Job ID = 2590588 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,659,061 reads read : 37,318,122 reads written : 18,659,061 reads 0-length : 18,659,061 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: 00:06:37 18659061 reads; of these: 18659061 (100.00%) were unpaired; of these: 394922 (2.12%) aligned 0 times 14638493 (78.45%) aligned exactly 1 time 3625646 (19.43%) aligned >1 times 97.88% overall alignment rate Time searching: 00:06:37 Overall time: 00:06:37 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] 5576676 / 18264139 = 0.3053 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 22:45:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923180/SRX4923180.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923180/SRX4923180.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923180/SRX4923180.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923180/SRX4923180.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 22:45:10: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:45:10: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:45:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923180/SRX4923180.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923180/SRX4923180.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923180/SRX4923180.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923180/SRX4923180.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 22:45:11: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:45:11: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:45:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923180/SRX4923180.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923180/SRX4923180.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923180/SRX4923180.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923180/SRX4923180.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 22:45:12: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:45:12: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:45:16: 1000000 INFO @ Mon, 12 Aug 2019 22:45:18: 1000000 INFO @ Mon, 12 Aug 2019 22:45:18: 1000000 INFO @ Mon, 12 Aug 2019 22:45:23: 2000000 INFO @ Mon, 12 Aug 2019 22:45:24: 2000000 INFO @ Mon, 12 Aug 2019 22:45:25: 2000000 INFO @ Mon, 12 Aug 2019 22:45:29: 3000000 INFO @ Mon, 12 Aug 2019 22:45:30: 3000000 INFO @ Mon, 12 Aug 2019 22:45:31: 3000000 INFO @ Mon, 12 Aug 2019 22:45:36: 4000000 INFO @ Mon, 12 Aug 2019 22:45:37: 4000000 INFO @ Mon, 12 Aug 2019 22:45:38: 4000000 INFO @ Mon, 12 Aug 2019 22:45:42: 5000000 INFO @ Mon, 12 Aug 2019 22:45:43: 5000000 INFO @ Mon, 12 Aug 2019 22:45:44: 5000000 INFO @ Mon, 12 Aug 2019 22:45:49: 6000000 INFO @ Mon, 12 Aug 2019 22:45:50: 6000000 INFO @ Mon, 12 Aug 2019 22:45:51: 6000000 INFO @ Mon, 12 Aug 2019 22:45:55: 7000000 INFO @ Mon, 12 Aug 2019 22:45:56: 7000000 INFO @ Mon, 12 Aug 2019 22:45:57: 7000000 INFO @ Mon, 12 Aug 2019 22:46:01: 8000000 INFO @ Mon, 12 Aug 2019 22:46:02: 8000000 INFO @ Mon, 12 Aug 2019 22:46:03: 8000000 INFO @ Mon, 12 Aug 2019 22:46:08: 9000000 INFO @ Mon, 12 Aug 2019 22:46:09: 9000000 INFO @ Mon, 12 Aug 2019 22:46:10: 9000000 INFO @ Mon, 12 Aug 2019 22:46:14: 10000000 INFO @ Mon, 12 Aug 2019 22:46:15: 10000000 INFO @ Mon, 12 Aug 2019 22:46:16: 10000000 INFO @ Mon, 12 Aug 2019 22:46:21: 11000000 INFO @ Mon, 12 Aug 2019 22:46:22: 11000000 INFO @ Mon, 12 Aug 2019 22:46:23: 11000000 INFO @ Mon, 12 Aug 2019 22:46:27: 12000000 INFO @ Mon, 12 Aug 2019 22:46:28: 12000000 INFO @ Mon, 12 Aug 2019 22:46:29: 12000000 INFO @ Mon, 12 Aug 2019 22:46:32: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:46:32: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:46:32: #1 total tags in treatment: 12687463 INFO @ Mon, 12 Aug 2019 22:46:32: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:46:32: #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 22:46:32: #1 tags after filtering in treatment: 12687463 INFO @ Mon, 12 Aug 2019 22:46:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:46:32: #1 finished! INFO @ Mon, 12 Aug 2019 22:46:32: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:46:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:46:33: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:46:33: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:46:33: #1 total tags in treatment: 12687463 INFO @ Mon, 12 Aug 2019 22:46:33: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:46:33: #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 22:46:33: #1 tags after filtering in treatment: 12687463 INFO @ Mon, 12 Aug 2019 22:46:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:46:33: #1 finished! INFO @ Mon, 12 Aug 2019 22:46:33: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:46:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:46:34: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:46:34: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:46:34: #1 total tags in treatment: 12687463 INFO @ Mon, 12 Aug 2019 22:46:34: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:46:34: #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 22:46:34: #1 tags after filtering in treatment: 12687463 INFO @ Mon, 12 Aug 2019 22:46:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:46:34: #1 finished! INFO @ Mon, 12 Aug 2019 22:46:34: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:46:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:46:34: #2 number of paired peaks: 7629 INFO @ Mon, 12 Aug 2019 22:46:34: start model_add_line... INFO @ Mon, 12 Aug 2019 22:46:34: start X-correlation... INFO @ Mon, 12 Aug 2019 22:46:34: end of X-cor INFO @ Mon, 12 Aug 2019 22:46:34: #2 finished! INFO @ Mon, 12 Aug 2019 22:46:34: #2 predicted fragment length is 135 bps INFO @ Mon, 12 Aug 2019 22:46:34: #2 alternative fragment length(s) may be 135 bps INFO @ Mon, 12 Aug 2019 22:46:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923180/SRX4923180.05_model.r INFO @ Mon, 12 Aug 2019 22:46:34: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:46:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:46:35: #2 number of paired peaks: 7629 INFO @ Mon, 12 Aug 2019 22:46:35: start model_add_line... INFO @ Mon, 12 Aug 2019 22:46:35: start X-correlation... INFO @ Mon, 12 Aug 2019 22:46:35: end of X-cor INFO @ Mon, 12 Aug 2019 22:46:35: #2 finished! INFO @ Mon, 12 Aug 2019 22:46:35: #2 predicted fragment length is 135 bps INFO @ Mon, 12 Aug 2019 22:46:35: #2 alternative fragment length(s) may be 135 bps INFO @ Mon, 12 Aug 2019 22:46:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923180/SRX4923180.10_model.r INFO @ Mon, 12 Aug 2019 22:46:35: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:46:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:46:36: #2 number of paired peaks: 7629 INFO @ Mon, 12 Aug 2019 22:46:36: start model_add_line... INFO @ Mon, 12 Aug 2019 22:46:36: start X-correlation... INFO @ Mon, 12 Aug 2019 22:46:36: end of X-cor INFO @ Mon, 12 Aug 2019 22:46:36: #2 finished! INFO @ Mon, 12 Aug 2019 22:46:36: #2 predicted fragment length is 135 bps INFO @ Mon, 12 Aug 2019 22:46:36: #2 alternative fragment length(s) may be 135 bps INFO @ Mon, 12 Aug 2019 22:46:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923180/SRX4923180.20_model.r INFO @ Mon, 12 Aug 2019 22:46:36: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:46:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:47:12: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:47:13: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:47:14: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:47:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923180/SRX4923180.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:47:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923180/SRX4923180.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:47:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923180/SRX4923180.05_summits.bed INFO @ Mon, 12 Aug 2019 22:47:30: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9223 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:47:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923180/SRX4923180.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:47:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923180/SRX4923180.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:47:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923180/SRX4923180.10_summits.bed INFO @ Mon, 12 Aug 2019 22:47:31: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8199 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:47:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923180/SRX4923180.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:47:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923180/SRX4923180.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:47:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923180/SRX4923180.20_summits.bed INFO @ Mon, 12 Aug 2019 22:47:32: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6638 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。