Job ID = 2590456 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,743,042 reads read : 27,486,084 reads written : 13,743,042 reads 0-length : 13,743,042 spots read : 13,751,561 reads read : 27,503,122 reads written : 13,751,561 reads 0-length : 13,751,561 spots read : 13,667,464 reads read : 27,334,928 reads written : 13,667,464 reads 0-length : 13,667,464 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: 00:00:01 Multiseed full-index search: 00:12:43 41162067 reads; of these: 41162067 (100.00%) were unpaired; of these: 1473326 (3.58%) aligned 0 times 33154993 (80.55%) aligned exactly 1 time 6533748 (15.87%) aligned >1 times 96.42% overall alignment rate Time searching: 00:12:44 Overall time: 00:12:44 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] 7473843 / 39688741 = 0.1883 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 22:18:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981688/SRX3981688.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981688/SRX3981688.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981688/SRX3981688.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981688/SRX3981688.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 22:18:51: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:18:51: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:18:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981688/SRX3981688.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981688/SRX3981688.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981688/SRX3981688.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981688/SRX3981688.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 22:18:52: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:18:52: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:18:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981688/SRX3981688.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981688/SRX3981688.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981688/SRX3981688.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981688/SRX3981688.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 22:18:53: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:18:53: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:18:59: 1000000 INFO @ Mon, 12 Aug 2019 22:19:00: 1000000 INFO @ Mon, 12 Aug 2019 22:19:01: 1000000 INFO @ Mon, 12 Aug 2019 22:19:06: 2000000 INFO @ Mon, 12 Aug 2019 22:19:08: 2000000 INFO @ Mon, 12 Aug 2019 22:19:09: 2000000 INFO @ Mon, 12 Aug 2019 22:19:14: 3000000 INFO @ Mon, 12 Aug 2019 22:19:16: 3000000 INFO @ Mon, 12 Aug 2019 22:19:17: 3000000 INFO @ Mon, 12 Aug 2019 22:19:21: 4000000 INFO @ Mon, 12 Aug 2019 22:19:24: 4000000 INFO @ Mon, 12 Aug 2019 22:19:25: 4000000 INFO @ Mon, 12 Aug 2019 22:19:29: 5000000 INFO @ Mon, 12 Aug 2019 22:19:32: 5000000 INFO @ Mon, 12 Aug 2019 22:19:33: 5000000 INFO @ Mon, 12 Aug 2019 22:19:37: 6000000 INFO @ Mon, 12 Aug 2019 22:19:40: 6000000 INFO @ Mon, 12 Aug 2019 22:19:40: 6000000 INFO @ Mon, 12 Aug 2019 22:19:45: 7000000 INFO @ Mon, 12 Aug 2019 22:19:47: 7000000 INFO @ Mon, 12 Aug 2019 22:19:48: 7000000 INFO @ Mon, 12 Aug 2019 22:19:53: 8000000 INFO @ Mon, 12 Aug 2019 22:19:55: 8000000 INFO @ Mon, 12 Aug 2019 22:19:56: 8000000 INFO @ Mon, 12 Aug 2019 22:20:02: 9000000 INFO @ Mon, 12 Aug 2019 22:20:03: 9000000 INFO @ Mon, 12 Aug 2019 22:20:03: 9000000 INFO @ Mon, 12 Aug 2019 22:20:11: 10000000 INFO @ Mon, 12 Aug 2019 22:20:11: 10000000 INFO @ Mon, 12 Aug 2019 22:20:11: 10000000 INFO @ Mon, 12 Aug 2019 22:20:19: 11000000 INFO @ Mon, 12 Aug 2019 22:20:19: 11000000 INFO @ Mon, 12 Aug 2019 22:20:19: 11000000 INFO @ Mon, 12 Aug 2019 22:20:26: 12000000 INFO @ Mon, 12 Aug 2019 22:20:27: 12000000 INFO @ Mon, 12 Aug 2019 22:20:28: 12000000 INFO @ Mon, 12 Aug 2019 22:20:34: 13000000 INFO @ Mon, 12 Aug 2019 22:20:34: 13000000 INFO @ Mon, 12 Aug 2019 22:20:37: 13000000 INFO @ Mon, 12 Aug 2019 22:20:42: 14000000 INFO @ Mon, 12 Aug 2019 22:20:42: 14000000 INFO @ Mon, 12 Aug 2019 22:20:45: 14000000 INFO @ Mon, 12 Aug 2019 22:20:50: 15000000 INFO @ Mon, 12 Aug 2019 22:20:50: 15000000 INFO @ Mon, 12 Aug 2019 22:20:54: 15000000 INFO @ Mon, 12 Aug 2019 22:20:58: 16000000 INFO @ Mon, 12 Aug 2019 22:20:58: 16000000 INFO @ Mon, 12 Aug 2019 22:21:03: 16000000 INFO @ Mon, 12 Aug 2019 22:21:05: 17000000 INFO @ Mon, 12 Aug 2019 22:21:05: 17000000 INFO @ Mon, 12 Aug 2019 22:21:11: 17000000 INFO @ Mon, 12 Aug 2019 22:21:13: 18000000 INFO @ Mon, 12 Aug 2019 22:21:13: 18000000 INFO @ Mon, 12 Aug 2019 22:21:20: 18000000 INFO @ Mon, 12 Aug 2019 22:21:21: 19000000 INFO @ Mon, 12 Aug 2019 22:21:21: 19000000 INFO @ Mon, 12 Aug 2019 22:21:29: 19000000 INFO @ Mon, 12 Aug 2019 22:21:30: 20000000 INFO @ Mon, 12 Aug 2019 22:21:30: 20000000 INFO @ Mon, 12 Aug 2019 22:21:38: 21000000 INFO @ Mon, 12 Aug 2019 22:21:38: 20000000 INFO @ Mon, 12 Aug 2019 22:21:38: 21000000 INFO @ Mon, 12 Aug 2019 22:21:46: 22000000 INFO @ Mon, 12 Aug 2019 22:21:46: 22000000 INFO @ Mon, 12 Aug 2019 22:21:46: 21000000 INFO @ Mon, 12 Aug 2019 22:21:54: 23000000 INFO @ Mon, 12 Aug 2019 22:21:55: 23000000 INFO @ Mon, 12 Aug 2019 22:21:55: 22000000 INFO @ Mon, 12 Aug 2019 22:22:03: 24000000 INFO @ Mon, 12 Aug 2019 22:22:03: 24000000 INFO @ Mon, 12 Aug 2019 22:22:04: 23000000 INFO @ Mon, 12 Aug 2019 22:22:11: 25000000 INFO @ Mon, 12 Aug 2019 22:22:13: 25000000 INFO @ Mon, 12 Aug 2019 22:22:14: 24000000 INFO @ Mon, 12 Aug 2019 22:22:19: 26000000 INFO @ Mon, 12 Aug 2019 22:22:23: 26000000 INFO @ Mon, 12 Aug 2019 22:22:24: 25000000 INFO @ Mon, 12 Aug 2019 22:22:27: 27000000 INFO @ Mon, 12 Aug 2019 22:22:34: 27000000 INFO @ Mon, 12 Aug 2019 22:22:34: 26000000 INFO @ Mon, 12 Aug 2019 22:22:36: 28000000 INFO @ Mon, 12 Aug 2019 22:22:44: 29000000 INFO @ Mon, 12 Aug 2019 22:22:44: 28000000 INFO @ Mon, 12 Aug 2019 22:22:44: 27000000 INFO @ Mon, 12 Aug 2019 22:22:52: 30000000 INFO @ Mon, 12 Aug 2019 22:22:54: 28000000 INFO @ Mon, 12 Aug 2019 22:22:54: 29000000 INFO @ Mon, 12 Aug 2019 22:23:00: 31000000 INFO @ Mon, 12 Aug 2019 22:23:04: 29000000 INFO @ Mon, 12 Aug 2019 22:23:04: 30000000 INFO @ Mon, 12 Aug 2019 22:23:08: 32000000 INFO @ Mon, 12 Aug 2019 22:23:10: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:23:10: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:23:10: #1 total tags in treatment: 32214898 INFO @ Mon, 12 Aug 2019 22:23:10: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:23:10: #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 22:23:11: #1 tags after filtering in treatment: 32214898 INFO @ Mon, 12 Aug 2019 22:23:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:23:11: #1 finished! INFO @ Mon, 12 Aug 2019 22:23:11: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:23:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:23:13: 30000000 INFO @ Mon, 12 Aug 2019 22:23:14: 31000000 INFO @ Mon, 12 Aug 2019 22:23:14: #2 number of paired peaks: 653 WARNING @ Mon, 12 Aug 2019 22:23:14: Fewer paired peaks (653) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 653 pairs to build model! INFO @ Mon, 12 Aug 2019 22:23:14: start model_add_line... INFO @ Mon, 12 Aug 2019 22:23:14: start X-correlation... INFO @ Mon, 12 Aug 2019 22:23:14: end of X-cor INFO @ Mon, 12 Aug 2019 22:23:14: #2 finished! INFO @ Mon, 12 Aug 2019 22:23:14: #2 predicted fragment length is 139 bps INFO @ Mon, 12 Aug 2019 22:23:14: #2 alternative fragment length(s) may be 4,127,139 bps INFO @ Mon, 12 Aug 2019 22:23:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981688/SRX3981688.10_model.r INFO @ Mon, 12 Aug 2019 22:23:14: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:23:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:23:22: 31000000 INFO @ Mon, 12 Aug 2019 22:23:23: 32000000 INFO @ Mon, 12 Aug 2019 22:23:25: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:23:25: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:23:25: #1 total tags in treatment: 32214898 INFO @ Mon, 12 Aug 2019 22:23:25: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:23:25: #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 22:23:26: #1 tags after filtering in treatment: 32214898 INFO @ Mon, 12 Aug 2019 22:23:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:23:26: #1 finished! INFO @ Mon, 12 Aug 2019 22:23:26: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:23:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:23:29: #2 number of paired peaks: 653 WARNING @ Mon, 12 Aug 2019 22:23:29: Fewer paired peaks (653) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 653 pairs to build model! INFO @ Mon, 12 Aug 2019 22:23:29: start model_add_line... INFO @ Mon, 12 Aug 2019 22:23:29: start X-correlation... INFO @ Mon, 12 Aug 2019 22:23:29: end of X-cor INFO @ Mon, 12 Aug 2019 22:23:29: #2 finished! INFO @ Mon, 12 Aug 2019 22:23:29: #2 predicted fragment length is 139 bps INFO @ Mon, 12 Aug 2019 22:23:29: #2 alternative fragment length(s) may be 4,127,139 bps INFO @ Mon, 12 Aug 2019 22:23:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981688/SRX3981688.20_model.r INFO @ Mon, 12 Aug 2019 22:23:29: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:23:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:23:31: 32000000 INFO @ Mon, 12 Aug 2019 22:23:33: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:23:33: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:23:33: #1 total tags in treatment: 32214898 INFO @ Mon, 12 Aug 2019 22:23:33: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:23:33: #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 22:23:34: #1 tags after filtering in treatment: 32214898 INFO @ Mon, 12 Aug 2019 22:23:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:23:34: #1 finished! INFO @ Mon, 12 Aug 2019 22:23:34: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:23:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:23:36: #2 number of paired peaks: 653 WARNING @ Mon, 12 Aug 2019 22:23:36: Fewer paired peaks (653) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 653 pairs to build model! INFO @ Mon, 12 Aug 2019 22:23:36: start model_add_line... INFO @ Mon, 12 Aug 2019 22:23:37: start X-correlation... INFO @ Mon, 12 Aug 2019 22:23:37: end of X-cor INFO @ Mon, 12 Aug 2019 22:23:37: #2 finished! INFO @ Mon, 12 Aug 2019 22:23:37: #2 predicted fragment length is 139 bps INFO @ Mon, 12 Aug 2019 22:23:37: #2 alternative fragment length(s) may be 4,127,139 bps INFO @ Mon, 12 Aug 2019 22:23:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981688/SRX3981688.05_model.r INFO @ Mon, 12 Aug 2019 22:23:37: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:23:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:24:36: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:24:50: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:24:58: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:25:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981688/SRX3981688.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:25:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981688/SRX3981688.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:25:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981688/SRX3981688.10_summits.bed INFO @ Mon, 12 Aug 2019 22:25:10: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (6291 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:25:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981688/SRX3981688.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:25:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981688/SRX3981688.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:25:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981688/SRX3981688.20_summits.bed INFO @ Mon, 12 Aug 2019 22:25:24: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2842 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:25:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981688/SRX3981688.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:25:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981688/SRX3981688.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:25:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981688/SRX3981688.05_summits.bed INFO @ Mon, 12 Aug 2019 22:25:33: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (9233 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。