Job ID = 1301545 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,812,532 reads read : 17,812,532 reads written : 17,812,532 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:05 17812532 reads; of these: 17812532 (100.00%) were unpaired; of these: 786519 (4.42%) aligned 0 times 15574326 (87.43%) aligned exactly 1 time 1451687 (8.15%) aligned >1 times 95.58% overall alignment rate Time searching: 00:05:06 Overall time: 00:05:06 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 8 files... [bam_rmdupse_core] 5284785 / 17026013 = 0.3104 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, 03 Jun 2019 20:10:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485221/SRX485221.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485221/SRX485221.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485221/SRX485221.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485221/SRX485221.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, 03 Jun 2019 20:10:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:10:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:10:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485221/SRX485221.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485221/SRX485221.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485221/SRX485221.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485221/SRX485221.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, 03 Jun 2019 20:10:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:10:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:10:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485221/SRX485221.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485221/SRX485221.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485221/SRX485221.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485221/SRX485221.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, 03 Jun 2019 20:10:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:10:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:10:10: 1000000 INFO @ Mon, 03 Jun 2019 20:10:10: 1000000 INFO @ Mon, 03 Jun 2019 20:10:12: 1000000 INFO @ Mon, 03 Jun 2019 20:10:18: 2000000 INFO @ Mon, 03 Jun 2019 20:10:18: 2000000 INFO @ Mon, 03 Jun 2019 20:10:21: 2000000 INFO @ Mon, 03 Jun 2019 20:10:27: 3000000 INFO @ Mon, 03 Jun 2019 20:10:27: 3000000 INFO @ Mon, 03 Jun 2019 20:10:31: 3000000 INFO @ Mon, 03 Jun 2019 20:10:35: 4000000 INFO @ Mon, 03 Jun 2019 20:10:35: 4000000 INFO @ Mon, 03 Jun 2019 20:10:41: 4000000 INFO @ Mon, 03 Jun 2019 20:10:43: 5000000 INFO @ Mon, 03 Jun 2019 20:10:43: 5000000 INFO @ Mon, 03 Jun 2019 20:10:51: 5000000 INFO @ Mon, 03 Jun 2019 20:10:52: 6000000 INFO @ Mon, 03 Jun 2019 20:10:52: 6000000 INFO @ Mon, 03 Jun 2019 20:11:00: 7000000 INFO @ Mon, 03 Jun 2019 20:11:00: 7000000 INFO @ Mon, 03 Jun 2019 20:11:01: 6000000 INFO @ Mon, 03 Jun 2019 20:11:08: 8000000 INFO @ Mon, 03 Jun 2019 20:11:08: 8000000 INFO @ Mon, 03 Jun 2019 20:11:10: 7000000 INFO @ Mon, 03 Jun 2019 20:11:17: 9000000 INFO @ Mon, 03 Jun 2019 20:11:17: 9000000 INFO @ Mon, 03 Jun 2019 20:11:18: 8000000 INFO @ Mon, 03 Jun 2019 20:11:25: 10000000 INFO @ Mon, 03 Jun 2019 20:11:25: 10000000 INFO @ Mon, 03 Jun 2019 20:11:27: 9000000 INFO @ Mon, 03 Jun 2019 20:11:33: 11000000 INFO @ Mon, 03 Jun 2019 20:11:33: 11000000 INFO @ Mon, 03 Jun 2019 20:11:36: 10000000 INFO @ Mon, 03 Jun 2019 20:11:39: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:11:39: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:11:39: #1 total tags in treatment: 11741228 INFO @ Mon, 03 Jun 2019 20:11:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:11:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 20:11:39: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:11:39: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:11:39: #1 total tags in treatment: 11741228 INFO @ Mon, 03 Jun 2019 20:11:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:11:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 20:11:39: #1 tags after filtering in treatment: 11741228 INFO @ Mon, 03 Jun 2019 20:11:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:11:39: #1 finished! INFO @ Mon, 03 Jun 2019 20:11:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:11:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:11:39: #1 tags after filtering in treatment: 11741228 INFO @ Mon, 03 Jun 2019 20:11:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:11:39: #1 finished! INFO @ Mon, 03 Jun 2019 20:11:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:11:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:11:41: #2 number of paired peaks: 10786 INFO @ Mon, 03 Jun 2019 20:11:41: start model_add_line... INFO @ Mon, 03 Jun 2019 20:11:41: #2 number of paired peaks: 10786 INFO @ Mon, 03 Jun 2019 20:11:41: start model_add_line... INFO @ Mon, 03 Jun 2019 20:11:42: start X-correlation... INFO @ Mon, 03 Jun 2019 20:11:42: start X-correlation... INFO @ Mon, 03 Jun 2019 20:11:42: end of X-cor INFO @ Mon, 03 Jun 2019 20:11:42: #2 finished! INFO @ Mon, 03 Jun 2019 20:11:42: #2 predicted fragment length is 230 bps INFO @ Mon, 03 Jun 2019 20:11:42: #2 alternative fragment length(s) may be 230 bps INFO @ Mon, 03 Jun 2019 20:11:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485221/SRX485221.05_model.r INFO @ Mon, 03 Jun 2019 20:11:42: end of X-cor INFO @ Mon, 03 Jun 2019 20:11:42: #2 finished! INFO @ Mon, 03 Jun 2019 20:11:42: #2 predicted fragment length is 230 bps INFO @ Mon, 03 Jun 2019 20:11:42: #2 alternative fragment length(s) may be 230 bps INFO @ Mon, 03 Jun 2019 20:11:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485221/SRX485221.20_model.r INFO @ Mon, 03 Jun 2019 20:11:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:11:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:11:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:11:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:11:45: 11000000 INFO @ Mon, 03 Jun 2019 20:11:52: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:11:52: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:11:52: #1 total tags in treatment: 11741228 INFO @ Mon, 03 Jun 2019 20:11:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:11:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 20:11:52: #1 tags after filtering in treatment: 11741228 INFO @ Mon, 03 Jun 2019 20:11:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:11:52: #1 finished! INFO @ Mon, 03 Jun 2019 20:11:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:11:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:11:54: #2 number of paired peaks: 10786 INFO @ Mon, 03 Jun 2019 20:11:54: start model_add_line... INFO @ Mon, 03 Jun 2019 20:11:54: start X-correlation... INFO @ Mon, 03 Jun 2019 20:11:54: end of X-cor INFO @ Mon, 03 Jun 2019 20:11:54: #2 finished! INFO @ Mon, 03 Jun 2019 20:11:54: #2 predicted fragment length is 230 bps INFO @ Mon, 03 Jun 2019 20:11:54: #2 alternative fragment length(s) may be 230 bps INFO @ Mon, 03 Jun 2019 20:11:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485221/SRX485221.10_model.r INFO @ Mon, 03 Jun 2019 20:11:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:11:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:12:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:12:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:12:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:12:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485221/SRX485221.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:12:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485221/SRX485221.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:12:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485221/SRX485221.20_summits.bed INFO @ Mon, 03 Jun 2019 20:12:40: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (6365 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:12:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485221/SRX485221.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:12:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485221/SRX485221.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:12:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485221/SRX485221.05_summits.bed INFO @ Mon, 03 Jun 2019 20:12:41: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7791 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:12:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485221/SRX485221.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:12:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485221/SRX485221.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:12:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485221/SRX485221.10_summits.bed INFO @ Mon, 03 Jun 2019 20:12:53: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (7311 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。