Job ID = 1295142 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 28,004,200 reads read : 56,008,400 reads written : 28,004,200 reads 0-length : 28,004,200 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: 00:09:50 28004200 reads; of these: 28004200 (100.00%) were unpaired; of these: 416304 (1.49%) aligned 0 times 25525281 (91.15%) aligned exactly 1 time 2062615 (7.37%) aligned >1 times 98.51% overall alignment rate Time searching: 00:09:50 Overall time: 00:09:50 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] 9827623 / 27587896 = 0.3562 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 12:40:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3279758/SRX3279758.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3279758/SRX3279758.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3279758/SRX3279758.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3279758/SRX3279758.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 12:40:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:40:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:40:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3279758/SRX3279758.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3279758/SRX3279758.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3279758/SRX3279758.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3279758/SRX3279758.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 12:40:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:40:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:40:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3279758/SRX3279758.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3279758/SRX3279758.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3279758/SRX3279758.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3279758/SRX3279758.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 12:40:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:40:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:40:55: 1000000 INFO @ Mon, 03 Jun 2019 12:40:57: 1000000 INFO @ Mon, 03 Jun 2019 12:41:00: 1000000 INFO @ Mon, 03 Jun 2019 12:41:03: 2000000 INFO @ Mon, 03 Jun 2019 12:41:07: 2000000 INFO @ Mon, 03 Jun 2019 12:41:14: 2000000 INFO @ Mon, 03 Jun 2019 12:41:14: 3000000 INFO @ Mon, 03 Jun 2019 12:41:18: 3000000 INFO @ Mon, 03 Jun 2019 12:41:24: 4000000 INFO @ Mon, 03 Jun 2019 12:41:27: 3000000 INFO @ Mon, 03 Jun 2019 12:41:29: 4000000 INFO @ Mon, 03 Jun 2019 12:41:33: 5000000 INFO @ Mon, 03 Jun 2019 12:41:40: 5000000 INFO @ Mon, 03 Jun 2019 12:41:41: 4000000 INFO @ Mon, 03 Jun 2019 12:41:42: 6000000 INFO @ Mon, 03 Jun 2019 12:41:51: 6000000 INFO @ Mon, 03 Jun 2019 12:41:52: 7000000 INFO @ Mon, 03 Jun 2019 12:41:55: 5000000 INFO @ Mon, 03 Jun 2019 12:42:01: 8000000 INFO @ Mon, 03 Jun 2019 12:42:02: 7000000 INFO @ Mon, 03 Jun 2019 12:42:09: 6000000 INFO @ Mon, 03 Jun 2019 12:42:11: 9000000 INFO @ Mon, 03 Jun 2019 12:42:12: 8000000 INFO @ Mon, 03 Jun 2019 12:42:20: 10000000 INFO @ Mon, 03 Jun 2019 12:42:22: 7000000 INFO @ Mon, 03 Jun 2019 12:42:24: 9000000 INFO @ Mon, 03 Jun 2019 12:42:29: 11000000 INFO @ Mon, 03 Jun 2019 12:42:35: 8000000 INFO @ Mon, 03 Jun 2019 12:42:35: 10000000 INFO @ Mon, 03 Jun 2019 12:42:39: 12000000 INFO @ Mon, 03 Jun 2019 12:42:46: 11000000 INFO @ Mon, 03 Jun 2019 12:42:48: 9000000 INFO @ Mon, 03 Jun 2019 12:42:48: 13000000 INFO @ Mon, 03 Jun 2019 12:42:57: 12000000 INFO @ Mon, 03 Jun 2019 12:42:58: 14000000 INFO @ Mon, 03 Jun 2019 12:43:01: 10000000 INFO @ Mon, 03 Jun 2019 12:43:08: 15000000 INFO @ Mon, 03 Jun 2019 12:43:08: 13000000 INFO @ Mon, 03 Jun 2019 12:43:14: 11000000 INFO @ Mon, 03 Jun 2019 12:43:18: 16000000 INFO @ Mon, 03 Jun 2019 12:43:20: 14000000 INFO @ Mon, 03 Jun 2019 12:43:27: 12000000 INFO @ Mon, 03 Jun 2019 12:43:28: 17000000 INFO @ Mon, 03 Jun 2019 12:43:33: 15000000 INFO @ Mon, 03 Jun 2019 12:43:36: #1 tag size is determined as 79 bps INFO @ Mon, 03 Jun 2019 12:43:36: #1 tag size = 79 INFO @ Mon, 03 Jun 2019 12:43:36: #1 total tags in treatment: 17760273 INFO @ Mon, 03 Jun 2019 12:43:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:43:36: #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 12:43:36: #1 tags after filtering in treatment: 17760273 INFO @ Mon, 03 Jun 2019 12:43:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:43:36: #1 finished! INFO @ Mon, 03 Jun 2019 12:43:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:43:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:43:39: #2 number of paired peaks: 14361 INFO @ Mon, 03 Jun 2019 12:43:39: start model_add_line... INFO @ Mon, 03 Jun 2019 12:43:40: 13000000 INFO @ Mon, 03 Jun 2019 12:43:40: start X-correlation... INFO @ Mon, 03 Jun 2019 12:43:40: end of X-cor INFO @ Mon, 03 Jun 2019 12:43:40: #2 finished! INFO @ Mon, 03 Jun 2019 12:43:40: #2 predicted fragment length is 164 bps INFO @ Mon, 03 Jun 2019 12:43:40: #2 alternative fragment length(s) may be 164 bps INFO @ Mon, 03 Jun 2019 12:43:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3279758/SRX3279758.10_model.r INFO @ Mon, 03 Jun 2019 12:43:40: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:43:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:43:45: 16000000 INFO @ Mon, 03 Jun 2019 12:43:53: 14000000 INFO @ Mon, 03 Jun 2019 12:43:56: 17000000 INFO @ Mon, 03 Jun 2019 12:44:05: #1 tag size is determined as 79 bps INFO @ Mon, 03 Jun 2019 12:44:05: #1 tag size = 79 INFO @ Mon, 03 Jun 2019 12:44:05: #1 total tags in treatment: 17760273 INFO @ Mon, 03 Jun 2019 12:44:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:44:05: #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 12:44:05: #1 tags after filtering in treatment: 17760273 INFO @ Mon, 03 Jun 2019 12:44:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:44:05: #1 finished! INFO @ Mon, 03 Jun 2019 12:44:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:44:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:44:07: 15000000 INFO @ Mon, 03 Jun 2019 12:44:08: #2 number of paired peaks: 14361 INFO @ Mon, 03 Jun 2019 12:44:08: start model_add_line... INFO @ Mon, 03 Jun 2019 12:44:09: start X-correlation... INFO @ Mon, 03 Jun 2019 12:44:09: end of X-cor INFO @ Mon, 03 Jun 2019 12:44:09: #2 finished! INFO @ Mon, 03 Jun 2019 12:44:09: #2 predicted fragment length is 164 bps INFO @ Mon, 03 Jun 2019 12:44:09: #2 alternative fragment length(s) may be 164 bps INFO @ Mon, 03 Jun 2019 12:44:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3279758/SRX3279758.05_model.r INFO @ Mon, 03 Jun 2019 12:44:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:44:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:44:20: 16000000 INFO @ Mon, 03 Jun 2019 12:44:33: 17000000 INFO @ Mon, 03 Jun 2019 12:44:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:44:43: #1 tag size is determined as 79 bps INFO @ Mon, 03 Jun 2019 12:44:43: #1 tag size = 79 INFO @ Mon, 03 Jun 2019 12:44:43: #1 total tags in treatment: 17760273 INFO @ Mon, 03 Jun 2019 12:44:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:44:43: #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 12:44:43: #1 tags after filtering in treatment: 17760273 INFO @ Mon, 03 Jun 2019 12:44:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:44:43: #1 finished! INFO @ Mon, 03 Jun 2019 12:44:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:44:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:44:47: #2 number of paired peaks: 14361 INFO @ Mon, 03 Jun 2019 12:44:47: start model_add_line... INFO @ Mon, 03 Jun 2019 12:44:47: start X-correlation... INFO @ Mon, 03 Jun 2019 12:44:47: end of X-cor INFO @ Mon, 03 Jun 2019 12:44:47: #2 finished! INFO @ Mon, 03 Jun 2019 12:44:47: #2 predicted fragment length is 164 bps INFO @ Mon, 03 Jun 2019 12:44:47: #2 alternative fragment length(s) may be 164 bps INFO @ Mon, 03 Jun 2019 12:44:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3279758/SRX3279758.20_model.r INFO @ Mon, 03 Jun 2019 12:44:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:44:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:45:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3279758/SRX3279758.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:45:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3279758/SRX3279758.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:45:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3279758/SRX3279758.10_summits.bed INFO @ Mon, 03 Jun 2019 12:45:04: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (8361 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 12:45:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:45:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3279758/SRX3279758.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:45:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3279758/SRX3279758.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:45:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3279758/SRX3279758.05_summits.bed INFO @ Mon, 03 Jun 2019 12:45:33: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (8808 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 03 Jun 2019 12:45:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:46:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3279758/SRX3279758.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:46:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3279758/SRX3279758.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:46:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3279758/SRX3279758.20_summits.bed INFO @ Mon, 03 Jun 2019 12:46:11: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (7784 records, 4 fields): 22 millis CompletedMACS2peakCalling