Job ID = 2590310 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,296,083 reads read : 21,296,083 reads written : 21,296,083 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: 00:07:15 21296083 reads; of these: 21296083 (100.00%) were unpaired; of these: 3403365 (15.98%) aligned 0 times 14177554 (66.57%) aligned exactly 1 time 3715164 (17.45%) aligned >1 times 84.02% overall alignment rate Time searching: 00:07:15 Overall time: 00:07:15 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] 4489378 / 17892718 = 0.2509 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 20:58:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331416/SRX331416.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331416/SRX331416.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331416/SRX331416.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331416/SRX331416.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 20:58:40: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:58:40: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:58:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331416/SRX331416.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331416/SRX331416.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331416/SRX331416.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331416/SRX331416.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 20:58:41: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:58:41: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:58:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331416/SRX331416.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331416/SRX331416.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331416/SRX331416.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331416/SRX331416.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 20:58:42: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:58:42: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:58:48: 1000000 INFO @ Mon, 12 Aug 2019 20:58:51: 1000000 INFO @ Mon, 12 Aug 2019 20:58:51: 1000000 INFO @ Mon, 12 Aug 2019 20:58:56: 2000000 INFO @ Mon, 12 Aug 2019 20:59:00: 2000000 INFO @ Mon, 12 Aug 2019 20:59:01: 2000000 INFO @ Mon, 12 Aug 2019 20:59:03: 3000000 INFO @ Mon, 12 Aug 2019 20:59:08: 3000000 INFO @ Mon, 12 Aug 2019 20:59:11: 4000000 INFO @ Mon, 12 Aug 2019 20:59:12: 3000000 INFO @ Mon, 12 Aug 2019 20:59:17: 4000000 INFO @ Mon, 12 Aug 2019 20:59:19: 5000000 INFO @ Mon, 12 Aug 2019 20:59:22: 4000000 INFO @ Mon, 12 Aug 2019 20:59:25: 5000000 INFO @ Mon, 12 Aug 2019 20:59:26: 6000000 INFO @ Mon, 12 Aug 2019 20:59:32: 5000000 INFO @ Mon, 12 Aug 2019 20:59:34: 6000000 INFO @ Mon, 12 Aug 2019 20:59:34: 7000000 INFO @ Mon, 12 Aug 2019 20:59:41: 8000000 INFO @ Mon, 12 Aug 2019 20:59:42: 6000000 INFO @ Mon, 12 Aug 2019 20:59:42: 7000000 INFO @ Mon, 12 Aug 2019 20:59:49: 9000000 INFO @ Mon, 12 Aug 2019 20:59:51: 8000000 INFO @ Mon, 12 Aug 2019 20:59:52: 7000000 INFO @ Mon, 12 Aug 2019 20:59:57: 10000000 INFO @ Mon, 12 Aug 2019 20:59:59: 9000000 INFO @ Mon, 12 Aug 2019 21:00:03: 8000000 INFO @ Mon, 12 Aug 2019 21:00:04: 11000000 INFO @ Mon, 12 Aug 2019 21:00:08: 10000000 INFO @ Mon, 12 Aug 2019 21:00:12: 12000000 INFO @ Mon, 12 Aug 2019 21:00:13: 9000000 INFO @ Mon, 12 Aug 2019 21:00:16: 11000000 INFO @ Mon, 12 Aug 2019 21:00:19: 13000000 INFO @ Mon, 12 Aug 2019 21:00:23: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:00:23: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:00:23: #1 total tags in treatment: 13403340 INFO @ Mon, 12 Aug 2019 21:00:23: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:00:23: #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 21:00:23: 10000000 INFO @ Mon, 12 Aug 2019 21:00:23: #1 tags after filtering in treatment: 13403340 INFO @ Mon, 12 Aug 2019 21:00:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:00:23: #1 finished! INFO @ Mon, 12 Aug 2019 21:00:23: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:00:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:00:25: 12000000 INFO @ Mon, 12 Aug 2019 21:00:25: #2 number of paired peaks: 8117 INFO @ Mon, 12 Aug 2019 21:00:25: start model_add_line... INFO @ Mon, 12 Aug 2019 21:00:25: start X-correlation... INFO @ Mon, 12 Aug 2019 21:00:25: end of X-cor INFO @ Mon, 12 Aug 2019 21:00:25: #2 finished! INFO @ Mon, 12 Aug 2019 21:00:25: #2 predicted fragment length is 245 bps INFO @ Mon, 12 Aug 2019 21:00:25: #2 alternative fragment length(s) may be 245 bps INFO @ Mon, 12 Aug 2019 21:00:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331416/SRX331416.05_model.r INFO @ Mon, 12 Aug 2019 21:00:25: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:00:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:00:33: 11000000 INFO @ Mon, 12 Aug 2019 21:00:33: 13000000 INFO @ Mon, 12 Aug 2019 21:00:36: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:00:36: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:00:36: #1 total tags in treatment: 13403340 INFO @ Mon, 12 Aug 2019 21:00:36: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:00:36: #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 21:00:37: #1 tags after filtering in treatment: 13403340 INFO @ Mon, 12 Aug 2019 21:00:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:00:37: #1 finished! INFO @ Mon, 12 Aug 2019 21:00:37: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:00:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:00:39: #2 number of paired peaks: 8117 INFO @ Mon, 12 Aug 2019 21:00:39: start model_add_line... INFO @ Mon, 12 Aug 2019 21:00:39: start X-correlation... INFO @ Mon, 12 Aug 2019 21:00:39: end of X-cor INFO @ Mon, 12 Aug 2019 21:00:39: #2 finished! INFO @ Mon, 12 Aug 2019 21:00:39: #2 predicted fragment length is 245 bps INFO @ Mon, 12 Aug 2019 21:00:39: #2 alternative fragment length(s) may be 245 bps INFO @ Mon, 12 Aug 2019 21:00:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331416/SRX331416.20_model.r INFO @ Mon, 12 Aug 2019 21:00:39: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:00:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:00:43: 12000000 INFO @ Mon, 12 Aug 2019 21:00:52: 13000000 INFO @ Mon, 12 Aug 2019 21:00:56: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:00:56: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:00:56: #1 total tags in treatment: 13403340 INFO @ Mon, 12 Aug 2019 21:00:56: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:00:56: #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 21:00:56: #1 tags after filtering in treatment: 13403340 INFO @ Mon, 12 Aug 2019 21:00:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:00:56: #1 finished! INFO @ Mon, 12 Aug 2019 21:00:56: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:00:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:00:58: #2 number of paired peaks: 8117 INFO @ Mon, 12 Aug 2019 21:00:58: start model_add_line... INFO @ Mon, 12 Aug 2019 21:00:59: start X-correlation... INFO @ Mon, 12 Aug 2019 21:00:59: end of X-cor INFO @ Mon, 12 Aug 2019 21:00:59: #2 finished! INFO @ Mon, 12 Aug 2019 21:00:59: #2 predicted fragment length is 245 bps INFO @ Mon, 12 Aug 2019 21:00:59: #2 alternative fragment length(s) may be 245 bps INFO @ Mon, 12 Aug 2019 21:00:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331416/SRX331416.10_model.r INFO @ Mon, 12 Aug 2019 21:00:59: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:00:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:01:20: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:01:34: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:01:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331416/SRX331416.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:01:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331416/SRX331416.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:01:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331416/SRX331416.05_summits.bed INFO @ Mon, 12 Aug 2019 21:01:41: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10293 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:01:53: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:01:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331416/SRX331416.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:01:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331416/SRX331416.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:01:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331416/SRX331416.20_summits.bed INFO @ Mon, 12 Aug 2019 21:01:53: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (6468 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 12 Aug 2019 21:02:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331416/SRX331416.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:02:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331416/SRX331416.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:02:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331416/SRX331416.10_summits.bed INFO @ Mon, 12 Aug 2019 21:02:13: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (8513 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。