Job ID = 2001535 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,307,892 reads read : 23,307,892 reads written : 23,307,892 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:09:31 23307892 reads; of these: 23307892 (100.00%) were unpaired; of these: 521884 (2.24%) aligned 0 times 16962619 (72.78%) aligned exactly 1 time 5823389 (24.98%) aligned >1 times 97.76% overall alignment rate Time searching: 00:09:34 Overall time: 00:09:34 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 8 files... [bam_rmdupse_core] 1240945 / 22786008 = 0.0545 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 04:46:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101878/ERX101878.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101878/ERX101878.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101878/ERX101878.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101878/ERX101878.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 04:46:09: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:46:09: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:46:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101878/ERX101878.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101878/ERX101878.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101878/ERX101878.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101878/ERX101878.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 04:46:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:46:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:46:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101878/ERX101878.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101878/ERX101878.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101878/ERX101878.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101878/ERX101878.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 04:46:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:46:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:46:19: 1000000 INFO @ Fri, 05 Jul 2019 04:46:20: 1000000 INFO @ Fri, 05 Jul 2019 04:46:21: 1000000 INFO @ Fri, 05 Jul 2019 04:46:28: 2000000 INFO @ Fri, 05 Jul 2019 04:46:29: 2000000 INFO @ Fri, 05 Jul 2019 04:46:30: 2000000 INFO @ Fri, 05 Jul 2019 04:46:38: 3000000 INFO @ Fri, 05 Jul 2019 04:46:40: 3000000 INFO @ Fri, 05 Jul 2019 04:46:40: 3000000 INFO @ Fri, 05 Jul 2019 04:46:47: 4000000 INFO @ Fri, 05 Jul 2019 04:46:49: 4000000 INFO @ Fri, 05 Jul 2019 04:46:50: 4000000 INFO @ Fri, 05 Jul 2019 04:46:57: 5000000 INFO @ Fri, 05 Jul 2019 04:46:58: 5000000 INFO @ Fri, 05 Jul 2019 04:47:00: 5000000 INFO @ Fri, 05 Jul 2019 04:47:06: 6000000 INFO @ Fri, 05 Jul 2019 04:47:08: 6000000 INFO @ Fri, 05 Jul 2019 04:47:10: 6000000 INFO @ Fri, 05 Jul 2019 04:47:15: 7000000 INFO @ Fri, 05 Jul 2019 04:47:16: 7000000 INFO @ Fri, 05 Jul 2019 04:47:20: 7000000 INFO @ Fri, 05 Jul 2019 04:47:24: 8000000 INFO @ Fri, 05 Jul 2019 04:47:25: 8000000 INFO @ Fri, 05 Jul 2019 04:47:30: 8000000 INFO @ Fri, 05 Jul 2019 04:47:33: 9000000 INFO @ Fri, 05 Jul 2019 04:47:34: 9000000 INFO @ Fri, 05 Jul 2019 04:47:40: 9000000 INFO @ Fri, 05 Jul 2019 04:47:42: 10000000 INFO @ Fri, 05 Jul 2019 04:47:43: 10000000 INFO @ Fri, 05 Jul 2019 04:47:51: 10000000 INFO @ Fri, 05 Jul 2019 04:47:51: 11000000 INFO @ Fri, 05 Jul 2019 04:47:52: 11000000 INFO @ Fri, 05 Jul 2019 04:48:00: 12000000 INFO @ Fri, 05 Jul 2019 04:48:00: 11000000 INFO @ Fri, 05 Jul 2019 04:48:01: 12000000 INFO @ Fri, 05 Jul 2019 04:48:08: 13000000 INFO @ Fri, 05 Jul 2019 04:48:09: 13000000 INFO @ Fri, 05 Jul 2019 04:48:10: 12000000 INFO @ Fri, 05 Jul 2019 04:48:18: 14000000 INFO @ Fri, 05 Jul 2019 04:48:19: 14000000 INFO @ Fri, 05 Jul 2019 04:48:20: 13000000 INFO @ Fri, 05 Jul 2019 04:48:26: 15000000 INFO @ Fri, 05 Jul 2019 04:48:27: 15000000 INFO @ Fri, 05 Jul 2019 04:48:29: 14000000 INFO @ Fri, 05 Jul 2019 04:48:36: 16000000 INFO @ Fri, 05 Jul 2019 04:48:36: 16000000 INFO @ Fri, 05 Jul 2019 04:48:39: 15000000 INFO @ Fri, 05 Jul 2019 04:48:45: 17000000 INFO @ Fri, 05 Jul 2019 04:48:45: 17000000 INFO @ Fri, 05 Jul 2019 04:48:48: 16000000 INFO @ Fri, 05 Jul 2019 04:48:53: 18000000 INFO @ Fri, 05 Jul 2019 04:48:53: 18000000 INFO @ Fri, 05 Jul 2019 04:48:57: 17000000 INFO @ Fri, 05 Jul 2019 04:49:02: 19000000 INFO @ Fri, 05 Jul 2019 04:49:02: 19000000 INFO @ Fri, 05 Jul 2019 04:49:07: 18000000 INFO @ Fri, 05 Jul 2019 04:49:10: 20000000 INFO @ Fri, 05 Jul 2019 04:49:12: 20000000 INFO @ Fri, 05 Jul 2019 04:49:17: 19000000 INFO @ Fri, 05 Jul 2019 04:49:18: 21000000 INFO @ Fri, 05 Jul 2019 04:49:23: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:49:23: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:49:23: #1 total tags in treatment: 21545063 INFO @ Fri, 05 Jul 2019 04:49:23: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:49:23: #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 04:49:23: 21000000 INFO @ Fri, 05 Jul 2019 04:49:23: #1 tags after filtering in treatment: 21544909 INFO @ Fri, 05 Jul 2019 04:49:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:49:23: #1 finished! INFO @ Fri, 05 Jul 2019 04:49:23: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:49:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:49:28: #2 number of paired peaks: 43349 INFO @ Fri, 05 Jul 2019 04:49:28: start model_add_line... INFO @ Fri, 05 Jul 2019 04:49:28: start X-correlation... INFO @ Fri, 05 Jul 2019 04:49:28: end of X-cor INFO @ Fri, 05 Jul 2019 04:49:28: #2 finished! INFO @ Fri, 05 Jul 2019 04:49:28: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 04:49:28: #2 alternative fragment length(s) may be 130 bps INFO @ Fri, 05 Jul 2019 04:49:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101878/ERX101878.20_model.r INFO @ Fri, 05 Jul 2019 04:49:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:49:28: 20000000 INFO @ Fri, 05 Jul 2019 04:49:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:49:29: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:49:29: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:49:29: #1 total tags in treatment: 21545063 INFO @ Fri, 05 Jul 2019 04:49:29: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:49:29: #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 04:49:29: #1 tags after filtering in treatment: 21544909 INFO @ Fri, 05 Jul 2019 04:49:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:49:29: #1 finished! INFO @ Fri, 05 Jul 2019 04:49:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:49:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:49:34: #2 number of paired peaks: 43349 INFO @ Fri, 05 Jul 2019 04:49:34: start model_add_line... INFO @ Fri, 05 Jul 2019 04:49:34: start X-correlation... INFO @ Fri, 05 Jul 2019 04:49:34: end of X-cor INFO @ Fri, 05 Jul 2019 04:49:34: #2 finished! INFO @ Fri, 05 Jul 2019 04:49:34: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 04:49:34: #2 alternative fragment length(s) may be 130 bps INFO @ Fri, 05 Jul 2019 04:49:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101878/ERX101878.10_model.r INFO @ Fri, 05 Jul 2019 04:49:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:49:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:49:37: 21000000 INFO @ Fri, 05 Jul 2019 04:49:42: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:49:42: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:49:42: #1 total tags in treatment: 21545063 INFO @ Fri, 05 Jul 2019 04:49:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:49:42: #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 04:49:42: #1 tags after filtering in treatment: 21544909 INFO @ Fri, 05 Jul 2019 04:49:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:49:42: #1 finished! INFO @ Fri, 05 Jul 2019 04:49:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:49:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:49:47: #2 number of paired peaks: 43349 INFO @ Fri, 05 Jul 2019 04:49:47: start model_add_line... INFO @ Fri, 05 Jul 2019 04:49:47: start X-correlation... INFO @ Fri, 05 Jul 2019 04:49:47: end of X-cor INFO @ Fri, 05 Jul 2019 04:49:47: #2 finished! INFO @ Fri, 05 Jul 2019 04:49:47: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 04:49:47: #2 alternative fragment length(s) may be 130 bps INFO @ Fri, 05 Jul 2019 04:49:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101878/ERX101878.05_model.r INFO @ Fri, 05 Jul 2019 04:49:47: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:49:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:50:37: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:50:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:50:57: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:51:11: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101878/ERX101878.20_peaks.xls INFO @ Fri, 05 Jul 2019 04:51:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101878/ERX101878.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:51:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101878/ERX101878.20_summits.bed INFO @ Fri, 05 Jul 2019 04:51:11: Done! pass1 - making usageList (25 chroms): 1 millis pass2 - checking and writing primary data (145 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:51:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101878/ERX101878.10_peaks.xls INFO @ Fri, 05 Jul 2019 04:51:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101878/ERX101878.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:51:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101878/ERX101878.10_summits.bed INFO @ Fri, 05 Jul 2019 04:51:19: Done! pass1 - making usageList (41 chroms): 2 millis pass2 - checking and writing primary data (1381 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:51:32: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101878/ERX101878.05_peaks.xls INFO @ Fri, 05 Jul 2019 04:51:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101878/ERX101878.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:51:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101878/ERX101878.05_summits.bed INFO @ Fri, 05 Jul 2019 04:51:32: Done! pass1 - making usageList (56 chroms): 3 millis pass2 - checking and writing primary data (5727 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。