Job ID = 2640705 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,356,276 reads read : 48,712,552 reads written : 24,356,276 reads 0-length : 24,356,276 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: 00:17:44 24356276 reads; of these: 24356276 (100.00%) were unpaired; of these: 495885 (2.04%) aligned 0 times 19917930 (81.78%) aligned exactly 1 time 3942461 (16.19%) aligned >1 times 97.96% overall alignment rate Time searching: 00:17:47 Overall time: 00:17:47 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] 2106566 / 23860391 = 0.0883 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:51:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375062/SRX5375062.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375062/SRX5375062.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375062/SRX5375062.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375062/SRX5375062.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 @ Sat, 24 Aug 2019 18:51:03: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:51:03: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:51:10: 1000000 INFO @ Sat, 24 Aug 2019 18:51:17: 2000000 INFO @ Sat, 24 Aug 2019 18:51:23: 3000000 INFO @ Sat, 24 Aug 2019 18:51:30: 4000000 INFO @ Sat, 24 Aug 2019 18:51:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375062/SRX5375062.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375062/SRX5375062.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375062/SRX5375062.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375062/SRX5375062.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 @ Sat, 24 Aug 2019 18:51:32: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:51:32: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:51:36: 5000000 INFO @ Sat, 24 Aug 2019 18:51:39: 1000000 INFO @ Sat, 24 Aug 2019 18:51:43: 6000000 INFO @ Sat, 24 Aug 2019 18:51:45: 2000000 INFO @ Sat, 24 Aug 2019 18:51:50: 7000000 INFO @ Sat, 24 Aug 2019 18:51:51: 3000000 INFO @ Sat, 24 Aug 2019 18:51:56: 8000000 INFO @ Sat, 24 Aug 2019 18:51:58: 4000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:52:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375062/SRX5375062.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375062/SRX5375062.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375062/SRX5375062.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375062/SRX5375062.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 @ Sat, 24 Aug 2019 18:52:02: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:52:02: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:52:03: 9000000 INFO @ Sat, 24 Aug 2019 18:52:04: 5000000 INFO @ Sat, 24 Aug 2019 18:52:09: 1000000 INFO @ Sat, 24 Aug 2019 18:52:10: 10000000 INFO @ Sat, 24 Aug 2019 18:52:10: 6000000 INFO @ Sat, 24 Aug 2019 18:52:16: 2000000 INFO @ Sat, 24 Aug 2019 18:52:16: 11000000 INFO @ Sat, 24 Aug 2019 18:52:17: 7000000 INFO @ Sat, 24 Aug 2019 18:52:23: 3000000 INFO @ Sat, 24 Aug 2019 18:52:23: 8000000 INFO @ Sat, 24 Aug 2019 18:52:23: 12000000 INFO @ Sat, 24 Aug 2019 18:52:29: 9000000 INFO @ Sat, 24 Aug 2019 18:52:30: 13000000 INFO @ Sat, 24 Aug 2019 18:52:30: 4000000 INFO @ Sat, 24 Aug 2019 18:52:36: 10000000 INFO @ Sat, 24 Aug 2019 18:52:36: 14000000 INFO @ Sat, 24 Aug 2019 18:52:36: 5000000 INFO @ Sat, 24 Aug 2019 18:52:42: 11000000 INFO @ Sat, 24 Aug 2019 18:52:43: 15000000 INFO @ Sat, 24 Aug 2019 18:52:43: 6000000 INFO @ Sat, 24 Aug 2019 18:52:48: 12000000 INFO @ Sat, 24 Aug 2019 18:52:49: 16000000 INFO @ Sat, 24 Aug 2019 18:52:50: 7000000 INFO @ Sat, 24 Aug 2019 18:52:55: 13000000 INFO @ Sat, 24 Aug 2019 18:52:56: 17000000 INFO @ Sat, 24 Aug 2019 18:52:57: 8000000 INFO @ Sat, 24 Aug 2019 18:53:01: 14000000 INFO @ Sat, 24 Aug 2019 18:53:02: 18000000 INFO @ Sat, 24 Aug 2019 18:53:03: 9000000 INFO @ Sat, 24 Aug 2019 18:53:07: 15000000 INFO @ Sat, 24 Aug 2019 18:53:09: 19000000 INFO @ Sat, 24 Aug 2019 18:53:10: 10000000 INFO @ Sat, 24 Aug 2019 18:53:13: 16000000 INFO @ Sat, 24 Aug 2019 18:53:15: 20000000 INFO @ Sat, 24 Aug 2019 18:53:17: 11000000 INFO @ Sat, 24 Aug 2019 18:53:20: 17000000 INFO @ Sat, 24 Aug 2019 18:53:22: 21000000 INFO @ Sat, 24 Aug 2019 18:53:24: 12000000 INFO @ Sat, 24 Aug 2019 18:53:26: 18000000 INFO @ Sat, 24 Aug 2019 18:53:27: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:53:27: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:53:27: #1 total tags in treatment: 21753825 INFO @ Sat, 24 Aug 2019 18:53:27: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:53:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:53:28: #1 tags after filtering in treatment: 21753622 INFO @ Sat, 24 Aug 2019 18:53:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:53:28: #1 finished! INFO @ Sat, 24 Aug 2019 18:53:28: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:53:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:53:30: 13000000 INFO @ Sat, 24 Aug 2019 18:53:32: 19000000 INFO @ Sat, 24 Aug 2019 18:53:34: #2 number of paired peaks: 93777 INFO @ Sat, 24 Aug 2019 18:53:34: start model_add_line... INFO @ Sat, 24 Aug 2019 18:53:35: start X-correlation... INFO @ Sat, 24 Aug 2019 18:53:35: end of X-cor INFO @ Sat, 24 Aug 2019 18:53:35: #2 finished! INFO @ Sat, 24 Aug 2019 18:53:35: #2 predicted fragment length is 179 bps INFO @ Sat, 24 Aug 2019 18:53:35: #2 alternative fragment length(s) may be 179 bps INFO @ Sat, 24 Aug 2019 18:53:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375062/SRX5375062.05_model.r INFO @ Sat, 24 Aug 2019 18:53:35: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:53:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:53:37: 14000000 INFO @ Sat, 24 Aug 2019 18:53:39: 20000000 INFO @ Sat, 24 Aug 2019 18:53:44: 15000000 INFO @ Sat, 24 Aug 2019 18:53:45: 21000000 INFO @ Sat, 24 Aug 2019 18:53:50: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:53:50: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:53:50: #1 total tags in treatment: 21753825 INFO @ Sat, 24 Aug 2019 18:53:50: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:53:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:53:50: 16000000 INFO @ Sat, 24 Aug 2019 18:53:51: #1 tags after filtering in treatment: 21753622 INFO @ Sat, 24 Aug 2019 18:53:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:53:51: #1 finished! INFO @ Sat, 24 Aug 2019 18:53:51: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:53:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:53:57: #2 number of paired peaks: 93777 INFO @ Sat, 24 Aug 2019 18:53:57: start model_add_line... INFO @ Sat, 24 Aug 2019 18:53:57: 17000000 INFO @ Sat, 24 Aug 2019 18:53:57: start X-correlation... INFO @ Sat, 24 Aug 2019 18:53:57: end of X-cor INFO @ Sat, 24 Aug 2019 18:53:57: #2 finished! INFO @ Sat, 24 Aug 2019 18:53:57: #2 predicted fragment length is 179 bps INFO @ Sat, 24 Aug 2019 18:53:57: #2 alternative fragment length(s) may be 179 bps INFO @ Sat, 24 Aug 2019 18:53:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375062/SRX5375062.10_model.r INFO @ Sat, 24 Aug 2019 18:53:57: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:53:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:54:03: 18000000 INFO @ Sat, 24 Aug 2019 18:54:10: 19000000 INFO @ Sat, 24 Aug 2019 18:54:17: 20000000 INFO @ Sat, 24 Aug 2019 18:54:23: 21000000 INFO @ Sat, 24 Aug 2019 18:54:29: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:54:29: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:54:29: #1 total tags in treatment: 21753825 INFO @ Sat, 24 Aug 2019 18:54:29: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:54:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:54:29: #1 tags after filtering in treatment: 21753622 INFO @ Sat, 24 Aug 2019 18:54:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:54:29: #1 finished! INFO @ Sat, 24 Aug 2019 18:54:29: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:54:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:54:35: #2 number of paired peaks: 93777 INFO @ Sat, 24 Aug 2019 18:54:35: start model_add_line... INFO @ Sat, 24 Aug 2019 18:54:36: start X-correlation... INFO @ Sat, 24 Aug 2019 18:54:36: end of X-cor INFO @ Sat, 24 Aug 2019 18:54:36: #2 finished! INFO @ Sat, 24 Aug 2019 18:54:36: #2 predicted fragment length is 179 bps INFO @ Sat, 24 Aug 2019 18:54:36: #2 alternative fragment length(s) may be 179 bps INFO @ Sat, 24 Aug 2019 18:54:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375062/SRX5375062.20_model.r INFO @ Sat, 24 Aug 2019 18:54:36: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:54:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:54:47: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:55:08: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:55:25: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375062/SRX5375062.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:55:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375062/SRX5375062.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:55:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375062/SRX5375062.05_summits.bed INFO @ Sat, 24 Aug 2019 18:55:26: Done! pass1 - making usageList (135 chroms): 12 millis pass2 - checking and writing primary data (46371 records, 4 fields): 64 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:55:44: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375062/SRX5375062.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:55:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375062/SRX5375062.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:55:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375062/SRX5375062.10_summits.bed INFO @ Sat, 24 Aug 2019 18:55:44: Done! pass1 - making usageList (99 chroms): 10 millis pass2 - checking and writing primary data (30112 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:55:46: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:56:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375062/SRX5375062.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:56:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375062/SRX5375062.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:56:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375062/SRX5375062.20_summits.bed INFO @ Sat, 24 Aug 2019 18:56:22: Done! pass1 - making usageList (62 chroms): 7 millis pass2 - checking and writing primary data (13839 records, 4 fields): 23 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。