Job ID = 2590455 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,170,440 reads read : 34,340,880 reads written : 17,170,440 reads 0-length : 17,170,440 spots read : 17,230,833 reads read : 34,461,666 reads written : 17,230,833 reads 0-length : 17,230,833 spots read : 17,087,076 reads read : 34,174,152 reads written : 17,087,076 reads 0-length : 17,087,076 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: 00:14:38 51488349 reads; of these: 51488349 (100.00%) were unpaired; of these: 1568689 (3.05%) aligned 0 times 41562635 (80.72%) aligned exactly 1 time 8357025 (16.23%) aligned >1 times 96.95% overall alignment rate Time searching: 00:14:38 Overall time: 00:14:38 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 24 files... [bam_rmdupse_core] 10813025 / 49919660 = 0.2166 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 22:24:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981687/SRX3981687.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981687/SRX3981687.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981687/SRX3981687.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981687/SRX3981687.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 22:24:37: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:24:37: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:24:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981687/SRX3981687.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981687/SRX3981687.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981687/SRX3981687.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981687/SRX3981687.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 22:24:38: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:24:38: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:24:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981687/SRX3981687.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981687/SRX3981687.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981687/SRX3981687.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981687/SRX3981687.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 22:24:39: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:24:39: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:24:45: 1000000 INFO @ Mon, 12 Aug 2019 22:24:46: 1000000 INFO @ Mon, 12 Aug 2019 22:24:47: 1000000 INFO @ Mon, 12 Aug 2019 22:24:52: 2000000 INFO @ Mon, 12 Aug 2019 22:24:53: 2000000 INFO @ Mon, 12 Aug 2019 22:24:54: 2000000 INFO @ Mon, 12 Aug 2019 22:25:00: 3000000 INFO @ Mon, 12 Aug 2019 22:25:01: 3000000 INFO @ Mon, 12 Aug 2019 22:25:02: 3000000 INFO @ Mon, 12 Aug 2019 22:25:08: 4000000 INFO @ Mon, 12 Aug 2019 22:25:08: 4000000 INFO @ Mon, 12 Aug 2019 22:25:09: 4000000 INFO @ Mon, 12 Aug 2019 22:25:15: 5000000 INFO @ Mon, 12 Aug 2019 22:25:16: 5000000 INFO @ Mon, 12 Aug 2019 22:25:16: 5000000 INFO @ Mon, 12 Aug 2019 22:25:23: 6000000 INFO @ Mon, 12 Aug 2019 22:25:23: 6000000 INFO @ Mon, 12 Aug 2019 22:25:24: 6000000 INFO @ Mon, 12 Aug 2019 22:25:30: 7000000 INFO @ Mon, 12 Aug 2019 22:25:30: 7000000 INFO @ Mon, 12 Aug 2019 22:25:31: 7000000 INFO @ Mon, 12 Aug 2019 22:25:38: 8000000 INFO @ Mon, 12 Aug 2019 22:25:38: 8000000 INFO @ Mon, 12 Aug 2019 22:25:39: 8000000 INFO @ Mon, 12 Aug 2019 22:25:45: 9000000 INFO @ Mon, 12 Aug 2019 22:25:45: 9000000 INFO @ Mon, 12 Aug 2019 22:25:47: 9000000 INFO @ Mon, 12 Aug 2019 22:25:52: 10000000 INFO @ Mon, 12 Aug 2019 22:25:53: 10000000 INFO @ Mon, 12 Aug 2019 22:25:56: 10000000 INFO @ Mon, 12 Aug 2019 22:26:00: 11000000 INFO @ Mon, 12 Aug 2019 22:26:00: 11000000 INFO @ Mon, 12 Aug 2019 22:26:04: 11000000 INFO @ Mon, 12 Aug 2019 22:26:07: 12000000 INFO @ Mon, 12 Aug 2019 22:26:08: 12000000 INFO @ Mon, 12 Aug 2019 22:26:13: 12000000 INFO @ Mon, 12 Aug 2019 22:26:15: 13000000 INFO @ Mon, 12 Aug 2019 22:26:15: 13000000 INFO @ Mon, 12 Aug 2019 22:26:21: 13000000 INFO @ Mon, 12 Aug 2019 22:26:22: 14000000 INFO @ Mon, 12 Aug 2019 22:26:23: 14000000 INFO @ Mon, 12 Aug 2019 22:26:30: 15000000 INFO @ Mon, 12 Aug 2019 22:26:30: 14000000 INFO @ Mon, 12 Aug 2019 22:26:30: 15000000 INFO @ Mon, 12 Aug 2019 22:26:37: 16000000 INFO @ Mon, 12 Aug 2019 22:26:37: 16000000 INFO @ Mon, 12 Aug 2019 22:26:38: 15000000 INFO @ Mon, 12 Aug 2019 22:26:44: 17000000 INFO @ Mon, 12 Aug 2019 22:26:45: 17000000 INFO @ Mon, 12 Aug 2019 22:26:47: 16000000 INFO @ Mon, 12 Aug 2019 22:26:52: 18000000 INFO @ Mon, 12 Aug 2019 22:26:52: 18000000 INFO @ Mon, 12 Aug 2019 22:26:55: 17000000 INFO @ Mon, 12 Aug 2019 22:27:00: 19000000 INFO @ Mon, 12 Aug 2019 22:27:01: 19000000 INFO @ Mon, 12 Aug 2019 22:27:04: 18000000 INFO @ Mon, 12 Aug 2019 22:27:08: 20000000 INFO @ Mon, 12 Aug 2019 22:27:08: 20000000 INFO @ Mon, 12 Aug 2019 22:27:12: 19000000 INFO @ Mon, 12 Aug 2019 22:27:15: 21000000 INFO @ Mon, 12 Aug 2019 22:27:16: 21000000 INFO @ Mon, 12 Aug 2019 22:27:20: 20000000 INFO @ Mon, 12 Aug 2019 22:27:22: 22000000 INFO @ Mon, 12 Aug 2019 22:27:23: 22000000 INFO @ Mon, 12 Aug 2019 22:27:29: 21000000 INFO @ Mon, 12 Aug 2019 22:27:30: 23000000 INFO @ Mon, 12 Aug 2019 22:27:30: 23000000 INFO @ Mon, 12 Aug 2019 22:27:36: 22000000 INFO @ Mon, 12 Aug 2019 22:27:37: 24000000 INFO @ Mon, 12 Aug 2019 22:27:38: 24000000 INFO @ Mon, 12 Aug 2019 22:27:44: 25000000 INFO @ Mon, 12 Aug 2019 22:27:44: 23000000 INFO @ Mon, 12 Aug 2019 22:27:45: 25000000 INFO @ Mon, 12 Aug 2019 22:27:51: 26000000 INFO @ Mon, 12 Aug 2019 22:27:52: 24000000 INFO @ Mon, 12 Aug 2019 22:27:52: 26000000 INFO @ Mon, 12 Aug 2019 22:27:58: 27000000 INFO @ Mon, 12 Aug 2019 22:28:00: 27000000 INFO @ Mon, 12 Aug 2019 22:28:01: 25000000 INFO @ Mon, 12 Aug 2019 22:28:06: 28000000 INFO @ Mon, 12 Aug 2019 22:28:08: 28000000 INFO @ Mon, 12 Aug 2019 22:28:09: 26000000 INFO @ Mon, 12 Aug 2019 22:28:13: 29000000 INFO @ Mon, 12 Aug 2019 22:28:15: 29000000 INFO @ Mon, 12 Aug 2019 22:28:18: 27000000 INFO @ Mon, 12 Aug 2019 22:28:20: 30000000 INFO @ Mon, 12 Aug 2019 22:28:22: 30000000 INFO @ Mon, 12 Aug 2019 22:28:27: 28000000 INFO @ Mon, 12 Aug 2019 22:28:28: 31000000 INFO @ Mon, 12 Aug 2019 22:28:30: 31000000 INFO @ Mon, 12 Aug 2019 22:28:35: 29000000 INFO @ Mon, 12 Aug 2019 22:28:35: 32000000 INFO @ Mon, 12 Aug 2019 22:28:37: 32000000 INFO @ Mon, 12 Aug 2019 22:28:42: 33000000 INFO @ Mon, 12 Aug 2019 22:28:43: 30000000 INFO @ Mon, 12 Aug 2019 22:28:45: 33000000 INFO @ Mon, 12 Aug 2019 22:28:50: 34000000 INFO @ Mon, 12 Aug 2019 22:28:52: 31000000 INFO @ Mon, 12 Aug 2019 22:28:52: 34000000 INFO @ Mon, 12 Aug 2019 22:28:57: 35000000 INFO @ Mon, 12 Aug 2019 22:29:00: 35000000 INFO @ Mon, 12 Aug 2019 22:29:00: 32000000 INFO @ Mon, 12 Aug 2019 22:29:05: 36000000 INFO @ Mon, 12 Aug 2019 22:29:07: 36000000 INFO @ Mon, 12 Aug 2019 22:29:09: 33000000 INFO @ Mon, 12 Aug 2019 22:29:12: 37000000 INFO @ Mon, 12 Aug 2019 22:29:14: 37000000 INFO @ Mon, 12 Aug 2019 22:29:18: 34000000 INFO @ Mon, 12 Aug 2019 22:29:19: 38000000 INFO @ Mon, 12 Aug 2019 22:29:22: 38000000 INFO @ Mon, 12 Aug 2019 22:29:26: 39000000 INFO @ Mon, 12 Aug 2019 22:29:27: 35000000 INFO @ Mon, 12 Aug 2019 22:29:28: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:29:28: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:29:28: #1 total tags in treatment: 39106635 INFO @ Mon, 12 Aug 2019 22:29:28: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:29:28: #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 22:29:28: #1 tags after filtering in treatment: 39106635 INFO @ Mon, 12 Aug 2019 22:29:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:29:28: #1 finished! INFO @ Mon, 12 Aug 2019 22:29:28: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:29:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:29:29: 39000000 INFO @ Mon, 12 Aug 2019 22:29:30: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:29:30: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:29:30: #1 total tags in treatment: 39106635 INFO @ Mon, 12 Aug 2019 22:29:30: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:29:30: #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 22:29:31: #1 tags after filtering in treatment: 39106635 INFO @ Mon, 12 Aug 2019 22:29:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:29:31: #1 finished! INFO @ Mon, 12 Aug 2019 22:29:31: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:29:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:29:32: #2 number of paired peaks: 192 WARNING @ Mon, 12 Aug 2019 22:29:32: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Mon, 12 Aug 2019 22:29:32: start model_add_line... INFO @ Mon, 12 Aug 2019 22:29:32: start X-correlation... INFO @ Mon, 12 Aug 2019 22:29:32: end of X-cor INFO @ Mon, 12 Aug 2019 22:29:32: #2 finished! INFO @ Mon, 12 Aug 2019 22:29:32: #2 predicted fragment length is 125 bps INFO @ Mon, 12 Aug 2019 22:29:32: #2 alternative fragment length(s) may be 3,125 bps INFO @ Mon, 12 Aug 2019 22:29:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981687/SRX3981687.10_model.r INFO @ Mon, 12 Aug 2019 22:29:32: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:29:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:29:34: #2 number of paired peaks: 192 WARNING @ Mon, 12 Aug 2019 22:29:34: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Mon, 12 Aug 2019 22:29:34: start model_add_line... INFO @ Mon, 12 Aug 2019 22:29:35: start X-correlation... INFO @ Mon, 12 Aug 2019 22:29:35: end of X-cor INFO @ Mon, 12 Aug 2019 22:29:35: #2 finished! INFO @ Mon, 12 Aug 2019 22:29:35: #2 predicted fragment length is 125 bps INFO @ Mon, 12 Aug 2019 22:29:35: #2 alternative fragment length(s) may be 3,125 bps INFO @ Mon, 12 Aug 2019 22:29:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981687/SRX3981687.05_model.r INFO @ Mon, 12 Aug 2019 22:29:35: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:29:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:29:35: 36000000 INFO @ Mon, 12 Aug 2019 22:29:43: 37000000 INFO @ Mon, 12 Aug 2019 22:29:52: 38000000 INFO @ Mon, 12 Aug 2019 22:30:00: 39000000 INFO @ Mon, 12 Aug 2019 22:30:02: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:30:02: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:30:02: #1 total tags in treatment: 39106635 INFO @ Mon, 12 Aug 2019 22:30:02: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:30:02: #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 22:30:02: #1 tags after filtering in treatment: 39106635 INFO @ Mon, 12 Aug 2019 22:30:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:30:02: #1 finished! INFO @ Mon, 12 Aug 2019 22:30:02: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:30:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:30:06: #2 number of paired peaks: 192 WARNING @ Mon, 12 Aug 2019 22:30:06: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Mon, 12 Aug 2019 22:30:06: start model_add_line... INFO @ Mon, 12 Aug 2019 22:30:06: start X-correlation... INFO @ Mon, 12 Aug 2019 22:30:06: end of X-cor INFO @ Mon, 12 Aug 2019 22:30:06: #2 finished! INFO @ Mon, 12 Aug 2019 22:30:06: #2 predicted fragment length is 125 bps INFO @ Mon, 12 Aug 2019 22:30:06: #2 alternative fragment length(s) may be 3,125 bps INFO @ Mon, 12 Aug 2019 22:30:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981687/SRX3981687.20_model.r INFO @ Mon, 12 Aug 2019 22:30:06: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:30:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:31:02: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:31:10: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:31:37: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:31:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981687/SRX3981687.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:31:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981687/SRX3981687.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:31:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981687/SRX3981687.10_summits.bed INFO @ Mon, 12 Aug 2019 22:31:41: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (6399 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:31:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981687/SRX3981687.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:31:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981687/SRX3981687.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:31:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981687/SRX3981687.05_summits.bed INFO @ Mon, 12 Aug 2019 22:31:50: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9696 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:32:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981687/SRX3981687.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:32:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981687/SRX3981687.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:32:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981687/SRX3981687.20_summits.bed INFO @ Mon, 12 Aug 2019 22:32:15: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2707 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。