Job ID = 4178533 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,595,355 reads read : 26,595,355 reads written : 26,595,355 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: 00:00:02 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:47 26595355 reads; of these: 26595355 (100.00%) were unpaired; of these: 3546916 (13.34%) aligned 0 times 17100129 (64.30%) aligned exactly 1 time 5948310 (22.37%) aligned >1 times 86.66% overall alignment rate Time searching: 00:07:50 Overall time: 00:07:55 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 12 files... [bam_rmdupse_core] 7097486 / 23048439 = 0.3079 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:06:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717049/SRX5717049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717049/SRX5717049.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717049/SRX5717049.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717049/SRX5717049.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 @ Thu, 05 Dec 2019 13:06:26: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:06:26: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:06:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717049/SRX5717049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717049/SRX5717049.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717049/SRX5717049.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717049/SRX5717049.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 @ Thu, 05 Dec 2019 13:06:28: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:06:28: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:06:30: 1000000 INFO @ Thu, 05 Dec 2019 13:06:33: 1000000 INFO @ Thu, 05 Dec 2019 13:06:35: 2000000 INFO @ Thu, 05 Dec 2019 13:06:38: 2000000 INFO @ Thu, 05 Dec 2019 13:06:40: 3000000 INFO @ Thu, 05 Dec 2019 13:06:43: 3000000 INFO @ Thu, 05 Dec 2019 13:06:44: 4000000 INFO @ Thu, 05 Dec 2019 13:06:48: 4000000 INFO @ Thu, 05 Dec 2019 13:06:49: 5000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:06:53: 5000000 INFO @ Thu, 05 Dec 2019 13:06:54: 6000000 INFO @ Thu, 05 Dec 2019 13:06:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717049/SRX5717049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717049/SRX5717049.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717049/SRX5717049.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717049/SRX5717049.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 @ Thu, 05 Dec 2019 13:06:54: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:06:54: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:06:59: 6000000 INFO @ Thu, 05 Dec 2019 13:06:59: 7000000 INFO @ Thu, 05 Dec 2019 13:07:01: 1000000 INFO @ Thu, 05 Dec 2019 13:07:04: 8000000 INFO @ Thu, 05 Dec 2019 13:07:04: 7000000 INFO @ Thu, 05 Dec 2019 13:07:06: 2000000 INFO @ Thu, 05 Dec 2019 13:07:08: 9000000 INFO @ Thu, 05 Dec 2019 13:07:09: 8000000 INFO @ Thu, 05 Dec 2019 13:07:12: 3000000 INFO @ Thu, 05 Dec 2019 13:07:13: 10000000 INFO @ Thu, 05 Dec 2019 13:07:15: 9000000 INFO @ Thu, 05 Dec 2019 13:07:17: 4000000 INFO @ Thu, 05 Dec 2019 13:07:18: 11000000 INFO @ Thu, 05 Dec 2019 13:07:20: 10000000 INFO @ Thu, 05 Dec 2019 13:07:22: 12000000 INFO @ Thu, 05 Dec 2019 13:07:23: 5000000 INFO @ Thu, 05 Dec 2019 13:07:26: 11000000 INFO @ Thu, 05 Dec 2019 13:07:27: 13000000 INFO @ Thu, 05 Dec 2019 13:07:28: 6000000 INFO @ Thu, 05 Dec 2019 13:07:31: 12000000 INFO @ Thu, 05 Dec 2019 13:07:32: 14000000 INFO @ Thu, 05 Dec 2019 13:07:34: 7000000 INFO @ Thu, 05 Dec 2019 13:07:36: 15000000 INFO @ Thu, 05 Dec 2019 13:07:37: 13000000 INFO @ Thu, 05 Dec 2019 13:07:39: 8000000 INFO @ Thu, 05 Dec 2019 13:07:41: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:07:41: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:07:41: #1 total tags in treatment: 15950953 INFO @ Thu, 05 Dec 2019 13:07:41: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:07:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:07:41: #1 tags after filtering in treatment: 15950953 INFO @ Thu, 05 Dec 2019 13:07:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:07:41: #1 finished! INFO @ Thu, 05 Dec 2019 13:07:41: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:07:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:07:42: 14000000 INFO @ Thu, 05 Dec 2019 13:07:42: #2 number of paired peaks: 741 WARNING @ Thu, 05 Dec 2019 13:07:42: Fewer paired peaks (741) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 741 pairs to build model! INFO @ Thu, 05 Dec 2019 13:07:42: start model_add_line... INFO @ Thu, 05 Dec 2019 13:07:42: start X-correlation... INFO @ Thu, 05 Dec 2019 13:07:42: end of X-cor INFO @ Thu, 05 Dec 2019 13:07:42: #2 finished! INFO @ Thu, 05 Dec 2019 13:07:42: #2 predicted fragment length is 144 bps INFO @ Thu, 05 Dec 2019 13:07:42: #2 alternative fragment length(s) may be 31,144,160,259,304,487,511,597 bps INFO @ Thu, 05 Dec 2019 13:07:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717049/SRX5717049.10_model.r INFO @ Thu, 05 Dec 2019 13:07:42: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:07:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:07:45: 9000000 INFO @ Thu, 05 Dec 2019 13:07:47: 15000000 INFO @ Thu, 05 Dec 2019 13:07:50: 10000000 INFO @ Thu, 05 Dec 2019 13:07:52: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:07:52: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:07:52: #1 total tags in treatment: 15950953 INFO @ Thu, 05 Dec 2019 13:07:52: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:07:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:07:53: #1 tags after filtering in treatment: 15950953 INFO @ Thu, 05 Dec 2019 13:07:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:07:53: #1 finished! INFO @ Thu, 05 Dec 2019 13:07:53: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:07:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:07:54: #2 number of paired peaks: 741 WARNING @ Thu, 05 Dec 2019 13:07:54: Fewer paired peaks (741) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 741 pairs to build model! INFO @ Thu, 05 Dec 2019 13:07:54: start model_add_line... INFO @ Thu, 05 Dec 2019 13:07:54: start X-correlation... INFO @ Thu, 05 Dec 2019 13:07:54: end of X-cor INFO @ Thu, 05 Dec 2019 13:07:54: #2 finished! INFO @ Thu, 05 Dec 2019 13:07:54: #2 predicted fragment length is 144 bps INFO @ Thu, 05 Dec 2019 13:07:54: #2 alternative fragment length(s) may be 31,144,160,259,304,487,511,597 bps INFO @ Thu, 05 Dec 2019 13:07:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717049/SRX5717049.05_model.r INFO @ Thu, 05 Dec 2019 13:07:55: 11000000 INFO @ Thu, 05 Dec 2019 13:08:00: 12000000 INFO @ Thu, 05 Dec 2019 13:08:00: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:08:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:08:05: 13000000 INFO @ Thu, 05 Dec 2019 13:08:11: 14000000 INFO @ Thu, 05 Dec 2019 13:08:13: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:08:15: 15000000 INFO @ Thu, 05 Dec 2019 13:08:20: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:08:20: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:08:20: #1 total tags in treatment: 15950953 INFO @ Thu, 05 Dec 2019 13:08:20: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:08:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:08:20: #1 tags after filtering in treatment: 15950953 INFO @ Thu, 05 Dec 2019 13:08:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:08:20: #1 finished! INFO @ Thu, 05 Dec 2019 13:08:20: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:08:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:08:22: #2 number of paired peaks: 741 WARNING @ Thu, 05 Dec 2019 13:08:22: Fewer paired peaks (741) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 741 pairs to build model! INFO @ Thu, 05 Dec 2019 13:08:22: start model_add_line... INFO @ Thu, 05 Dec 2019 13:08:22: start X-correlation... INFO @ Thu, 05 Dec 2019 13:08:22: end of X-cor INFO @ Thu, 05 Dec 2019 13:08:22: #2 finished! INFO @ Thu, 05 Dec 2019 13:08:22: #2 predicted fragment length is 144 bps INFO @ Thu, 05 Dec 2019 13:08:22: #2 alternative fragment length(s) may be 31,144,160,259,304,487,511,597 bps INFO @ Thu, 05 Dec 2019 13:08:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717049/SRX5717049.20_model.r INFO @ Thu, 05 Dec 2019 13:08:22: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:08:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:08:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717049/SRX5717049.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:08:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717049/SRX5717049.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:08:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717049/SRX5717049.10_summits.bed INFO @ Thu, 05 Dec 2019 13:08:30: Done! INFO @ Thu, 05 Dec 2019 13:08:32: #3 Call peaks for each chromosome... pass1 - making usageList (12 chroms): 8 millis pass2 - checking and writing primary data (1003 records, 4 fields): 49 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:08:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717049/SRX5717049.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:08:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717049/SRX5717049.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:08:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717049/SRX5717049.05_summits.bed INFO @ Thu, 05 Dec 2019 13:08:49: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2077 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:08:52: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:09:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717049/SRX5717049.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:09:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717049/SRX5717049.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:09:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717049/SRX5717049.20_summits.bed INFO @ Thu, 05 Dec 2019 13:09:08: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (397 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。