Job ID = 2001710 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 45,506,621 reads read : 45,506,621 reads written : 45,506,621 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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:59:47 45506621 reads; of these: 45506621 (100.00%) were unpaired; of these: 1108111 (2.44%) aligned 0 times 34122033 (74.98%) aligned exactly 1 time 10276477 (22.58%) aligned >1 times 97.56% overall alignment rate Time searching: 00:59:50 Overall time: 00:59:50 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 20 files... [bam_rmdupse_core] 4559802 / 44398510 = 0.1027 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 11:00:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102018/ERX102018.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102018/ERX102018.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102018/ERX102018.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102018/ERX102018.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 11:00:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:00:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:00:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102018/ERX102018.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102018/ERX102018.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102018/ERX102018.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102018/ERX102018.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 11:00:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:00:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:00:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102018/ERX102018.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102018/ERX102018.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102018/ERX102018.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102018/ERX102018.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 11:00:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:00:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:01:03: 1000000 INFO @ Fri, 05 Jul 2019 11:01:04: 1000000 INFO @ Fri, 05 Jul 2019 11:01:06: 1000000 INFO @ Fri, 05 Jul 2019 11:01:10: 2000000 INFO @ Fri, 05 Jul 2019 11:01:11: 2000000 INFO @ Fri, 05 Jul 2019 11:01:13: 2000000 INFO @ Fri, 05 Jul 2019 11:01:17: 3000000 INFO @ Fri, 05 Jul 2019 11:01:18: 3000000 INFO @ Fri, 05 Jul 2019 11:01:21: 3000000 INFO @ Fri, 05 Jul 2019 11:01:24: 4000000 INFO @ Fri, 05 Jul 2019 11:01:25: 4000000 INFO @ Fri, 05 Jul 2019 11:01:29: 4000000 INFO @ Fri, 05 Jul 2019 11:01:31: 5000000 INFO @ Fri, 05 Jul 2019 11:01:32: 5000000 INFO @ Fri, 05 Jul 2019 11:01:37: 5000000 INFO @ Fri, 05 Jul 2019 11:01:38: 6000000 INFO @ Fri, 05 Jul 2019 11:01:39: 6000000 INFO @ Fri, 05 Jul 2019 11:01:44: 6000000 INFO @ Fri, 05 Jul 2019 11:01:45: 7000000 INFO @ Fri, 05 Jul 2019 11:01:46: 7000000 INFO @ Fri, 05 Jul 2019 11:01:52: 7000000 INFO @ Fri, 05 Jul 2019 11:01:53: 8000000 INFO @ Fri, 05 Jul 2019 11:01:54: 8000000 INFO @ Fri, 05 Jul 2019 11:02:00: 9000000 INFO @ Fri, 05 Jul 2019 11:02:00: 8000000 INFO @ Fri, 05 Jul 2019 11:02:01: 9000000 INFO @ Fri, 05 Jul 2019 11:02:07: 10000000 INFO @ Fri, 05 Jul 2019 11:02:08: 9000000 INFO @ Fri, 05 Jul 2019 11:02:08: 10000000 INFO @ Fri, 05 Jul 2019 11:02:14: 11000000 INFO @ Fri, 05 Jul 2019 11:02:15: 11000000 INFO @ Fri, 05 Jul 2019 11:02:15: 10000000 INFO @ Fri, 05 Jul 2019 11:02:21: 12000000 INFO @ Fri, 05 Jul 2019 11:02:22: 12000000 INFO @ Fri, 05 Jul 2019 11:02:23: 11000000 INFO @ Fri, 05 Jul 2019 11:02:28: 13000000 INFO @ Fri, 05 Jul 2019 11:02:29: 13000000 INFO @ Fri, 05 Jul 2019 11:02:31: 12000000 INFO @ Fri, 05 Jul 2019 11:02:35: 14000000 INFO @ Fri, 05 Jul 2019 11:02:36: 14000000 INFO @ Fri, 05 Jul 2019 11:02:38: 13000000 INFO @ Fri, 05 Jul 2019 11:02:42: 15000000 INFO @ Fri, 05 Jul 2019 11:02:43: 15000000 INFO @ Fri, 05 Jul 2019 11:02:46: 14000000 INFO @ Fri, 05 Jul 2019 11:02:49: 16000000 INFO @ Fri, 05 Jul 2019 11:02:50: 16000000 INFO @ Fri, 05 Jul 2019 11:02:53: 15000000 INFO @ Fri, 05 Jul 2019 11:02:56: 17000000 INFO @ Fri, 05 Jul 2019 11:02:57: 17000000 INFO @ Fri, 05 Jul 2019 11:03:01: 16000000 INFO @ Fri, 05 Jul 2019 11:03:03: 18000000 INFO @ Fri, 05 Jul 2019 11:03:04: 18000000 INFO @ Fri, 05 Jul 2019 11:03:09: 17000000 INFO @ Fri, 05 Jul 2019 11:03:11: 19000000 INFO @ Fri, 05 Jul 2019 11:03:11: 19000000 INFO @ Fri, 05 Jul 2019 11:03:16: 18000000 INFO @ Fri, 05 Jul 2019 11:03:18: 20000000 INFO @ Fri, 05 Jul 2019 11:03:19: 20000000 INFO @ Fri, 05 Jul 2019 11:03:24: 19000000 INFO @ Fri, 05 Jul 2019 11:03:25: 21000000 INFO @ Fri, 05 Jul 2019 11:03:26: 21000000 INFO @ Fri, 05 Jul 2019 11:03:32: 22000000 INFO @ Fri, 05 Jul 2019 11:03:32: 20000000 INFO @ Fri, 05 Jul 2019 11:03:33: 22000000 INFO @ Fri, 05 Jul 2019 11:03:39: 23000000 INFO @ Fri, 05 Jul 2019 11:03:40: 21000000 INFO @ Fri, 05 Jul 2019 11:03:40: 23000000 INFO @ Fri, 05 Jul 2019 11:03:46: 24000000 INFO @ Fri, 05 Jul 2019 11:03:47: 24000000 INFO @ Fri, 05 Jul 2019 11:03:48: 22000000 INFO @ Fri, 05 Jul 2019 11:03:54: 25000000 INFO @ Fri, 05 Jul 2019 11:03:54: 25000000 INFO @ Fri, 05 Jul 2019 11:03:56: 23000000 INFO @ Fri, 05 Jul 2019 11:04:01: 26000000 INFO @ Fri, 05 Jul 2019 11:04:02: 26000000 INFO @ Fri, 05 Jul 2019 11:04:03: 24000000 INFO @ Fri, 05 Jul 2019 11:04:08: 27000000 INFO @ Fri, 05 Jul 2019 11:04:09: 27000000 INFO @ Fri, 05 Jul 2019 11:04:11: 25000000 INFO @ Fri, 05 Jul 2019 11:04:15: 28000000 INFO @ Fri, 05 Jul 2019 11:04:16: 28000000 INFO @ Fri, 05 Jul 2019 11:04:19: 26000000 INFO @ Fri, 05 Jul 2019 11:04:22: 29000000 INFO @ Fri, 05 Jul 2019 11:04:23: 29000000 INFO @ Fri, 05 Jul 2019 11:04:27: 27000000 INFO @ Fri, 05 Jul 2019 11:04:29: 30000000 INFO @ Fri, 05 Jul 2019 11:04:30: 30000000 INFO @ Fri, 05 Jul 2019 11:04:35: 28000000 INFO @ Fri, 05 Jul 2019 11:04:36: 31000000 INFO @ Fri, 05 Jul 2019 11:04:37: 31000000 INFO @ Fri, 05 Jul 2019 11:04:43: 29000000 INFO @ Fri, 05 Jul 2019 11:04:43: 32000000 INFO @ Fri, 05 Jul 2019 11:04:44: 32000000 INFO @ Fri, 05 Jul 2019 11:04:50: 30000000 INFO @ Fri, 05 Jul 2019 11:04:51: 33000000 INFO @ Fri, 05 Jul 2019 11:04:51: 33000000 INFO @ Fri, 05 Jul 2019 11:04:58: 34000000 INFO @ Fri, 05 Jul 2019 11:04:58: 31000000 INFO @ Fri, 05 Jul 2019 11:04:59: 34000000 INFO @ Fri, 05 Jul 2019 11:05:05: 35000000 INFO @ Fri, 05 Jul 2019 11:05:06: 35000000 INFO @ Fri, 05 Jul 2019 11:05:06: 32000000 INFO @ Fri, 05 Jul 2019 11:05:12: 36000000 INFO @ Fri, 05 Jul 2019 11:05:13: 36000000 INFO @ Fri, 05 Jul 2019 11:05:14: 33000000 INFO @ Fri, 05 Jul 2019 11:05:19: 37000000 INFO @ Fri, 05 Jul 2019 11:05:20: 37000000 INFO @ Fri, 05 Jul 2019 11:05:21: 34000000 INFO @ Fri, 05 Jul 2019 11:05:27: 38000000 INFO @ Fri, 05 Jul 2019 11:05:28: 38000000 INFO @ Fri, 05 Jul 2019 11:05:29: 35000000 INFO @ Fri, 05 Jul 2019 11:05:34: 39000000 INFO @ Fri, 05 Jul 2019 11:05:35: 39000000 INFO @ Fri, 05 Jul 2019 11:05:37: 36000000 INFO @ Fri, 05 Jul 2019 11:05:40: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 11:05:40: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 11:05:40: #1 total tags in treatment: 39838708 INFO @ Fri, 05 Jul 2019 11:05:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:05:40: #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 11:05:41: #1 tags after filtering in treatment: 39838587 INFO @ Fri, 05 Jul 2019 11:05:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:05:41: #1 finished! INFO @ Fri, 05 Jul 2019 11:05:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:05:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:05:41: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 11:05:41: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 11:05:41: #1 total tags in treatment: 39838708 INFO @ Fri, 05 Jul 2019 11:05:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:05:41: #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 11:05:42: #1 tags after filtering in treatment: 39838587 INFO @ Fri, 05 Jul 2019 11:05:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:05:42: #1 finished! INFO @ Fri, 05 Jul 2019 11:05:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:05:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:05:45: 37000000 INFO @ Fri, 05 Jul 2019 11:05:48: #2 number of paired peaks: 55514 INFO @ Fri, 05 Jul 2019 11:05:48: start model_add_line... INFO @ Fri, 05 Jul 2019 11:05:49: start X-correlation... INFO @ Fri, 05 Jul 2019 11:05:49: end of X-cor INFO @ Fri, 05 Jul 2019 11:05:49: #2 finished! INFO @ Fri, 05 Jul 2019 11:05:49: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 11:05:49: #2 alternative fragment length(s) may be 2,132,507 bps INFO @ Fri, 05 Jul 2019 11:05:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102018/ERX102018.05_model.r INFO @ Fri, 05 Jul 2019 11:05:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:05:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:05:49: #2 number of paired peaks: 55514 INFO @ Fri, 05 Jul 2019 11:05:49: start model_add_line... INFO @ Fri, 05 Jul 2019 11:05:50: start X-correlation... INFO @ Fri, 05 Jul 2019 11:05:50: end of X-cor INFO @ Fri, 05 Jul 2019 11:05:50: #2 finished! INFO @ Fri, 05 Jul 2019 11:05:50: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 11:05:50: #2 alternative fragment length(s) may be 2,132,507 bps INFO @ Fri, 05 Jul 2019 11:05:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102018/ERX102018.10_model.r INFO @ Fri, 05 Jul 2019 11:05:50: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:05:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:05:53: 38000000 INFO @ Fri, 05 Jul 2019 11:06:01: 39000000 INFO @ Fri, 05 Jul 2019 11:06:08: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 11:06:08: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 11:06:08: #1 total tags in treatment: 39838708 INFO @ Fri, 05 Jul 2019 11:06:08: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:06:08: #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 11:06:09: #1 tags after filtering in treatment: 39838587 INFO @ Fri, 05 Jul 2019 11:06:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:06:09: #1 finished! INFO @ Fri, 05 Jul 2019 11:06:09: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:06:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:06:15: #2 number of paired peaks: 55514 INFO @ Fri, 05 Jul 2019 11:06:15: start model_add_line... INFO @ Fri, 05 Jul 2019 11:06:16: start X-correlation... INFO @ Fri, 05 Jul 2019 11:06:16: end of X-cor INFO @ Fri, 05 Jul 2019 11:06:16: #2 finished! INFO @ Fri, 05 Jul 2019 11:06:16: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 11:06:16: #2 alternative fragment length(s) may be 2,132,507 bps INFO @ Fri, 05 Jul 2019 11:06:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102018/ERX102018.20_model.r INFO @ Fri, 05 Jul 2019 11:06:16: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:06:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:07:52: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:07:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:08:20: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:08:57: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102018/ERX102018.05_peaks.xls INFO @ Fri, 05 Jul 2019 11:08:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102018/ERX102018.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:08:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102018/ERX102018.05_summits.bed INFO @ Fri, 05 Jul 2019 11:08:57: Done! INFO @ Fri, 05 Jul 2019 11:08:57: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102018/ERX102018.10_peaks.xls pass1 - making usageList (113 chroms): 5 millis pass2 - checking and writing primary data (12254 records, 4 fields): 21 millis INFO @ Fri, 05 Jul 2019 11:08:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102018/ERX102018.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:08:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102018/ERX102018.10_summits.bed INFO @ Fri, 05 Jul 2019 11:08:58: Done! pass1 - making usageList (67 chroms): 2 millis pass2 - checking and writing primary data (3870 records, 4 fields): 13 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 11:09:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102018/ERX102018.20_peaks.xls INFO @ Fri, 05 Jul 2019 11:09:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102018/ERX102018.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:09:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102018/ERX102018.20_summits.bed INFO @ Fri, 05 Jul 2019 11:09:23: Done! pass1 - making usageList (38 chroms): 2 millis pass2 - checking and writing primary data (625 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。