Job ID = 4178599 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,128,443 reads read : 25,128,443 reads written : 25,128,443 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: 00:06:30 25128443 reads; of these: 25128443 (100.00%) were unpaired; of these: 1890600 (7.52%) aligned 0 times 20304246 (80.80%) aligned exactly 1 time 2933597 (11.67%) aligned >1 times 92.48% overall alignment rate Time searching: 00:06:30 Overall time: 00:06:30 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 12 files... [bam_rmdupse_core] 12470703 / 23237843 = 0.5367 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:34:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6468478/SRX6468478.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6468478/SRX6468478.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6468478/SRX6468478.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6468478/SRX6468478.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 13:34:55: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:34:55: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:35:03: 1000000 INFO @ Thu, 05 Dec 2019 13:35:10: 2000000 INFO @ Thu, 05 Dec 2019 13:35:18: 3000000 INFO @ Thu, 05 Dec 2019 13:35:25: 4000000 INFO @ Thu, 05 Dec 2019 13:35:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6468478/SRX6468478.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6468478/SRX6468478.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6468478/SRX6468478.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6468478/SRX6468478.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 13:35:25: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:35:25: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:35:32: 1000000 INFO @ Thu, 05 Dec 2019 13:35:33: 5000000 INFO @ Thu, 05 Dec 2019 13:35:39: 2000000 INFO @ Thu, 05 Dec 2019 13:35:40: 6000000 INFO @ Thu, 05 Dec 2019 13:35:46: 3000000 INFO @ Thu, 05 Dec 2019 13:35:48: 7000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:35:53: 4000000 INFO @ Thu, 05 Dec 2019 13:35:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6468478/SRX6468478.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6468478/SRX6468478.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6468478/SRX6468478.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6468478/SRX6468478.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 13:35:55: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:35:55: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:35:57: 8000000 INFO @ Thu, 05 Dec 2019 13:36:00: 5000000 INFO @ Thu, 05 Dec 2019 13:36:02: 1000000 INFO @ Thu, 05 Dec 2019 13:36:05: 9000000 INFO @ Thu, 05 Dec 2019 13:36:08: 6000000 INFO @ Thu, 05 Dec 2019 13:36:10: 2000000 INFO @ Thu, 05 Dec 2019 13:36:14: 10000000 INFO @ Thu, 05 Dec 2019 13:36:15: 7000000 INFO @ Thu, 05 Dec 2019 13:36:18: 3000000 INFO @ Thu, 05 Dec 2019 13:36:20: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:36:20: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:36:20: #1 total tags in treatment: 10767140 INFO @ Thu, 05 Dec 2019 13:36:20: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:36:20: #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 13:36:20: #1 tags after filtering in treatment: 10767140 INFO @ Thu, 05 Dec 2019 13:36:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:36:20: #1 finished! INFO @ Thu, 05 Dec 2019 13:36:20: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:36:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:36:21: #2 number of paired peaks: 5540 INFO @ Thu, 05 Dec 2019 13:36:21: start model_add_line... INFO @ Thu, 05 Dec 2019 13:36:22: start X-correlation... INFO @ Thu, 05 Dec 2019 13:36:22: end of X-cor INFO @ Thu, 05 Dec 2019 13:36:22: #2 finished! INFO @ Thu, 05 Dec 2019 13:36:22: #2 predicted fragment length is 139 bps INFO @ Thu, 05 Dec 2019 13:36:22: #2 alternative fragment length(s) may be 139 bps INFO @ Thu, 05 Dec 2019 13:36:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6468478/SRX6468478.05_model.r INFO @ Thu, 05 Dec 2019 13:36:22: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:36:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:36:23: 8000000 INFO @ Thu, 05 Dec 2019 13:36:25: 4000000 INFO @ Thu, 05 Dec 2019 13:36:30: 9000000 INFO @ Thu, 05 Dec 2019 13:36:32: 5000000 INFO @ Thu, 05 Dec 2019 13:36:37: 10000000 INFO @ Thu, 05 Dec 2019 13:36:39: 6000000 INFO @ Thu, 05 Dec 2019 13:36:42: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:36:42: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:36:42: #1 total tags in treatment: 10767140 INFO @ Thu, 05 Dec 2019 13:36:42: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:36:42: #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 13:36:42: #1 tags after filtering in treatment: 10767140 INFO @ Thu, 05 Dec 2019 13:36:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:36:42: #1 finished! INFO @ Thu, 05 Dec 2019 13:36:42: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:36:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:36:44: #2 number of paired peaks: 5540 INFO @ Thu, 05 Dec 2019 13:36:44: start model_add_line... INFO @ Thu, 05 Dec 2019 13:36:44: start X-correlation... INFO @ Thu, 05 Dec 2019 13:36:44: end of X-cor INFO @ Thu, 05 Dec 2019 13:36:44: #2 finished! INFO @ Thu, 05 Dec 2019 13:36:44: #2 predicted fragment length is 139 bps INFO @ Thu, 05 Dec 2019 13:36:44: #2 alternative fragment length(s) may be 139 bps INFO @ Thu, 05 Dec 2019 13:36:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6468478/SRX6468478.10_model.r INFO @ Thu, 05 Dec 2019 13:36:44: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:36:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:36:44: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:36:46: 7000000 INFO @ Thu, 05 Dec 2019 13:36:52: 8000000 INFO @ Thu, 05 Dec 2019 13:36:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6468478/SRX6468478.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:36:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6468478/SRX6468478.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:36:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6468478/SRX6468478.05_summits.bed INFO @ Thu, 05 Dec 2019 13:36:58: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7881 records, 4 fields): 185 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:36:59: 9000000 INFO @ Thu, 05 Dec 2019 13:37:05: 10000000 INFO @ Thu, 05 Dec 2019 13:37:06: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:37:10: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:37:10: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:37:10: #1 total tags in treatment: 10767140 INFO @ Thu, 05 Dec 2019 13:37:10: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:37:10: #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 13:37:10: #1 tags after filtering in treatment: 10767140 INFO @ Thu, 05 Dec 2019 13:37:10: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:37:10: #1 finished! INFO @ Thu, 05 Dec 2019 13:37:10: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:37:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:37:11: #2 number of paired peaks: 5540 INFO @ Thu, 05 Dec 2019 13:37:11: start model_add_line... INFO @ Thu, 05 Dec 2019 13:37:12: start X-correlation... INFO @ Thu, 05 Dec 2019 13:37:12: end of X-cor INFO @ Thu, 05 Dec 2019 13:37:12: #2 finished! INFO @ Thu, 05 Dec 2019 13:37:12: #2 predicted fragment length is 139 bps INFO @ Thu, 05 Dec 2019 13:37:12: #2 alternative fragment length(s) may be 139 bps INFO @ Thu, 05 Dec 2019 13:37:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6468478/SRX6468478.20_model.r INFO @ Thu, 05 Dec 2019 13:37:12: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:37:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:37:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6468478/SRX6468478.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:37:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6468478/SRX6468478.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:37:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6468478/SRX6468478.10_summits.bed INFO @ Thu, 05 Dec 2019 13:37:19: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6749 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:37:34: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:37:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6468478/SRX6468478.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:37:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6468478/SRX6468478.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:37:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6468478/SRX6468478.20_summits.bed INFO @ Thu, 05 Dec 2019 13:37:46: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4153 records, 4 fields): 101 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。