Job ID = 2590674 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 40,574,216 reads read : 81,148,432 reads written : 40,574,216 reads 0-length : 40,574,216 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: 00:16:25 40574216 reads; of these: 40574216 (100.00%) were unpaired; of these: 5585224 (13.77%) aligned 0 times 25479816 (62.80%) aligned exactly 1 time 9509176 (23.44%) aligned >1 times 86.23% overall alignment rate Time searching: 00:16:25 Overall time: 00:16:25 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 16 files... [bam_rmdupse_core] 19067618 / 34988992 = 0.5450 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 23:35:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011021/SRX5011021.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011021/SRX5011021.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011021/SRX5011021.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011021/SRX5011021.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 23:35:18: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:35:18: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:35:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011021/SRX5011021.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011021/SRX5011021.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011021/SRX5011021.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011021/SRX5011021.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 23:35:19: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:35:19: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:35:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011021/SRX5011021.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011021/SRX5011021.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011021/SRX5011021.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011021/SRX5011021.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 23:35:20: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:35:20: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:35:26: 1000000 INFO @ Mon, 12 Aug 2019 23:35:27: 1000000 INFO @ Mon, 12 Aug 2019 23:35:28: 1000000 INFO @ Mon, 12 Aug 2019 23:35:32: 2000000 INFO @ Mon, 12 Aug 2019 23:35:36: 2000000 INFO @ Mon, 12 Aug 2019 23:35:36: 2000000 INFO @ Mon, 12 Aug 2019 23:35:38: 3000000 INFO @ Mon, 12 Aug 2019 23:35:44: 3000000 INFO @ Mon, 12 Aug 2019 23:35:44: 3000000 INFO @ Mon, 12 Aug 2019 23:35:45: 4000000 INFO @ Mon, 12 Aug 2019 23:35:51: 5000000 INFO @ Mon, 12 Aug 2019 23:35:52: 4000000 INFO @ Mon, 12 Aug 2019 23:35:52: 4000000 INFO @ Mon, 12 Aug 2019 23:35:57: 6000000 INFO @ Mon, 12 Aug 2019 23:36:00: 5000000 INFO @ Mon, 12 Aug 2019 23:36:00: 5000000 INFO @ Mon, 12 Aug 2019 23:36:04: 7000000 INFO @ Mon, 12 Aug 2019 23:36:08: 6000000 INFO @ Mon, 12 Aug 2019 23:36:08: 6000000 INFO @ Mon, 12 Aug 2019 23:36:10: 8000000 INFO @ Mon, 12 Aug 2019 23:36:16: 7000000 INFO @ Mon, 12 Aug 2019 23:36:16: 9000000 INFO @ Mon, 12 Aug 2019 23:36:17: 7000000 INFO @ Mon, 12 Aug 2019 23:36:23: 10000000 INFO @ Mon, 12 Aug 2019 23:36:23: 8000000 INFO @ Mon, 12 Aug 2019 23:36:25: 8000000 INFO @ Mon, 12 Aug 2019 23:36:29: 11000000 INFO @ Mon, 12 Aug 2019 23:36:31: 9000000 INFO @ Mon, 12 Aug 2019 23:36:33: 9000000 INFO @ Mon, 12 Aug 2019 23:36:35: 12000000 INFO @ Mon, 12 Aug 2019 23:36:39: 10000000 INFO @ Mon, 12 Aug 2019 23:36:41: 10000000 INFO @ Mon, 12 Aug 2019 23:36:42: 13000000 INFO @ Mon, 12 Aug 2019 23:36:47: 11000000 INFO @ Mon, 12 Aug 2019 23:36:48: 14000000 INFO @ Mon, 12 Aug 2019 23:36:49: 11000000 INFO @ Mon, 12 Aug 2019 23:36:54: 15000000 INFO @ Mon, 12 Aug 2019 23:36:55: 12000000 INFO @ Mon, 12 Aug 2019 23:36:57: 12000000 INFO @ Mon, 12 Aug 2019 23:37:00: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:37:00: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:37:00: #1 total tags in treatment: 15921374 INFO @ Mon, 12 Aug 2019 23:37:00: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:37:00: #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 23:37:01: #1 tags after filtering in treatment: 15921374 INFO @ Mon, 12 Aug 2019 23:37:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:37:01: #1 finished! INFO @ Mon, 12 Aug 2019 23:37:01: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:37:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:37:02: #2 number of paired peaks: 1247 INFO @ Mon, 12 Aug 2019 23:37:02: start model_add_line... INFO @ Mon, 12 Aug 2019 23:37:02: start X-correlation... INFO @ Mon, 12 Aug 2019 23:37:02: end of X-cor INFO @ Mon, 12 Aug 2019 23:37:02: #2 finished! INFO @ Mon, 12 Aug 2019 23:37:02: #2 predicted fragment length is 140 bps INFO @ Mon, 12 Aug 2019 23:37:02: #2 alternative fragment length(s) may be 140 bps INFO @ Mon, 12 Aug 2019 23:37:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011021/SRX5011021.05_model.r INFO @ Mon, 12 Aug 2019 23:37:02: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:37:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:37:03: 13000000 INFO @ Mon, 12 Aug 2019 23:37:04: 13000000 INFO @ Mon, 12 Aug 2019 23:37:10: 14000000 INFO @ Mon, 12 Aug 2019 23:37:12: 14000000 INFO @ Mon, 12 Aug 2019 23:37:18: 15000000 INFO @ Mon, 12 Aug 2019 23:37:20: 15000000 INFO @ Mon, 12 Aug 2019 23:37:25: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:37:25: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:37:25: #1 total tags in treatment: 15921374 INFO @ Mon, 12 Aug 2019 23:37:25: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:37:25: #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 23:37:26: #1 tags after filtering in treatment: 15921374 INFO @ Mon, 12 Aug 2019 23:37:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:37:26: #1 finished! INFO @ Mon, 12 Aug 2019 23:37:26: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:37:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:37:27: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:37:27: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:37:27: #1 total tags in treatment: 15921374 INFO @ Mon, 12 Aug 2019 23:37:27: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:37:27: #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 23:37:27: #2 number of paired peaks: 1247 INFO @ Mon, 12 Aug 2019 23:37:27: start model_add_line... INFO @ Mon, 12 Aug 2019 23:37:27: start X-correlation... INFO @ Mon, 12 Aug 2019 23:37:27: end of X-cor INFO @ Mon, 12 Aug 2019 23:37:27: #2 finished! INFO @ Mon, 12 Aug 2019 23:37:27: #2 predicted fragment length is 140 bps INFO @ Mon, 12 Aug 2019 23:37:27: #2 alternative fragment length(s) may be 140 bps INFO @ Mon, 12 Aug 2019 23:37:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011021/SRX5011021.20_model.r INFO @ Mon, 12 Aug 2019 23:37:28: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:37:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:37:28: #1 tags after filtering in treatment: 15921374 INFO @ Mon, 12 Aug 2019 23:37:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:37:28: #1 finished! INFO @ Mon, 12 Aug 2019 23:37:28: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:37:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:37:29: #2 number of paired peaks: 1247 INFO @ Mon, 12 Aug 2019 23:37:29: start model_add_line... INFO @ Mon, 12 Aug 2019 23:37:29: start X-correlation... INFO @ Mon, 12 Aug 2019 23:37:29: end of X-cor INFO @ Mon, 12 Aug 2019 23:37:29: #2 finished! INFO @ Mon, 12 Aug 2019 23:37:29: #2 predicted fragment length is 140 bps INFO @ Mon, 12 Aug 2019 23:37:29: #2 alternative fragment length(s) may be 140 bps INFO @ Mon, 12 Aug 2019 23:37:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011021/SRX5011021.10_model.r INFO @ Mon, 12 Aug 2019 23:37:29: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:37:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:37:48: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:38:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011021/SRX5011021.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:38:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011021/SRX5011021.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:38:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011021/SRX5011021.05_summits.bed INFO @ Mon, 12 Aug 2019 23:38:09: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (9302 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:38:13: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:38:16: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:38:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011021/SRX5011021.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:38:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011021/SRX5011021.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:38:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011021/SRX5011021.20_summits.bed INFO @ Mon, 12 Aug 2019 23:38:34: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2434 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:38:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011021/SRX5011021.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:38:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011021/SRX5011021.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:38:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011021/SRX5011021.10_summits.bed INFO @ Mon, 12 Aug 2019 23:38:40: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5386 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。