Job ID = 2590504 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,396,581 reads read : 26,793,162 reads written : 13,396,581 reads 0-length : 13,396,581 spots read : 13,600,143 reads read : 27,200,286 reads written : 13,600,143 reads 0-length : 13,600,143 spots read : 13,616,459 reads read : 27,232,918 reads written : 13,616,459 reads 0-length : 13,616,459 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:13:44 40613183 reads; of these: 40613183 (100.00%) were unpaired; of these: 1059703 (2.61%) aligned 0 times 31285177 (77.03%) aligned exactly 1 time 8268303 (20.36%) aligned >1 times 97.39% overall alignment rate Time searching: 00:13:45 Overall time: 00:13:45 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 20 files... [bam_rmdupse_core] 13264653 / 39553480 = 0.3354 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 22:41:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981731/SRX3981731.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981731/SRX3981731.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981731/SRX3981731.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981731/SRX3981731.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 22:41:22: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:41:22: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:41:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981731/SRX3981731.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981731/SRX3981731.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981731/SRX3981731.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981731/SRX3981731.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 22:41:23: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:41:23: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:41:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981731/SRX3981731.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981731/SRX3981731.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981731/SRX3981731.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981731/SRX3981731.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 22:41:24: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:41:24: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:41:31: 1000000 INFO @ Mon, 12 Aug 2019 22:41:32: 1000000 INFO @ Mon, 12 Aug 2019 22:41:33: 1000000 INFO @ Mon, 12 Aug 2019 22:41:39: 2000000 INFO @ Mon, 12 Aug 2019 22:41:42: 2000000 INFO @ Mon, 12 Aug 2019 22:41:43: 2000000 INFO @ Mon, 12 Aug 2019 22:41:49: 3000000 INFO @ Mon, 12 Aug 2019 22:41:53: 3000000 INFO @ Mon, 12 Aug 2019 22:41:53: 3000000 INFO @ Mon, 12 Aug 2019 22:41:58: 4000000 INFO @ Mon, 12 Aug 2019 22:42:03: 4000000 INFO @ Mon, 12 Aug 2019 22:42:03: 4000000 INFO @ Mon, 12 Aug 2019 22:42:07: 5000000 INFO @ Mon, 12 Aug 2019 22:42:13: 5000000 INFO @ Mon, 12 Aug 2019 22:42:13: 5000000 INFO @ Mon, 12 Aug 2019 22:42:15: 6000000 INFO @ Mon, 12 Aug 2019 22:42:22: 6000000 INFO @ Mon, 12 Aug 2019 22:42:23: 7000000 INFO @ Mon, 12 Aug 2019 22:42:23: 6000000 INFO @ Mon, 12 Aug 2019 22:42:31: 8000000 INFO @ Mon, 12 Aug 2019 22:42:32: 7000000 INFO @ Mon, 12 Aug 2019 22:42:33: 7000000 INFO @ Mon, 12 Aug 2019 22:42:38: 9000000 INFO @ Mon, 12 Aug 2019 22:42:41: 8000000 INFO @ Mon, 12 Aug 2019 22:42:43: 8000000 INFO @ Mon, 12 Aug 2019 22:42:46: 10000000 INFO @ Mon, 12 Aug 2019 22:42:50: 9000000 INFO @ Mon, 12 Aug 2019 22:42:53: 9000000 INFO @ Mon, 12 Aug 2019 22:42:54: 11000000 INFO @ Mon, 12 Aug 2019 22:43:00: 10000000 INFO @ Mon, 12 Aug 2019 22:43:02: 12000000 INFO @ Mon, 12 Aug 2019 22:43:02: 10000000 INFO @ Mon, 12 Aug 2019 22:43:09: 11000000 INFO @ Mon, 12 Aug 2019 22:43:09: 13000000 INFO @ Mon, 12 Aug 2019 22:43:12: 11000000 INFO @ Mon, 12 Aug 2019 22:43:17: 14000000 INFO @ Mon, 12 Aug 2019 22:43:18: 12000000 INFO @ Mon, 12 Aug 2019 22:43:22: 12000000 INFO @ Mon, 12 Aug 2019 22:43:25: 15000000 INFO @ Mon, 12 Aug 2019 22:43:27: 13000000 INFO @ Mon, 12 Aug 2019 22:43:31: 13000000 INFO @ Mon, 12 Aug 2019 22:43:32: 16000000 INFO @ Mon, 12 Aug 2019 22:43:37: 14000000 INFO @ Mon, 12 Aug 2019 22:43:40: 17000000 INFO @ Mon, 12 Aug 2019 22:43:41: 14000000 INFO @ Mon, 12 Aug 2019 22:43:46: 15000000 INFO @ Mon, 12 Aug 2019 22:43:48: 18000000 INFO @ Mon, 12 Aug 2019 22:43:51: 15000000 INFO @ Mon, 12 Aug 2019 22:43:55: 19000000 INFO @ Mon, 12 Aug 2019 22:43:56: 16000000 INFO @ Mon, 12 Aug 2019 22:44:01: 16000000 INFO @ Mon, 12 Aug 2019 22:44:03: 20000000 INFO @ Mon, 12 Aug 2019 22:44:05: 17000000 INFO @ Mon, 12 Aug 2019 22:44:10: 21000000 INFO @ Mon, 12 Aug 2019 22:44:11: 17000000 INFO @ Mon, 12 Aug 2019 22:44:14: 18000000 INFO @ Mon, 12 Aug 2019 22:44:19: 22000000 INFO @ Mon, 12 Aug 2019 22:44:21: 18000000 INFO @ Mon, 12 Aug 2019 22:44:23: 19000000 INFO @ Mon, 12 Aug 2019 22:44:26: 23000000 INFO @ Mon, 12 Aug 2019 22:44:30: 19000000 INFO @ Mon, 12 Aug 2019 22:44:33: 20000000 INFO @ Mon, 12 Aug 2019 22:44:34: 24000000 INFO @ Mon, 12 Aug 2019 22:44:40: 20000000 INFO @ Mon, 12 Aug 2019 22:44:41: 25000000 INFO @ Mon, 12 Aug 2019 22:44:42: 21000000 INFO @ Mon, 12 Aug 2019 22:44:49: 26000000 INFO @ Mon, 12 Aug 2019 22:44:50: 21000000 INFO @ Mon, 12 Aug 2019 22:44:51: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:44:51: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:44:51: #1 total tags in treatment: 26288827 INFO @ Mon, 12 Aug 2019 22:44:51: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:44:51: #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 22:44:51: 22000000 INFO @ Mon, 12 Aug 2019 22:44:51: #1 tags after filtering in treatment: 26288827 INFO @ Mon, 12 Aug 2019 22:44:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:44:51: #1 finished! INFO @ Mon, 12 Aug 2019 22:44:51: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:44:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:44:54: #2 number of paired peaks: 3383 INFO @ Mon, 12 Aug 2019 22:44:54: start model_add_line... INFO @ Mon, 12 Aug 2019 22:44:55: start X-correlation... INFO @ Mon, 12 Aug 2019 22:44:55: end of X-cor INFO @ Mon, 12 Aug 2019 22:44:55: #2 finished! INFO @ Mon, 12 Aug 2019 22:44:55: #2 predicted fragment length is 215 bps INFO @ Mon, 12 Aug 2019 22:44:55: #2 alternative fragment length(s) may be 215 bps INFO @ Mon, 12 Aug 2019 22:44:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981731/SRX3981731.10_model.r INFO @ Mon, 12 Aug 2019 22:44:55: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:44:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:44:59: 22000000 INFO @ Mon, 12 Aug 2019 22:45:01: 23000000 INFO @ Mon, 12 Aug 2019 22:45:09: 23000000 INFO @ Mon, 12 Aug 2019 22:45:10: 24000000 INFO @ Mon, 12 Aug 2019 22:45:19: 24000000 INFO @ Mon, 12 Aug 2019 22:45:19: 25000000 INFO @ Mon, 12 Aug 2019 22:45:28: 26000000 INFO @ Mon, 12 Aug 2019 22:45:28: 25000000 INFO @ Mon, 12 Aug 2019 22:45:31: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:45:31: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:45:31: #1 total tags in treatment: 26288827 INFO @ Mon, 12 Aug 2019 22:45:31: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:45:31: #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 22:45:31: #1 tags after filtering in treatment: 26288827 INFO @ Mon, 12 Aug 2019 22:45:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:45:31: #1 finished! INFO @ Mon, 12 Aug 2019 22:45:31: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:45:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:45:34: #2 number of paired peaks: 3383 INFO @ Mon, 12 Aug 2019 22:45:34: start model_add_line... INFO @ Mon, 12 Aug 2019 22:45:34: start X-correlation... INFO @ Mon, 12 Aug 2019 22:45:34: end of X-cor INFO @ Mon, 12 Aug 2019 22:45:34: #2 finished! INFO @ Mon, 12 Aug 2019 22:45:34: #2 predicted fragment length is 215 bps INFO @ Mon, 12 Aug 2019 22:45:34: #2 alternative fragment length(s) may be 215 bps INFO @ Mon, 12 Aug 2019 22:45:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981731/SRX3981731.20_model.r INFO @ Mon, 12 Aug 2019 22:45:34: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:45:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:45:37: 26000000 INFO @ Mon, 12 Aug 2019 22:45:40: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:45:40: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:45:40: #1 total tags in treatment: 26288827 INFO @ Mon, 12 Aug 2019 22:45:40: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:45:40: #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 22:45:41: #1 tags after filtering in treatment: 26288827 INFO @ Mon, 12 Aug 2019 22:45:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:45:41: #1 finished! INFO @ Mon, 12 Aug 2019 22:45:41: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:45:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:45:43: #2 number of paired peaks: 3383 INFO @ Mon, 12 Aug 2019 22:45:43: start model_add_line... INFO @ Mon, 12 Aug 2019 22:45:44: start X-correlation... INFO @ Mon, 12 Aug 2019 22:45:44: end of X-cor INFO @ Mon, 12 Aug 2019 22:45:44: #2 finished! INFO @ Mon, 12 Aug 2019 22:45:44: #2 predicted fragment length is 215 bps INFO @ Mon, 12 Aug 2019 22:45:44: #2 alternative fragment length(s) may be 215 bps INFO @ Mon, 12 Aug 2019 22:45:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981731/SRX3981731.05_model.r INFO @ Mon, 12 Aug 2019 22:45:44: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:45:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:46:24: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:46:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981731/SRX3981731.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:46:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981731/SRX3981731.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:46:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981731/SRX3981731.10_summits.bed INFO @ Mon, 12 Aug 2019 22:46:54: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (7739 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:47:03: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:47:12: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:47:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981731/SRX3981731.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:47:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981731/SRX3981731.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:47:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981731/SRX3981731.20_summits.bed INFO @ Mon, 12 Aug 2019 22:47:33: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5209 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:47:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981731/SRX3981731.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:47:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981731/SRX3981731.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:47:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981731/SRX3981731.05_summits.bed INFO @ Mon, 12 Aug 2019 22:47:43: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (10197 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。