Job ID = 2590848 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,927,894 reads read : 23,927,894 reads written : 23,927,894 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: 00:07:43 23927894 reads; of these: 23927894 (100.00%) were unpaired; of these: 4537128 (18.96%) aligned 0 times 14752207 (61.65%) aligned exactly 1 time 4638559 (19.39%) aligned >1 times 81.04% overall alignment rate Time searching: 00:07:43 Overall time: 00:07:43 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] 11612937 / 19390766 = 0.5989 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 23:54:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011082/SRX5011082.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011082/SRX5011082.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011082/SRX5011082.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011082/SRX5011082.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 23:54:10: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:54:10: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:54:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011082/SRX5011082.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011082/SRX5011082.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011082/SRX5011082.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011082/SRX5011082.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 23:54:11: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:54:11: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:54:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011082/SRX5011082.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011082/SRX5011082.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011082/SRX5011082.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011082/SRX5011082.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 23:54:12: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:54:12: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:54:19: 1000000 INFO @ Mon, 12 Aug 2019 23:54:19: 1000000 INFO @ Mon, 12 Aug 2019 23:54:21: 1000000 INFO @ Mon, 12 Aug 2019 23:54:26: 2000000 INFO @ Mon, 12 Aug 2019 23:54:27: 2000000 INFO @ Mon, 12 Aug 2019 23:54:29: 2000000 INFO @ Mon, 12 Aug 2019 23:54:33: 3000000 INFO @ Mon, 12 Aug 2019 23:54:35: 3000000 INFO @ Mon, 12 Aug 2019 23:54:37: 3000000 INFO @ Mon, 12 Aug 2019 23:54:40: 4000000 INFO @ Mon, 12 Aug 2019 23:54:43: 4000000 INFO @ Mon, 12 Aug 2019 23:54:45: 4000000 INFO @ Mon, 12 Aug 2019 23:54:47: 5000000 INFO @ Mon, 12 Aug 2019 23:54:51: 5000000 INFO @ Mon, 12 Aug 2019 23:54:53: 5000000 INFO @ Mon, 12 Aug 2019 23:54:54: 6000000 INFO @ Mon, 12 Aug 2019 23:55:00: 6000000 INFO @ Mon, 12 Aug 2019 23:55:01: 7000000 INFO @ Mon, 12 Aug 2019 23:55:02: 6000000 INFO @ Mon, 12 Aug 2019 23:55:07: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:55:07: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:55:07: #1 total tags in treatment: 7777829 INFO @ Mon, 12 Aug 2019 23:55:07: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:55:07: #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 23:55:07: #1 tags after filtering in treatment: 7777829 INFO @ Mon, 12 Aug 2019 23:55:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:55:07: #1 finished! INFO @ Mon, 12 Aug 2019 23:55:07: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:55:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:55:08: 7000000 INFO @ Mon, 12 Aug 2019 23:55:08: #2 number of paired peaks: 2971 INFO @ Mon, 12 Aug 2019 23:55:08: start model_add_line... INFO @ Mon, 12 Aug 2019 23:55:08: start X-correlation... INFO @ Mon, 12 Aug 2019 23:55:08: end of X-cor INFO @ Mon, 12 Aug 2019 23:55:08: #2 finished! INFO @ Mon, 12 Aug 2019 23:55:08: #2 predicted fragment length is 130 bps INFO @ Mon, 12 Aug 2019 23:55:08: #2 alternative fragment length(s) may be 130 bps INFO @ Mon, 12 Aug 2019 23:55:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011082/SRX5011082.10_model.r INFO @ Mon, 12 Aug 2019 23:55:08: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:55:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:55:10: 7000000 INFO @ Mon, 12 Aug 2019 23:55:14: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:55:14: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:55:14: #1 total tags in treatment: 7777829 INFO @ Mon, 12 Aug 2019 23:55:14: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:55:14: #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 23:55:14: #1 tags after filtering in treatment: 7777829 INFO @ Mon, 12 Aug 2019 23:55:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:55:14: #1 finished! INFO @ Mon, 12 Aug 2019 23:55:14: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:55:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:55:15: #2 number of paired peaks: 2971 INFO @ Mon, 12 Aug 2019 23:55:15: start model_add_line... INFO @ Mon, 12 Aug 2019 23:55:15: start X-correlation... INFO @ Mon, 12 Aug 2019 23:55:15: end of X-cor INFO @ Mon, 12 Aug 2019 23:55:15: #2 finished! INFO @ Mon, 12 Aug 2019 23:55:15: #2 predicted fragment length is 130 bps INFO @ Mon, 12 Aug 2019 23:55:15: #2 alternative fragment length(s) may be 130 bps INFO @ Mon, 12 Aug 2019 23:55:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011082/SRX5011082.05_model.r INFO @ Mon, 12 Aug 2019 23:55:15: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:55:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:55:17: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:55:17: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:55:17: #1 total tags in treatment: 7777829 INFO @ Mon, 12 Aug 2019 23:55:17: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:55:17: #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 23:55:17: #1 tags after filtering in treatment: 7777829 INFO @ Mon, 12 Aug 2019 23:55:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:55:17: #1 finished! INFO @ Mon, 12 Aug 2019 23:55:17: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:55:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:55:18: #2 number of paired peaks: 2971 INFO @ Mon, 12 Aug 2019 23:55:18: start model_add_line... INFO @ Mon, 12 Aug 2019 23:55:18: start X-correlation... INFO @ Mon, 12 Aug 2019 23:55:18: end of X-cor INFO @ Mon, 12 Aug 2019 23:55:18: #2 finished! INFO @ Mon, 12 Aug 2019 23:55:18: #2 predicted fragment length is 130 bps INFO @ Mon, 12 Aug 2019 23:55:18: #2 alternative fragment length(s) may be 130 bps INFO @ Mon, 12 Aug 2019 23:55:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011082/SRX5011082.20_model.r INFO @ Mon, 12 Aug 2019 23:55:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:55:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:55:32: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:55:39: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:55:42: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:55:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011082/SRX5011082.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:55:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011082/SRX5011082.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:55:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011082/SRX5011082.10_summits.bed INFO @ Mon, 12 Aug 2019 23:55:44: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5765 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:55:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011082/SRX5011082.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:55:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011082/SRX5011082.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:55:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011082/SRX5011082.05_summits.bed INFO @ Mon, 12 Aug 2019 23:55:51: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (9452 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:55:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011082/SRX5011082.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:55:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011082/SRX5011082.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:55:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011082/SRX5011082.20_summits.bed INFO @ Mon, 12 Aug 2019 23:55:54: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3114 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。