Job ID = 2003606 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,016,427 reads read : 19,016,427 reads written : 19,016,427 spots read : 13,196,217 reads read : 13,196,217 reads written : 13,196,217 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:51:07 32212644 reads; of these: 32212644 (100.00%) were unpaired; of these: 3843808 (11.93%) aligned 0 times 22182835 (68.86%) aligned exactly 1 time 6186001 (19.20%) aligned >1 times 88.07% overall alignment rate Time searching: 00:51:08 Overall time: 00:51:08 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4458804 / 28368836 = 0.1572 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 @ Fri, 05 Jul 2019 14:05:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX204152/SRX204152.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX204152/SRX204152.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX204152/SRX204152.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX204152/SRX204152.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 14:05:02: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:05:02: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:05:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX204152/SRX204152.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX204152/SRX204152.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX204152/SRX204152.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX204152/SRX204152.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 14:05:03: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:05:03: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:05:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX204152/SRX204152.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX204152/SRX204152.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX204152/SRX204152.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX204152/SRX204152.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 14:05:04: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:05:04: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:05:12: 1000000 INFO @ Fri, 05 Jul 2019 14:05:12: 1000000 INFO @ Fri, 05 Jul 2019 14:05:13: 1000000 INFO @ Fri, 05 Jul 2019 14:05:20: 2000000 INFO @ Fri, 05 Jul 2019 14:05:21: 2000000 INFO @ Fri, 05 Jul 2019 14:05:24: 2000000 INFO @ Fri, 05 Jul 2019 14:05:28: 3000000 INFO @ Fri, 05 Jul 2019 14:05:30: 3000000 INFO @ Fri, 05 Jul 2019 14:05:34: 3000000 INFO @ Fri, 05 Jul 2019 14:05:36: 4000000 INFO @ Fri, 05 Jul 2019 14:05:38: 4000000 INFO @ Fri, 05 Jul 2019 14:05:43: 5000000 INFO @ Fri, 05 Jul 2019 14:05:43: 4000000 INFO @ Fri, 05 Jul 2019 14:05:47: 5000000 INFO @ Fri, 05 Jul 2019 14:05:51: 6000000 INFO @ Fri, 05 Jul 2019 14:05:53: 5000000 INFO @ Fri, 05 Jul 2019 14:05:55: 6000000 INFO @ Fri, 05 Jul 2019 14:05:58: 7000000 INFO @ Fri, 05 Jul 2019 14:06:03: 6000000 INFO @ Fri, 05 Jul 2019 14:06:04: 7000000 INFO @ Fri, 05 Jul 2019 14:06:06: 8000000 INFO @ Fri, 05 Jul 2019 14:06:13: 8000000 INFO @ Fri, 05 Jul 2019 14:06:13: 7000000 INFO @ Fri, 05 Jul 2019 14:06:13: 9000000 INFO @ Fri, 05 Jul 2019 14:06:21: 10000000 INFO @ Fri, 05 Jul 2019 14:06:21: 9000000 INFO @ Fri, 05 Jul 2019 14:06:23: 8000000 INFO @ Fri, 05 Jul 2019 14:06:29: 11000000 INFO @ Fri, 05 Jul 2019 14:06:30: 10000000 INFO @ Fri, 05 Jul 2019 14:06:32: 9000000 INFO @ Fri, 05 Jul 2019 14:06:37: 12000000 INFO @ Fri, 05 Jul 2019 14:06:39: 11000000 INFO @ Fri, 05 Jul 2019 14:06:42: 10000000 INFO @ Fri, 05 Jul 2019 14:06:44: 13000000 INFO @ Fri, 05 Jul 2019 14:06:47: 12000000 INFO @ Fri, 05 Jul 2019 14:06:52: 14000000 INFO @ Fri, 05 Jul 2019 14:06:53: 11000000 INFO @ Fri, 05 Jul 2019 14:06:56: 13000000 INFO @ Fri, 05 Jul 2019 14:06:59: 15000000 INFO @ Fri, 05 Jul 2019 14:07:03: 12000000 INFO @ Fri, 05 Jul 2019 14:07:05: 14000000 INFO @ Fri, 05 Jul 2019 14:07:07: 16000000 INFO @ Fri, 05 Jul 2019 14:07:13: 13000000 INFO @ Fri, 05 Jul 2019 14:07:14: 15000000 INFO @ Fri, 05 Jul 2019 14:07:15: 17000000 INFO @ Fri, 05 Jul 2019 14:07:22: 18000000 INFO @ Fri, 05 Jul 2019 14:07:22: 16000000 INFO @ Fri, 05 Jul 2019 14:07:23: 14000000 INFO @ Fri, 05 Jul 2019 14:07:30: 19000000 INFO @ Fri, 05 Jul 2019 14:07:31: 17000000 INFO @ Fri, 05 Jul 2019 14:07:33: 15000000 INFO @ Fri, 05 Jul 2019 14:07:38: 20000000 INFO @ Fri, 05 Jul 2019 14:07:39: 18000000 INFO @ Fri, 05 Jul 2019 14:07:43: 16000000 INFO @ Fri, 05 Jul 2019 14:07:46: 21000000 INFO @ Fri, 05 Jul 2019 14:07:47: 19000000 INFO @ Fri, 05 Jul 2019 14:07:52: 17000000 INFO @ Fri, 05 Jul 2019 14:07:54: 22000000 INFO @ Fri, 05 Jul 2019 14:07:56: 20000000 INFO @ Fri, 05 Jul 2019 14:08:01: 23000000 INFO @ Fri, 05 Jul 2019 14:08:02: 18000000 INFO @ Fri, 05 Jul 2019 14:08:05: 21000000 INFO @ Fri, 05 Jul 2019 14:08:09: #1 tag size is determined as 55 bps INFO @ Fri, 05 Jul 2019 14:08:09: #1 tag size = 55 INFO @ Fri, 05 Jul 2019 14:08:09: #1 total tags in treatment: 23910032 INFO @ Fri, 05 Jul 2019 14:08:09: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:08:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 14:08:09: #1 tags after filtering in treatment: 23909886 INFO @ Fri, 05 Jul 2019 14:08:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:08:09: #1 finished! INFO @ Fri, 05 Jul 2019 14:08:09: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:08:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:08:11: 19000000 INFO @ Fri, 05 Jul 2019 14:08:14: 22000000 INFO @ Fri, 05 Jul 2019 14:08:15: #2 number of paired peaks: 59585 INFO @ Fri, 05 Jul 2019 14:08:15: start model_add_line... INFO @ Fri, 05 Jul 2019 14:08:15: start X-correlation... INFO @ Fri, 05 Jul 2019 14:08:15: end of X-cor INFO @ Fri, 05 Jul 2019 14:08:15: #2 finished! INFO @ Fri, 05 Jul 2019 14:08:15: #2 predicted fragment length is 225 bps INFO @ Fri, 05 Jul 2019 14:08:15: #2 alternative fragment length(s) may be 225 bps INFO @ Fri, 05 Jul 2019 14:08:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX204152/SRX204152.20_model.r INFO @ Fri, 05 Jul 2019 14:08:15: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:08:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:08:22: 20000000 INFO @ Fri, 05 Jul 2019 14:08:23: 23000000 INFO @ Fri, 05 Jul 2019 14:08:31: #1 tag size is determined as 55 bps INFO @ Fri, 05 Jul 2019 14:08:31: #1 tag size = 55 INFO @ Fri, 05 Jul 2019 14:08:31: #1 total tags in treatment: 23910032 INFO @ Fri, 05 Jul 2019 14:08:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:08:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 14:08:31: #1 tags after filtering in treatment: 23909886 INFO @ Fri, 05 Jul 2019 14:08:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:08:31: #1 finished! INFO @ Fri, 05 Jul 2019 14:08:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:08:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:08:33: 21000000 INFO @ Fri, 05 Jul 2019 14:08:37: #2 number of paired peaks: 59585 INFO @ Fri, 05 Jul 2019 14:08:37: start model_add_line... INFO @ Fri, 05 Jul 2019 14:08:37: start X-correlation... INFO @ Fri, 05 Jul 2019 14:08:37: end of X-cor INFO @ Fri, 05 Jul 2019 14:08:37: #2 finished! INFO @ Fri, 05 Jul 2019 14:08:37: #2 predicted fragment length is 225 bps INFO @ Fri, 05 Jul 2019 14:08:37: #2 alternative fragment length(s) may be 225 bps INFO @ Fri, 05 Jul 2019 14:08:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX204152/SRX204152.10_model.r INFO @ Fri, 05 Jul 2019 14:08:37: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:08:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:08:43: 22000000 INFO @ Fri, 05 Jul 2019 14:08:53: 23000000 INFO @ Fri, 05 Jul 2019 14:09:03: #1 tag size is determined as 55 bps INFO @ Fri, 05 Jul 2019 14:09:03: #1 tag size = 55 INFO @ Fri, 05 Jul 2019 14:09:03: #1 total tags in treatment: 23910032 INFO @ Fri, 05 Jul 2019 14:09:03: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:09:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 14:09:03: #1 tags after filtering in treatment: 23909886 INFO @ Fri, 05 Jul 2019 14:09:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:09:03: #1 finished! INFO @ Fri, 05 Jul 2019 14:09:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:09:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:09:09: #2 number of paired peaks: 59585 INFO @ Fri, 05 Jul 2019 14:09:09: start model_add_line... INFO @ Fri, 05 Jul 2019 14:09:09: start X-correlation... INFO @ Fri, 05 Jul 2019 14:09:09: end of X-cor INFO @ Fri, 05 Jul 2019 14:09:09: #2 finished! INFO @ Fri, 05 Jul 2019 14:09:09: #2 predicted fragment length is 225 bps INFO @ Fri, 05 Jul 2019 14:09:09: #2 alternative fragment length(s) may be 225 bps INFO @ Fri, 05 Jul 2019 14:09:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX204152/SRX204152.05_model.r INFO @ Fri, 05 Jul 2019 14:09:09: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:09:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:09:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:09:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:10:12: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX204152/SRX204152.20_peaks.xls INFO @ Fri, 05 Jul 2019 14:10:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX204152/SRX204152.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:10:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX204152/SRX204152.20_summits.bed INFO @ Fri, 05 Jul 2019 14:10:12: Done! pass1 - making usageList (31 chroms): 4 millis pass2 - checking and writing primary data (861 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 14:10:29: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:10:34: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX204152/SRX204152.10_peaks.xls INFO @ Fri, 05 Jul 2019 14:10:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX204152/SRX204152.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:10:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX204152/SRX204152.10_summits.bed INFO @ Fri, 05 Jul 2019 14:10:34: Done! pass1 - making usageList (52 chroms): 3 millis pass2 - checking and writing primary data (3376 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 14:11:11: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX204152/SRX204152.05_peaks.xls INFO @ Fri, 05 Jul 2019 14:11:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX204152/SRX204152.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:11:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX204152/SRX204152.05_summits.bed INFO @ Fri, 05 Jul 2019 14:11:11: Done! pass1 - making usageList (88 chroms): 5 millis pass2 - checking and writing primary data (15819 records, 4 fields): 74 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。