000000 INFO @ Mon, 12 Aug 2019 23:22:05: 24000000 INFO @ Mon, 12 Aug 2019 23:22:11: 25000000 INFO @ Mon, 12 Aug 2019 23:22:12: 24000000 INFO @ Mon, 12 Aug 2019 23:22:12: 25000000 INFO @ Mon, 12 Aug 2019 23:22:17: 26000000 INFO @ Mon, 12 Aug 2019 23:22:18: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:22:18: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:22:18: #1 total tags in treatment: 26009493 INFO @ Mon, 12 Aug 2019 23:22:18: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:22:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:22:18: #1 tags after filtering in treatment: 26009493 INFO @ Mon, 12 Aug 2019 23:22:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:22:18: #1 finished! INFO @ Mon, 12 Aug 2019 23:22:18: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:22:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:22:19: 26000000 INFO @ Mon, 12 Aug 2019 23:22:19: 25000000 INFO @ Mon, 12 Aug 2019 23:22:19: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:22:19: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:22:19: #1 total tags in treatment: 26009493 INFO @ Mon, 12 Aug 2019 23:22:19: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:22:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:22:19: #1 tags after filtering in treatment: 26009493 INFO @ Mon, 12 Aug 2019 23:22:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:22:19: #1 finished! INFO @ Mon, 12 Aug 2019 23:22:19: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:22:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:22:22: #2 number of paired peaks: 10239 INFO @ Mon, 12 Aug 2019 23:22:22: start model_add_line... INFO @ Mon, 12 Aug 2019 23:22:23: start X-correlation... INFO @ Mon, 12 Aug 2019 23:22:23: end of X-cor INFO @ Mon, 12 Aug 2019 23:22:23: #2 finished! INFO @ Mon, 12 Aug 2019 23:22:23: #2 predicted fragment length is 139 bps INFO @ Mon, 12 Aug 2019 23:22:23: #2 alternative fragment length(s) may be 139 bps INFO @ Mon, 12 Aug 2019 23:22:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923190/SRX4923190.10_model.r INFO @ Mon, 12 Aug 2019 23:22:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:22:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:22:23: #2 number of paired peaks: 10239 INFO @ Mon, 12 Aug 2019 23:22:23: start model_add_line... INFO @ Mon, 12 Aug 2019 23:22:24: start X-correlation... INFO @ Mon, 12 Aug 2019 23:22:24: end of X-cor INFO @ Mon, 12 Aug 2019 23:22:24: #2 finished! INFO @ Mon, 12 Aug 2019 23:22:24: #2 predicted fragment length is 139 bps INFO @ Mon, 12 Aug 2019 23:22:24: #2 alternative fragment length(s) may be 139 bps INFO @ Mon, 12 Aug 2019 23:22:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923190/SRX4923190.20_model.r INFO @ Mon, 12 Aug 2019 23:22:24: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:22:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:22:26: 26000000 INFO @ Mon, 12 Aug 2019 23:22:26: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:22:26: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:22:26: #1 total tags in treatment: 26009493 INFO @ Mon, 12 Aug 2019 23:22:26: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:22:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:22:27: #1 tags after filtering in treatment: 26009493 INFO @ Mon, 12 Aug 2019 23:22:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:22:27: #1 finished! INFO @ Mon, 12 Aug 2019 23:22:27: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:22:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:22:30: #2 number of paired peaks: 10239 INFO @ Mon, 12 Aug 2019 23:22:30: start model_add_line... INFO @ Mon, 12 Aug 2019 23:22:31: start X-correlation... INFO @ Mon, 12 Aug 2019 23:22:31: end of X-cor INFO @ Mon, 12 Aug 2019 23:22:31: #2 finished! INFO @ Mon, 12 Aug 2019 23:22:31: #2 predicted fragment length is 139 bps INFO @ Mon, 12 Aug 2019 23:22:31: #2 alternative fragment length(s) may be 139 bps INFO @ Mon, 12 Aug 2019 23:22:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923190/SRX4923190.05_model.r INFO @ Mon, 12 Aug 2019 23:22:31: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:22:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:23:35: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:23:35: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:23:42: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:24:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923190/SRX4923190.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:24:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923190/SRX4923190.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:24:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923190/SRX4923190.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:24:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923190/SRX4923190.20_summits.bed INFO @ Mon, 12 Aug 2019 23:24:06: Done! INFO @ Mon, 12 Aug 2019 23:24:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923190/SRX4923190.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:24:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923190/SRX4923190.10_summits.bed INFO @ Mon, 12 Aug 2019 23:24:06: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (8865 records, 4 fields): 13 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (11309 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:24:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923190/SRX4923190.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:24:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923190/SRX4923190.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:24:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923190/SRX4923190.05_summits.bed INFO @ Mon, 12 Aug 2019 23:24:14: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (13480 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。