Job ID = 2590306 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,513,994 reads read : 18,513,994 reads written : 18,513,994 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: 00:07:01 18513994 reads; of these: 18513994 (100.00%) were unpaired; of these: 712202 (3.85%) aligned 0 times 13383267 (72.29%) aligned exactly 1 time 4418525 (23.87%) aligned >1 times 96.15% overall alignment rate Time searching: 00:07:01 Overall time: 00:07:01 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] 4108955 / 17801792 = 0.2308 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 20:52:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318801/SRX318801.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318801/SRX318801.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318801/SRX318801.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318801/SRX318801.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 20:52:49: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:52:49: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:52:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318801/SRX318801.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318801/SRX318801.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318801/SRX318801.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318801/SRX318801.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 20:52:50: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:52:50: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:52:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318801/SRX318801.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318801/SRX318801.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318801/SRX318801.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318801/SRX318801.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 20:52:51: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:52:51: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:52:58: 1000000 INFO @ Mon, 12 Aug 2019 20:52:59: 1000000 INFO @ Mon, 12 Aug 2019 20:53:01: 1000000 INFO @ Mon, 12 Aug 2019 20:53:05: 2000000 INFO @ Mon, 12 Aug 2019 20:53:07: 2000000 INFO @ Mon, 12 Aug 2019 20:53:11: 2000000 INFO @ Mon, 12 Aug 2019 20:53:12: 3000000 INFO @ Mon, 12 Aug 2019 20:53:16: 3000000 INFO @ Mon, 12 Aug 2019 20:53:19: 4000000 INFO @ Mon, 12 Aug 2019 20:53:20: 3000000 INFO @ Mon, 12 Aug 2019 20:53:25: 4000000 INFO @ Mon, 12 Aug 2019 20:53:26: 5000000 INFO @ Mon, 12 Aug 2019 20:53:30: 4000000 INFO @ Mon, 12 Aug 2019 20:53:33: 6000000 INFO @ Mon, 12 Aug 2019 20:53:34: 5000000 INFO @ Mon, 12 Aug 2019 20:53:39: 5000000 INFO @ Mon, 12 Aug 2019 20:53:40: 7000000 INFO @ Mon, 12 Aug 2019 20:53:42: 6000000 INFO @ Mon, 12 Aug 2019 20:53:47: 8000000 INFO @ Mon, 12 Aug 2019 20:53:48: 6000000 INFO @ Mon, 12 Aug 2019 20:53:51: 7000000 INFO @ Mon, 12 Aug 2019 20:53:55: 9000000 INFO @ Mon, 12 Aug 2019 20:53:58: 7000000 INFO @ Mon, 12 Aug 2019 20:54:00: 8000000 INFO @ Mon, 12 Aug 2019 20:54:02: 10000000 INFO @ Mon, 12 Aug 2019 20:54:07: 8000000 INFO @ Mon, 12 Aug 2019 20:54:09: 11000000 INFO @ Mon, 12 Aug 2019 20:54:09: 9000000 INFO @ Mon, 12 Aug 2019 20:54:16: 12000000 INFO @ Mon, 12 Aug 2019 20:54:17: 9000000 INFO @ Mon, 12 Aug 2019 20:54:18: 10000000 INFO @ Mon, 12 Aug 2019 20:54:23: 13000000 INFO @ Mon, 12 Aug 2019 20:54:26: 10000000 INFO @ Mon, 12 Aug 2019 20:54:27: 11000000 INFO @ Mon, 12 Aug 2019 20:54:28: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:54:28: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:54:28: #1 total tags in treatment: 13692837 INFO @ Mon, 12 Aug 2019 20:54:28: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:54:28: #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 20:54:28: #1 tags after filtering in treatment: 13692837 INFO @ Mon, 12 Aug 2019 20:54:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:54:28: #1 finished! INFO @ Mon, 12 Aug 2019 20:54:28: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:54:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:54:30: #2 number of paired peaks: 5242 INFO @ Mon, 12 Aug 2019 20:54:30: start model_add_line... INFO @ Mon, 12 Aug 2019 20:54:30: start X-correlation... INFO @ Mon, 12 Aug 2019 20:54:30: end of X-cor INFO @ Mon, 12 Aug 2019 20:54:30: #2 finished! INFO @ Mon, 12 Aug 2019 20:54:30: #2 predicted fragment length is 218 bps INFO @ Mon, 12 Aug 2019 20:54:30: #2 alternative fragment length(s) may be 218 bps INFO @ Mon, 12 Aug 2019 20:54:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318801/SRX318801.10_model.r INFO @ Mon, 12 Aug 2019 20:54:30: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:54:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:54:35: 11000000 INFO @ Mon, 12 Aug 2019 20:54:36: 12000000 INFO @ Mon, 12 Aug 2019 20:54:43: 12000000 INFO @ Mon, 12 Aug 2019 20:54:44: 13000000 INFO @ Mon, 12 Aug 2019 20:54:50: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:54:50: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:54:50: #1 total tags in treatment: 13692837 INFO @ Mon, 12 Aug 2019 20:54:50: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:54:50: #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 20:54:50: #1 tags after filtering in treatment: 13692837 INFO @ Mon, 12 Aug 2019 20:54:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:54:50: #1 finished! INFO @ Mon, 12 Aug 2019 20:54:50: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:54:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:54:51: 13000000 INFO @ Mon, 12 Aug 2019 20:54:52: #2 number of paired peaks: 5242 INFO @ Mon, 12 Aug 2019 20:54:52: start model_add_line... INFO @ Mon, 12 Aug 2019 20:54:52: start X-correlation... INFO @ Mon, 12 Aug 2019 20:54:52: end of X-cor INFO @ Mon, 12 Aug 2019 20:54:52: #2 finished! INFO @ Mon, 12 Aug 2019 20:54:52: #2 predicted fragment length is 218 bps INFO @ Mon, 12 Aug 2019 20:54:52: #2 alternative fragment length(s) may be 218 bps INFO @ Mon, 12 Aug 2019 20:54:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318801/SRX318801.05_model.r INFO @ Mon, 12 Aug 2019 20:54:52: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:54:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:54:57: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:54:57: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:54:57: #1 total tags in treatment: 13692837 INFO @ Mon, 12 Aug 2019 20:54:57: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:54:57: #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 20:54:57: #1 tags after filtering in treatment: 13692837 INFO @ Mon, 12 Aug 2019 20:54:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:54:57: #1 finished! INFO @ Mon, 12 Aug 2019 20:54:57: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:54:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:54:59: #2 number of paired peaks: 5242 INFO @ Mon, 12 Aug 2019 20:54:59: start model_add_line... INFO @ Mon, 12 Aug 2019 20:54:59: start X-correlation... INFO @ Mon, 12 Aug 2019 20:54:59: end of X-cor INFO @ Mon, 12 Aug 2019 20:54:59: #2 finished! INFO @ Mon, 12 Aug 2019 20:54:59: #2 predicted fragment length is 218 bps INFO @ Mon, 12 Aug 2019 20:54:59: #2 alternative fragment length(s) may be 218 bps INFO @ Mon, 12 Aug 2019 20:54:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318801/SRX318801.20_model.r INFO @ Mon, 12 Aug 2019 20:54:59: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:54:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:55:20: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:55:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318801/SRX318801.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:55:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318801/SRX318801.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:55:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318801/SRX318801.10_summits.bed INFO @ Mon, 12 Aug 2019 20:55:40: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7559 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:55:41: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:55:49: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:56:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318801/SRX318801.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:56:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318801/SRX318801.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:56:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318801/SRX318801.05_summits.bed INFO @ Mon, 12 Aug 2019 20:56:02: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (9554 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:56:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318801/SRX318801.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:56:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318801/SRX318801.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:56:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318801/SRX318801.20_summits.bed INFO @ Mon, 12 Aug 2019 20:56:09: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5379 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。