Job ID = 2001658 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,659,787 reads read : 26,659,787 reads written : 26,659,787 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: 00:10:11 26659787 reads; of these: 26659787 (100.00%) were unpaired; of these: 592028 (2.22%) aligned 0 times 19846830 (74.44%) aligned exactly 1 time 6220929 (23.33%) aligned >1 times 97.78% overall alignment rate Time searching: 00:10:14 Overall time: 00:10:14 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] 1878499 / 26067759 = 0.0721 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 07:49:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101973/ERX101973.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101973/ERX101973.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101973/ERX101973.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101973/ERX101973.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 07:49:04: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:49:04: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:49:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101973/ERX101973.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101973/ERX101973.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101973/ERX101973.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101973/ERX101973.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 07:49:05: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:49:05: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:49:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101973/ERX101973.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101973/ERX101973.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101973/ERX101973.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101973/ERX101973.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 07:49:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:49:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:49:11: 1000000 INFO @ Fri, 05 Jul 2019 07:49:13: 1000000 INFO @ Fri, 05 Jul 2019 07:49:13: 1000000 INFO @ Fri, 05 Jul 2019 07:49:18: 2000000 INFO @ Fri, 05 Jul 2019 07:49:19: 2000000 INFO @ Fri, 05 Jul 2019 07:49:20: 2000000 INFO @ Fri, 05 Jul 2019 07:49:25: 3000000 INFO @ Fri, 05 Jul 2019 07:49:26: 3000000 INFO @ Fri, 05 Jul 2019 07:49:27: 3000000 INFO @ Fri, 05 Jul 2019 07:49:31: 4000000 INFO @ Fri, 05 Jul 2019 07:49:34: 4000000 INFO @ Fri, 05 Jul 2019 07:49:34: 4000000 INFO @ Fri, 05 Jul 2019 07:49:38: 5000000 INFO @ Fri, 05 Jul 2019 07:49:40: 5000000 INFO @ Fri, 05 Jul 2019 07:49:41: 5000000 INFO @ Fri, 05 Jul 2019 07:49:44: 6000000 INFO @ Fri, 05 Jul 2019 07:49:47: 6000000 INFO @ Fri, 05 Jul 2019 07:49:49: 6000000 INFO @ Fri, 05 Jul 2019 07:49:50: 7000000 INFO @ Fri, 05 Jul 2019 07:49:54: 7000000 INFO @ Fri, 05 Jul 2019 07:49:56: 8000000 INFO @ Fri, 05 Jul 2019 07:49:56: 7000000 INFO @ Fri, 05 Jul 2019 07:50:00: 8000000 INFO @ Fri, 05 Jul 2019 07:50:03: 9000000 INFO @ Fri, 05 Jul 2019 07:50:04: 8000000 INFO @ Fri, 05 Jul 2019 07:50:07: 9000000 INFO @ Fri, 05 Jul 2019 07:50:09: 10000000 INFO @ Fri, 05 Jul 2019 07:50:11: 9000000 INFO @ Fri, 05 Jul 2019 07:50:14: 10000000 INFO @ Fri, 05 Jul 2019 07:50:15: 11000000 INFO @ Fri, 05 Jul 2019 07:50:19: 10000000 INFO @ Fri, 05 Jul 2019 07:50:21: 11000000 INFO @ Fri, 05 Jul 2019 07:50:21: 12000000 INFO @ Fri, 05 Jul 2019 07:50:27: 11000000 INFO @ Fri, 05 Jul 2019 07:50:27: 12000000 INFO @ Fri, 05 Jul 2019 07:50:28: 13000000 INFO @ Fri, 05 Jul 2019 07:50:34: 14000000 INFO @ Fri, 05 Jul 2019 07:50:34: 12000000 INFO @ Fri, 05 Jul 2019 07:50:34: 13000000 INFO @ Fri, 05 Jul 2019 07:50:40: 15000000 INFO @ Fri, 05 Jul 2019 07:50:41: 14000000 INFO @ Fri, 05 Jul 2019 07:50:42: 13000000 INFO @ Fri, 05 Jul 2019 07:50:46: 16000000 INFO @ Fri, 05 Jul 2019 07:50:48: 15000000 INFO @ Fri, 05 Jul 2019 07:50:49: 14000000 INFO @ Fri, 05 Jul 2019 07:50:53: 17000000 INFO @ Fri, 05 Jul 2019 07:50:54: 16000000 INFO @ Fri, 05 Jul 2019 07:50:56: 15000000 INFO @ Fri, 05 Jul 2019 07:50:59: 18000000 INFO @ Fri, 05 Jul 2019 07:51:01: 17000000 INFO @ Fri, 05 Jul 2019 07:51:03: 16000000 INFO @ Fri, 05 Jul 2019 07:51:06: 19000000 INFO @ Fri, 05 Jul 2019 07:51:08: 18000000 INFO @ Fri, 05 Jul 2019 07:51:11: 17000000 INFO @ Fri, 05 Jul 2019 07:51:12: 20000000 INFO @ Fri, 05 Jul 2019 07:51:15: 19000000 INFO @ Fri, 05 Jul 2019 07:51:18: 21000000 INFO @ Fri, 05 Jul 2019 07:51:18: 18000000 INFO @ Fri, 05 Jul 2019 07:51:21: 20000000 INFO @ Fri, 05 Jul 2019 07:51:24: 22000000 INFO @ Fri, 05 Jul 2019 07:51:26: 19000000 INFO @ Fri, 05 Jul 2019 07:51:28: 21000000 INFO @ Fri, 05 Jul 2019 07:51:31: 23000000 INFO @ Fri, 05 Jul 2019 07:51:33: 20000000 INFO @ Fri, 05 Jul 2019 07:51:35: 22000000 INFO @ Fri, 05 Jul 2019 07:51:37: 24000000 INFO @ Fri, 05 Jul 2019 07:51:39: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 07:51:39: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 07:51:39: #1 total tags in treatment: 24189260 INFO @ Fri, 05 Jul 2019 07:51:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:51:39: #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 07:51:39: #1 tags after filtering in treatment: 24189096 INFO @ Fri, 05 Jul 2019 07:51:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:51:39: #1 finished! INFO @ Fri, 05 Jul 2019 07:51:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:51:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:51:41: 21000000 INFO @ Fri, 05 Jul 2019 07:51:42: 23000000 INFO @ Fri, 05 Jul 2019 07:51:44: #2 number of paired peaks: 57781 INFO @ Fri, 05 Jul 2019 07:51:44: start model_add_line... INFO @ Fri, 05 Jul 2019 07:51:45: start X-correlation... INFO @ Fri, 05 Jul 2019 07:51:45: end of X-cor INFO @ Fri, 05 Jul 2019 07:51:45: #2 finished! INFO @ Fri, 05 Jul 2019 07:51:45: #2 predicted fragment length is 129 bps INFO @ Fri, 05 Jul 2019 07:51:45: #2 alternative fragment length(s) may be 4,129,498 bps INFO @ Fri, 05 Jul 2019 07:51:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101973/ERX101973.10_model.r INFO @ Fri, 05 Jul 2019 07:51:45: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:51:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:51:49: 24000000 INFO @ Fri, 05 Jul 2019 07:51:49: 22000000 INFO @ Fri, 05 Jul 2019 07:51:50: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 07:51:50: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 07:51:50: #1 total tags in treatment: 24189260 INFO @ Fri, 05 Jul 2019 07:51:50: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:51:50: #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 07:51:51: #1 tags after filtering in treatment: 24189096 INFO @ Fri, 05 Jul 2019 07:51:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:51:51: #1 finished! INFO @ Fri, 05 Jul 2019 07:51:51: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:51:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:51:56: #2 number of paired peaks: 57781 INFO @ Fri, 05 Jul 2019 07:51:56: start model_add_line... INFO @ Fri, 05 Jul 2019 07:51:56: start X-correlation... INFO @ Fri, 05 Jul 2019 07:51:56: end of X-cor INFO @ Fri, 05 Jul 2019 07:51:56: #2 finished! INFO @ Fri, 05 Jul 2019 07:51:56: #2 predicted fragment length is 129 bps INFO @ Fri, 05 Jul 2019 07:51:56: #2 alternative fragment length(s) may be 4,129,498 bps INFO @ Fri, 05 Jul 2019 07:51:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101973/ERX101973.20_model.r INFO @ Fri, 05 Jul 2019 07:51:56: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:51:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:51:56: 23000000 INFO @ Fri, 05 Jul 2019 07:52:04: 24000000 INFO @ Fri, 05 Jul 2019 07:52:05: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 07:52:05: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 07:52:05: #1 total tags in treatment: 24189260 INFO @ Fri, 05 Jul 2019 07:52:05: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:52:05: #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 07:52:06: #1 tags after filtering in treatment: 24189096 INFO @ Fri, 05 Jul 2019 07:52:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:52:06: #1 finished! INFO @ Fri, 05 Jul 2019 07:52:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:52:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:52:11: #2 number of paired peaks: 57781 INFO @ Fri, 05 Jul 2019 07:52:11: start model_add_line... INFO @ Fri, 05 Jul 2019 07:52:11: start X-correlation... INFO @ Fri, 05 Jul 2019 07:52:11: end of X-cor INFO @ Fri, 05 Jul 2019 07:52:11: #2 finished! INFO @ Fri, 05 Jul 2019 07:52:11: #2 predicted fragment length is 129 bps INFO @ Fri, 05 Jul 2019 07:52:11: #2 alternative fragment length(s) may be 4,129,498 bps INFO @ Fri, 05 Jul 2019 07:52:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101973/ERX101973.05_model.r INFO @ Fri, 05 Jul 2019 07:52:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:52:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:53:01: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:53:12: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:53:27: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:53:41: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101973/ERX101973.10_peaks.xls INFO @ Fri, 05 Jul 2019 07:53:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101973/ERX101973.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:53:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101973/ERX101973.10_summits.bed INFO @ Fri, 05 Jul 2019 07:53:41: Done! pass1 - making usageList (39 chroms): 2 millis pass2 - checking and writing primary data (1389 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 07:53:50: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101973/ERX101973.20_peaks.xls INFO @ Fri, 05 Jul 2019 07:53:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101973/ERX101973.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:53:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101973/ERX101973.20_summits.bed INFO @ Fri, 05 Jul 2019 07:53:50: Done! pass1 - making usageList (29 chroms): 1 millis pass2 - checking and writing primary data (164 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 07:54:05: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101973/ERX101973.05_peaks.xls INFO @ Fri, 05 Jul 2019 07:54:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101973/ERX101973.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:54:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101973/ERX101973.05_summits.bed INFO @ Fri, 05 Jul 2019 07:54:05: Done! pass1 - making usageList (66 chroms): 3 millis pass2 - checking and writing primary data (6259 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。