Job ID = 1294220 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 33,841,224 reads read : 33,841,224 reads written : 33,841,224 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:55 33841224 reads; of these: 33841224 (100.00%) were unpaired; of these: 1521100 (4.49%) aligned 0 times 25673475 (75.86%) aligned exactly 1 time 6646649 (19.64%) aligned >1 times 95.51% overall alignment rate Time searching: 00:09:55 Overall time: 00:09:55 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 16 files... [bam_rmdupse_core] 12054736 / 32320124 = 0.3730 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 05:53:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201897/SRX201897.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201897/SRX201897.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201897/SRX201897.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201897/SRX201897.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 05:53:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:53:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:53:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201897/SRX201897.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201897/SRX201897.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201897/SRX201897.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201897/SRX201897.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 05:53:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:53:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:53:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201897/SRX201897.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201897/SRX201897.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201897/SRX201897.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201897/SRX201897.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 05:53:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:53:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:54:00: 1000000 INFO @ Mon, 03 Jun 2019 05:54:01: 1000000 INFO @ Mon, 03 Jun 2019 05:54:02: 1000000 INFO @ Mon, 03 Jun 2019 05:54:09: 2000000 INFO @ Mon, 03 Jun 2019 05:54:09: 2000000 INFO @ Mon, 03 Jun 2019 05:54:11: 2000000 INFO @ Mon, 03 Jun 2019 05:54:19: 3000000 INFO @ Mon, 03 Jun 2019 05:54:19: 3000000 INFO @ Mon, 03 Jun 2019 05:54:21: 3000000 INFO @ Mon, 03 Jun 2019 05:54:27: 4000000 INFO @ Mon, 03 Jun 2019 05:54:28: 4000000 INFO @ Mon, 03 Jun 2019 05:54:31: 4000000 INFO @ Mon, 03 Jun 2019 05:54:36: 5000000 INFO @ Mon, 03 Jun 2019 05:54:37: 5000000 INFO @ Mon, 03 Jun 2019 05:54:40: 5000000 INFO @ Mon, 03 Jun 2019 05:54:44: 6000000 INFO @ Mon, 03 Jun 2019 05:54:45: 6000000 INFO @ Mon, 03 Jun 2019 05:54:49: 6000000 INFO @ Mon, 03 Jun 2019 05:54:53: 7000000 INFO @ Mon, 03 Jun 2019 05:54:54: 7000000 INFO @ Mon, 03 Jun 2019 05:54:59: 7000000 INFO @ Mon, 03 Jun 2019 05:55:01: 8000000 INFO @ Mon, 03 Jun 2019 05:55:03: 8000000 INFO @ Mon, 03 Jun 2019 05:55:08: 8000000 INFO @ Mon, 03 Jun 2019 05:55:11: 9000000 INFO @ Mon, 03 Jun 2019 05:55:12: 9000000 INFO @ Mon, 03 Jun 2019 05:55:18: 9000000 INFO @ Mon, 03 Jun 2019 05:55:20: 10000000 INFO @ Mon, 03 Jun 2019 05:55:22: 10000000 INFO @ Mon, 03 Jun 2019 05:55:28: 10000000 INFO @ Mon, 03 Jun 2019 05:55:30: 11000000 INFO @ Mon, 03 Jun 2019 05:55:31: 11000000 INFO @ Mon, 03 Jun 2019 05:55:38: 11000000 INFO @ Mon, 03 Jun 2019 05:55:39: 12000000 INFO @ Mon, 03 Jun 2019 05:55:41: 12000000 INFO @ Mon, 03 Jun 2019 05:55:48: 12000000 INFO @ Mon, 03 Jun 2019 05:55:49: 13000000 INFO @ Mon, 03 Jun 2019 05:55:50: 13000000 INFO @ Mon, 03 Jun 2019 05:55:57: 13000000 INFO @ Mon, 03 Jun 2019 05:55:58: 14000000 INFO @ Mon, 03 Jun 2019 05:56:00: 14000000 INFO @ Mon, 03 Jun 2019 05:56:06: 15000000 INFO @ Mon, 03 Jun 2019 05:56:07: 14000000 INFO @ Mon, 03 Jun 2019 05:56:08: 15000000 INFO @ Mon, 03 Jun 2019 05:56:14: 16000000 INFO @ Mon, 03 Jun 2019 05:56:16: 15000000 INFO @ Mon, 03 Jun 2019 05:56:16: 16000000 INFO @ Mon, 03 Jun 2019 05:56:22: 17000000 INFO @ Mon, 03 Jun 2019 05:56:25: 17000000 INFO @ Mon, 03 Jun 2019 05:56:26: 16000000 INFO @ Mon, 03 Jun 2019 05:56:31: 18000000 INFO @ Mon, 03 Jun 2019 05:56:35: 18000000 INFO @ Mon, 03 Jun 2019 05:56:36: 17000000 INFO @ Mon, 03 Jun 2019 05:56:40: 19000000 INFO @ Mon, 03 Jun 2019 05:56:43: 19000000 INFO @ Mon, 03 Jun 2019 05:56:45: 18000000 INFO @ Mon, 03 Jun 2019 05:56:48: 20000000 INFO @ Mon, 03 Jun 2019 05:56:50: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:56:50: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:56:50: #1 total tags in treatment: 20265388 INFO @ Mon, 03 Jun 2019 05:56:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:56:50: #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 05:56:51: #1 tags after filtering in treatment: 20265388 INFO @ Mon, 03 Jun 2019 05:56:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:56:51: #1 finished! INFO @ Mon, 03 Jun 2019 05:56:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:56:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:56:52: 20000000 INFO @ Mon, 03 Jun 2019 05:56:53: #2 number of paired peaks: 3175 INFO @ Mon, 03 Jun 2019 05:56:53: start model_add_line... INFO @ Mon, 03 Jun 2019 05:56:53: start X-correlation... INFO @ Mon, 03 Jun 2019 05:56:53: end of X-cor INFO @ Mon, 03 Jun 2019 05:56:53: #2 finished! INFO @ Mon, 03 Jun 2019 05:56:53: #2 predicted fragment length is 221 bps INFO @ Mon, 03 Jun 2019 05:56:53: #2 alternative fragment length(s) may be 221 bps INFO @ Mon, 03 Jun 2019 05:56:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201897/SRX201897.10_model.r INFO @ Mon, 03 Jun 2019 05:56:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:56:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:56:54: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:56:54: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:56:54: #1 total tags in treatment: 20265388 INFO @ Mon, 03 Jun 2019 05:56:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:56:54: #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 05:56:54: 19000000 INFO @ Mon, 03 Jun 2019 05:56:55: #1 tags after filtering in treatment: 20265388 INFO @ Mon, 03 Jun 2019 05:56:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:56:55: #1 finished! INFO @ Mon, 03 Jun 2019 05:56:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:56:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:56:57: #2 number of paired peaks: 3175 INFO @ Mon, 03 Jun 2019 05:56:57: start model_add_line... INFO @ Mon, 03 Jun 2019 05:56:57: start X-correlation... INFO @ Mon, 03 Jun 2019 05:56:57: end of X-cor INFO @ Mon, 03 Jun 2019 05:56:57: #2 finished! INFO @ Mon, 03 Jun 2019 05:56:57: #2 predicted fragment length is 221 bps INFO @ Mon, 03 Jun 2019 05:56:57: #2 alternative fragment length(s) may be 221 bps INFO @ Mon, 03 Jun 2019 05:56:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201897/SRX201897.05_model.r INFO @ Mon, 03 Jun 2019 05:56:57: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:56:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:57:04: 20000000 INFO @ Mon, 03 Jun 2019 05:57:06: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:57:06: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:57:06: #1 total tags in treatment: 20265388 INFO @ Mon, 03 Jun 2019 05:57:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:57:06: #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 05:57:07: #1 tags after filtering in treatment: 20265388 INFO @ Mon, 03 Jun 2019 05:57:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:57:07: #1 finished! INFO @ Mon, 03 Jun 2019 05:57:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:57:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:57:09: #2 number of paired peaks: 3175 INFO @ Mon, 03 Jun 2019 05:57:09: start model_add_line... INFO @ Mon, 03 Jun 2019 05:57:09: start X-correlation... INFO @ Mon, 03 Jun 2019 05:57:09: end of X-cor INFO @ Mon, 03 Jun 2019 05:57:09: #2 finished! INFO @ Mon, 03 Jun 2019 05:57:09: #2 predicted fragment length is 221 bps INFO @ Mon, 03 Jun 2019 05:57:09: #2 alternative fragment length(s) may be 221 bps INFO @ Mon, 03 Jun 2019 05:57:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201897/SRX201897.20_model.r INFO @ Mon, 03 Jun 2019 05:57:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:57:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:58:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:58:06: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:58:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:58:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201897/SRX201897.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:58:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201897/SRX201897.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:58:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201897/SRX201897.10_summits.bed INFO @ Mon, 03 Jun 2019 05:58:32: Done! pass1 - making usageList (13 chroms): 4 millis pass2 - checking and writing primary data (7742 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:58:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201897/SRX201897.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:58:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201897/SRX201897.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:58:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201897/SRX201897.05_summits.bed INFO @ Mon, 03 Jun 2019 05:58:35: Done! pass1 - making usageList (13 chroms): 5 millis pass2 - checking and writing primary data (9028 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:58:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201897/SRX201897.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:58:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201897/SRX201897.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:58:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201897/SRX201897.20_summits.bed INFO @ Mon, 03 Jun 2019 05:58:45: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6390 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。