Job ID = 4178564 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 35,746,292 reads read : 71,492,584 reads written : 35,746,292 reads 0-length : 35,746,292 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: 00:10:42 35746292 reads; of these: 35746292 (100.00%) were unpaired; of these: 2579502 (7.22%) aligned 0 times 28384009 (79.40%) aligned exactly 1 time 4782781 (13.38%) aligned >1 times 92.78% overall alignment rate Time searching: 00:10:42 Overall time: 00:10:42 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] 14055678 / 33166790 = 0.4238 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:37:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827836/SRX5827836.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827836/SRX5827836.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827836/SRX5827836.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827836/SRX5827836.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 13:37:54: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:37:54: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:38:08: 1000000 INFO @ Thu, 05 Dec 2019 13:38:17: 2000000 INFO @ Thu, 05 Dec 2019 13:38:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827836/SRX5827836.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827836/SRX5827836.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827836/SRX5827836.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827836/SRX5827836.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 13:38:22: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:38:22: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:38:28: 3000000 INFO @ Thu, 05 Dec 2019 13:38:33: 1000000 INFO @ Thu, 05 Dec 2019 13:38:41: 4000000 INFO @ Thu, 05 Dec 2019 13:38:43: 2000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:38:51: 5000000 INFO @ Thu, 05 Dec 2019 13:38:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827836/SRX5827836.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827836/SRX5827836.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827836/SRX5827836.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827836/SRX5827836.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 13:38:52: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:38:52: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:38:53: 3000000 INFO @ Thu, 05 Dec 2019 13:39:02: 1000000 INFO @ Thu, 05 Dec 2019 13:39:03: 6000000 INFO @ Thu, 05 Dec 2019 13:39:03: 4000000 INFO @ Thu, 05 Dec 2019 13:39:12: 2000000 INFO @ Thu, 05 Dec 2019 13:39:14: 5000000 INFO @ Thu, 05 Dec 2019 13:39:14: 7000000 INFO @ Thu, 05 Dec 2019 13:39:23: 3000000 INFO @ Thu, 05 Dec 2019 13:39:25: 6000000 INFO @ Thu, 05 Dec 2019 13:39:25: 8000000 INFO @ Thu, 05 Dec 2019 13:39:33: 4000000 INFO @ Thu, 05 Dec 2019 13:39:36: 7000000 INFO @ Thu, 05 Dec 2019 13:39:37: 9000000 INFO @ Thu, 05 Dec 2019 13:39:42: 5000000 INFO @ Thu, 05 Dec 2019 13:39:47: 8000000 INFO @ Thu, 05 Dec 2019 13:39:48: 10000000 INFO @ Thu, 05 Dec 2019 13:39:52: 6000000 INFO @ Thu, 05 Dec 2019 13:39:57: 9000000 INFO @ Thu, 05 Dec 2019 13:39:59: 11000000 INFO @ Thu, 05 Dec 2019 13:40:04: 7000000 INFO @ Thu, 05 Dec 2019 13:40:08: 10000000 INFO @ Thu, 05 Dec 2019 13:40:10: 12000000 INFO @ Thu, 05 Dec 2019 13:40:14: 8000000 INFO @ Thu, 05 Dec 2019 13:40:18: 11000000 INFO @ Thu, 05 Dec 2019 13:40:21: 13000000 INFO @ Thu, 05 Dec 2019 13:40:24: 9000000 INFO @ Thu, 05 Dec 2019 13:40:28: 12000000 INFO @ Thu, 05 Dec 2019 13:40:34: 10000000 INFO @ Thu, 05 Dec 2019 13:40:34: 14000000 INFO @ Thu, 05 Dec 2019 13:40:39: 13000000 INFO @ Thu, 05 Dec 2019 13:40:43: 11000000 INFO @ Thu, 05 Dec 2019 13:40:46: 15000000 INFO @ Thu, 05 Dec 2019 13:40:50: 14000000 INFO @ Thu, 05 Dec 2019 13:40:53: 12000000 INFO @ Thu, 05 Dec 2019 13:40:57: 16000000 INFO @ Thu, 05 Dec 2019 13:41:01: 15000000 INFO @ Thu, 05 Dec 2019 13:41:02: 13000000 INFO @ Thu, 05 Dec 2019 13:41:08: 17000000 INFO @ Thu, 05 Dec 2019 13:41:12: 14000000 INFO @ Thu, 05 Dec 2019 13:41:12: 16000000 INFO @ Thu, 05 Dec 2019 13:41:20: 18000000 INFO @ Thu, 05 Dec 2019 13:41:21: 15000000 INFO @ Thu, 05 Dec 2019 13:41:23: 17000000 INFO @ Thu, 05 Dec 2019 13:41:31: 16000000 INFO @ Thu, 05 Dec 2019 13:41:31: 19000000 INFO @ Thu, 05 Dec 2019 13:41:32: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:41:32: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:41:32: #1 total tags in treatment: 19111112 INFO @ Thu, 05 Dec 2019 13:41:32: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:41:32: #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 13:41:33: #1 tags after filtering in treatment: 19111112 INFO @ Thu, 05 Dec 2019 13:41:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:41:33: #1 finished! INFO @ Thu, 05 Dec 2019 13:41:33: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:41:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:41:34: 18000000 INFO @ Thu, 05 Dec 2019 13:41:35: #2 number of paired peaks: 1579 INFO @ Thu, 05 Dec 2019 13:41:35: start model_add_line... INFO @ Thu, 05 Dec 2019 13:41:35: start X-correlation... INFO @ Thu, 05 Dec 2019 13:41:35: end of X-cor INFO @ Thu, 05 Dec 2019 13:41:35: #2 finished! INFO @ Thu, 05 Dec 2019 13:41:35: #2 predicted fragment length is 165 bps INFO @ Thu, 05 Dec 2019 13:41:35: #2 alternative fragment length(s) may be 165 bps INFO @ Thu, 05 Dec 2019 13:41:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827836/SRX5827836.05_model.r INFO @ Thu, 05 Dec 2019 13:41:35: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:41:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:41:42: 17000000 INFO @ Thu, 05 Dec 2019 13:41:44: 19000000 INFO @ Thu, 05 Dec 2019 13:41:45: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:41:45: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:41:45: #1 total tags in treatment: 19111112 INFO @ Thu, 05 Dec 2019 13:41:45: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:41:45: #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 13:41:46: #1 tags after filtering in treatment: 19111112 INFO @ Thu, 05 Dec 2019 13:41:46: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:41:46: #1 finished! INFO @ Thu, 05 Dec 2019 13:41:46: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:41:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:41:47: #2 number of paired peaks: 1579 INFO @ Thu, 05 Dec 2019 13:41:47: start model_add_line... INFO @ Thu, 05 Dec 2019 13:41:48: start X-correlation... INFO @ Thu, 05 Dec 2019 13:41:48: end of X-cor INFO @ Thu, 05 Dec 2019 13:41:48: #2 finished! INFO @ Thu, 05 Dec 2019 13:41:48: #2 predicted fragment length is 165 bps INFO @ Thu, 05 Dec 2019 13:41:48: #2 alternative fragment length(s) may be 165 bps INFO @ Thu, 05 Dec 2019 13:41:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827836/SRX5827836.10_model.r INFO @ Thu, 05 Dec 2019 13:41:48: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:41:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:41:51: 18000000 INFO @ Thu, 05 Dec 2019 13:42:00: 19000000 INFO @ Thu, 05 Dec 2019 13:42:01: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:42:01: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:42:01: #1 total tags in treatment: 19111112 INFO @ Thu, 05 Dec 2019 13:42:01: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:42:01: #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 13:42:02: #1 tags after filtering in treatment: 19111112 INFO @ Thu, 05 Dec 2019 13:42:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:42:02: #1 finished! INFO @ Thu, 05 Dec 2019 13:42:02: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:42:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:42:03: #2 number of paired peaks: 1579 INFO @ Thu, 05 Dec 2019 13:42:03: start model_add_line... INFO @ Thu, 05 Dec 2019 13:42:04: start X-correlation... INFO @ Thu, 05 Dec 2019 13:42:04: end of X-cor INFO @ Thu, 05 Dec 2019 13:42:04: #2 finished! INFO @ Thu, 05 Dec 2019 13:42:04: #2 predicted fragment length is 165 bps INFO @ Thu, 05 Dec 2019 13:42:04: #2 alternative fragment length(s) may be 165 bps INFO @ Thu, 05 Dec 2019 13:42:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827836/SRX5827836.20_model.r INFO @ Thu, 05 Dec 2019 13:42:04: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:42:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:42:36: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:42:44: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:43:00: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:43:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827836/SRX5827836.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:43:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827836/SRX5827836.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:43:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827836/SRX5827836.05_summits.bed INFO @ Thu, 05 Dec 2019 13:43:08: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6150 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:43:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827836/SRX5827836.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:43:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827836/SRX5827836.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:43:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827836/SRX5827836.10_summits.bed INFO @ Thu, 05 Dec 2019 13:43:11: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3808 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:43:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827836/SRX5827836.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:43:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827836/SRX5827836.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:43:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827836/SRX5827836.20_summits.bed INFO @ Thu, 05 Dec 2019 13:43:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2165 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。