Job ID = 2590677 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 37,082,776 reads read : 74,165,552 reads written : 37,082,776 reads 0-length : 37,082,776 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:13:47 37082776 reads; of these: 37082776 (100.00%) were unpaired; of these: 4174231 (11.26%) aligned 0 times 24027159 (64.79%) aligned exactly 1 time 8881386 (23.95%) aligned >1 times 88.74% overall alignment rate Time searching: 00:13:47 Overall time: 00:13:47 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] 17157815 / 32908545 = 0.5214 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 23:34:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011024/SRX5011024.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011024/SRX5011024.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011024/SRX5011024.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011024/SRX5011024.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 23:34:00: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:34:00: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:34:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011024/SRX5011024.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011024/SRX5011024.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011024/SRX5011024.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011024/SRX5011024.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 23:34:00: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:34:00: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:34:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011024/SRX5011024.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011024/SRX5011024.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011024/SRX5011024.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011024/SRX5011024.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 23:34:01: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:34:01: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:34:10: 1000000 INFO @ Mon, 12 Aug 2019 23:34:10: 1000000 INFO @ Mon, 12 Aug 2019 23:34:12: 1000000 INFO @ Mon, 12 Aug 2019 23:34:18: 2000000 INFO @ Mon, 12 Aug 2019 23:34:20: 2000000 INFO @ Mon, 12 Aug 2019 23:34:23: 2000000 INFO @ Mon, 12 Aug 2019 23:34:26: 3000000 INFO @ Mon, 12 Aug 2019 23:34:29: 3000000 INFO @ Mon, 12 Aug 2019 23:34:33: 4000000 INFO @ Mon, 12 Aug 2019 23:34:34: 3000000 INFO @ Mon, 12 Aug 2019 23:34:38: 4000000 INFO @ Mon, 12 Aug 2019 23:34:41: 5000000 INFO @ Mon, 12 Aug 2019 23:34:45: 4000000 INFO @ Mon, 12 Aug 2019 23:34:47: 5000000 INFO @ Mon, 12 Aug 2019 23:34:49: 6000000 INFO @ Mon, 12 Aug 2019 23:34:55: 6000000 INFO @ Mon, 12 Aug 2019 23:34:55: 5000000 INFO @ Mon, 12 Aug 2019 23:34:57: 7000000 INFO @ Mon, 12 Aug 2019 23:35:04: 7000000 INFO @ Mon, 12 Aug 2019 23:35:05: 8000000 INFO @ Mon, 12 Aug 2019 23:35:06: 6000000 INFO @ Mon, 12 Aug 2019 23:35:13: 9000000 INFO @ Mon, 12 Aug 2019 23:35:14: 8000000 INFO @ Mon, 12 Aug 2019 23:35:17: 7000000 INFO @ Mon, 12 Aug 2019 23:35:21: 10000000 INFO @ Mon, 12 Aug 2019 23:35:23: 9000000 INFO @ Mon, 12 Aug 2019 23:35:28: 8000000 INFO @ Mon, 12 Aug 2019 23:35:29: 11000000 INFO @ Mon, 12 Aug 2019 23:35:32: 10000000 INFO @ Mon, 12 Aug 2019 23:35:37: 12000000 INFO @ Mon, 12 Aug 2019 23:35:40: 9000000 INFO @ Mon, 12 Aug 2019 23:35:42: 11000000 INFO @ Mon, 12 Aug 2019 23:35:46: 13000000 INFO @ Mon, 12 Aug 2019 23:35:51: 12000000 INFO @ Mon, 12 Aug 2019 23:35:51: 10000000 INFO @ Mon, 12 Aug 2019 23:35:54: 14000000 INFO @ Mon, 12 Aug 2019 23:36:01: 13000000 INFO @ Mon, 12 Aug 2019 23:36:02: 15000000 INFO @ Mon, 12 Aug 2019 23:36:03: 11000000 INFO @ Mon, 12 Aug 2019 23:36:08: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:36:08: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:36:08: #1 total tags in treatment: 15750730 INFO @ Mon, 12 Aug 2019 23:36:08: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:36:08: #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 23:36:08: #1 tags after filtering in treatment: 15750730 INFO @ Mon, 12 Aug 2019 23:36:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:36:08: #1 finished! INFO @ Mon, 12 Aug 2019 23:36:08: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:36:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:36:10: #2 number of paired peaks: 1217 INFO @ Mon, 12 Aug 2019 23:36:10: start model_add_line... INFO @ Mon, 12 Aug 2019 23:36:10: start X-correlation... INFO @ Mon, 12 Aug 2019 23:36:10: end of X-cor INFO @ Mon, 12 Aug 2019 23:36:10: #2 finished! INFO @ Mon, 12 Aug 2019 23:36:10: #2 predicted fragment length is 161 bps INFO @ Mon, 12 Aug 2019 23:36:10: #2 alternative fragment length(s) may be 161 bps INFO @ Mon, 12 Aug 2019 23:36:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011024/SRX5011024.20_model.r INFO @ Mon, 12 Aug 2019 23:36:10: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:36:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:36:10: 14000000 INFO @ Mon, 12 Aug 2019 23:36:14: 12000000 INFO @ Mon, 12 Aug 2019 23:36:19: 15000000 INFO @ Mon, 12 Aug 2019 23:36:26: 13000000 INFO @ Mon, 12 Aug 2019 23:36:26: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:36:26: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:36:26: #1 total tags in treatment: 15750730 INFO @ Mon, 12 Aug 2019 23:36:26: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:36:26: #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 23:36:27: #1 tags after filtering in treatment: 15750730 INFO @ Mon, 12 Aug 2019 23:36:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:36:27: #1 finished! INFO @ Mon, 12 Aug 2019 23:36:27: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:36:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:36:28: #2 number of paired peaks: 1217 INFO @ Mon, 12 Aug 2019 23:36:28: start model_add_line... INFO @ Mon, 12 Aug 2019 23:36:28: start X-correlation... INFO @ Mon, 12 Aug 2019 23:36:28: end of X-cor INFO @ Mon, 12 Aug 2019 23:36:28: #2 finished! INFO @ Mon, 12 Aug 2019 23:36:28: #2 predicted fragment length is 161 bps INFO @ Mon, 12 Aug 2019 23:36:28: #2 alternative fragment length(s) may be 161 bps INFO @ Mon, 12 Aug 2019 23:36:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011024/SRX5011024.10_model.r INFO @ Mon, 12 Aug 2019 23:36:28: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:36:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:36:37: 14000000 INFO @ Mon, 12 Aug 2019 23:36:47: 15000000 INFO @ Mon, 12 Aug 2019 23:36:55: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:36:55: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:36:55: #1 total tags in treatment: 15750730 INFO @ Mon, 12 Aug 2019 23:36:55: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:36:55: #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 23:36:55: #1 tags after filtering in treatment: 15750730 INFO @ Mon, 12 Aug 2019 23:36:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:36:55: #1 finished! INFO @ Mon, 12 Aug 2019 23:36:55: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:36:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:36:56: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:36:57: #2 number of paired peaks: 1217 INFO @ Mon, 12 Aug 2019 23:36:57: start model_add_line... INFO @ Mon, 12 Aug 2019 23:36:57: start X-correlation... INFO @ Mon, 12 Aug 2019 23:36:57: end of X-cor INFO @ Mon, 12 Aug 2019 23:36:57: #2 finished! INFO @ Mon, 12 Aug 2019 23:36:57: #2 predicted fragment length is 161 bps INFO @ Mon, 12 Aug 2019 23:36:57: #2 alternative fragment length(s) may be 161 bps INFO @ Mon, 12 Aug 2019 23:36:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011024/SRX5011024.05_model.r INFO @ Mon, 12 Aug 2019 23:36:57: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:36:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:37:14: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:37:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011024/SRX5011024.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:37:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011024/SRX5011024.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:37:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011024/SRX5011024.20_summits.bed INFO @ Mon, 12 Aug 2019 23:37:17: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2598 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:37:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011024/SRX5011024.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:37:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011024/SRX5011024.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:37:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011024/SRX5011024.10_summits.bed INFO @ Mon, 12 Aug 2019 23:37:36: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4648 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:37:42: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:38:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011024/SRX5011024.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:38:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011024/SRX5011024.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:38:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011024/SRX5011024.05_summits.bed INFO @ Mon, 12 Aug 2019 23:38:06: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7836 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。