Job ID = 2003698 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 76,965,850 reads read : 153,931,700 reads written : 76,965,850 reads 0-length : 76,965,850 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: 00:00:00 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:22:53 76965850 reads; of these: 76965850 (100.00%) were unpaired; of these: 3931465 (5.11%) aligned 0 times 55628482 (72.28%) aligned exactly 1 time 17405903 (22.62%) aligned >1 times 94.89% overall alignment rate Time searching: 01:22:56 Overall time: 01:22:56 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 32 files... [bam_rmdupse_core] 46174361 / 73034385 = 0.6322 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 15:49:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4370838/SRX4370838.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4370838/SRX4370838.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4370838/SRX4370838.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4370838/SRX4370838.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 15:49:39: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:49:39: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:49:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4370838/SRX4370838.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4370838/SRX4370838.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4370838/SRX4370838.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4370838/SRX4370838.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 15:49:40: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:49:40: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:49:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4370838/SRX4370838.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4370838/SRX4370838.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4370838/SRX4370838.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4370838/SRX4370838.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 15:49:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:49:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:49:50: 1000000 INFO @ Fri, 05 Jul 2019 15:49:52: 1000000 INFO @ Fri, 05 Jul 2019 15:49:53: 1000000 INFO @ Fri, 05 Jul 2019 15:50:00: 2000000 INFO @ Fri, 05 Jul 2019 15:50:03: 2000000 INFO @ Fri, 05 Jul 2019 15:50:06: 2000000 INFO @ Fri, 05 Jul 2019 15:50:09: 3000000 INFO @ Fri, 05 Jul 2019 15:50:14: 3000000 INFO @ Fri, 05 Jul 2019 15:50:19: 4000000 INFO @ Fri, 05 Jul 2019 15:50:19: 3000000 INFO @ Fri, 05 Jul 2019 15:50:24: 4000000 INFO @ Fri, 05 Jul 2019 15:50:28: 5000000 INFO @ Fri, 05 Jul 2019 15:50:32: 4000000 INFO @ Fri, 05 Jul 2019 15:50:34: 5000000 INFO @ Fri, 05 Jul 2019 15:50:38: 6000000 INFO @ Fri, 05 Jul 2019 15:50:45: 6000000 INFO @ Fri, 05 Jul 2019 15:50:46: 5000000 INFO @ Fri, 05 Jul 2019 15:50:47: 7000000 INFO @ Fri, 05 Jul 2019 15:50:55: 7000000 INFO @ Fri, 05 Jul 2019 15:50:56: 8000000 INFO @ Fri, 05 Jul 2019 15:50:59: 6000000 INFO @ Fri, 05 Jul 2019 15:51:06: 9000000 INFO @ Fri, 05 Jul 2019 15:51:06: 8000000 INFO @ Fri, 05 Jul 2019 15:51:12: 7000000 INFO @ Fri, 05 Jul 2019 15:51:15: 10000000 INFO @ Fri, 05 Jul 2019 15:51:16: 9000000 INFO @ Fri, 05 Jul 2019 15:51:24: 11000000 INFO @ Fri, 05 Jul 2019 15:51:25: 8000000 INFO @ Fri, 05 Jul 2019 15:51:27: 10000000 INFO @ Fri, 05 Jul 2019 15:51:33: 12000000 INFO @ Fri, 05 Jul 2019 15:51:37: 11000000 INFO @ Fri, 05 Jul 2019 15:51:39: 9000000 INFO @ Fri, 05 Jul 2019 15:51:43: 13000000 INFO @ Fri, 05 Jul 2019 15:51:48: 12000000 INFO @ Fri, 05 Jul 2019 15:51:52: 10000000 INFO @ Fri, 05 Jul 2019 15:51:52: 14000000 INFO @ Fri, 05 Jul 2019 15:51:58: 13000000 INFO @ Fri, 05 Jul 2019 15:52:01: 15000000 INFO @ Fri, 05 Jul 2019 15:52:05: 11000000 INFO @ Fri, 05 Jul 2019 15:52:09: 14000000 INFO @ Fri, 05 Jul 2019 15:52:11: 16000000 INFO @ Fri, 05 Jul 2019 15:52:18: 12000000 INFO @ Fri, 05 Jul 2019 15:52:19: 15000000 INFO @ Fri, 05 Jul 2019 15:52:20: 17000000 INFO @ Fri, 05 Jul 2019 15:52:29: 18000000 INFO @ Fri, 05 Jul 2019 15:52:30: 16000000 INFO @ Fri, 05 Jul 2019 15:52:31: 13000000 INFO @ Fri, 05 Jul 2019 15:52:38: 19000000 INFO @ Fri, 05 Jul 2019 15:52:40: 17000000 INFO @ Fri, 05 Jul 2019 15:52:45: 14000000 INFO @ Fri, 05 Jul 2019 15:52:48: 20000000 INFO @ Fri, 05 Jul 2019 15:52:50: 18000000 INFO @ Fri, 05 Jul 2019 15:52:57: 21000000 INFO @ Fri, 05 Jul 2019 15:52:58: 15000000 INFO @ Fri, 05 Jul 2019 15:53:00: 19000000 INFO @ Fri, 05 Jul 2019 15:53:06: 22000000 INFO @ Fri, 05 Jul 2019 15:53:11: 20000000 INFO @ Fri, 05 Jul 2019 15:53:11: 16000000 INFO @ Fri, 05 Jul 2019 15:53:16: 23000000 INFO @ Fri, 05 Jul 2019 15:53:21: 21000000 INFO @ Fri, 05 Jul 2019 15:53:24: 17000000 INFO @ Fri, 05 Jul 2019 15:53:25: 24000000 INFO @ Fri, 05 Jul 2019 15:53:32: 22000000 INFO @ Fri, 05 Jul 2019 15:53:35: 25000000 INFO @ Fri, 05 Jul 2019 15:53:37: 18000000 INFO @ Fri, 05 Jul 2019 15:53:42: 23000000 INFO @ Fri, 05 Jul 2019 15:53:44: 26000000 INFO @ Fri, 05 Jul 2019 15:53:50: 19000000 INFO @ Fri, 05 Jul 2019 15:53:52: 24000000 INFO @ Fri, 05 Jul 2019 15:53:53: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:53:53: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:53:53: #1 total tags in treatment: 26860024 INFO @ Fri, 05 Jul 2019 15:53:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:53:53: #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 15:53:54: #1 tags after filtering in treatment: 26859945 INFO @ Fri, 05 Jul 2019 15:53:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:53:54: #1 finished! INFO @ Fri, 05 Jul 2019 15:53:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:53:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:53:58: #2 number of paired peaks: 23400 INFO @ Fri, 05 Jul 2019 15:53:58: start model_add_line... INFO @ Fri, 05 Jul 2019 15:53:58: start X-correlation... INFO @ Fri, 05 Jul 2019 15:53:58: end of X-cor INFO @ Fri, 05 Jul 2019 15:53:58: #2 finished! INFO @ Fri, 05 Jul 2019 15:53:58: #2 predicted fragment length is 156 bps INFO @ Fri, 05 Jul 2019 15:53:58: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 05 Jul 2019 15:53:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4370838/SRX4370838.10_model.r INFO @ Fri, 05 Jul 2019 15:53:58: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:53:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:54:03: 20000000 INFO @ Fri, 05 Jul 2019 15:54:03: 25000000 INFO @ Fri, 05 Jul 2019 15:54:13: 26000000 INFO @ Fri, 05 Jul 2019 15:54:16: 21000000 INFO @ Fri, 05 Jul 2019 15:54:22: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:54:22: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:54:22: #1 total tags in treatment: 26860024 INFO @ Fri, 05 Jul 2019 15:54:22: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:54:22: #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 15:54:23: #1 tags after filtering in treatment: 26859945 INFO @ Fri, 05 Jul 2019 15:54:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:54:23: #1 finished! INFO @ Fri, 05 Jul 2019 15:54:23: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:54:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:54:27: #2 number of paired peaks: 23400 INFO @ Fri, 05 Jul 2019 15:54:27: start model_add_line... INFO @ Fri, 05 Jul 2019 15:54:27: start X-correlation... INFO @ Fri, 05 Jul 2019 15:54:27: end of X-cor INFO @ Fri, 05 Jul 2019 15:54:27: #2 finished! INFO @ Fri, 05 Jul 2019 15:54:27: #2 predicted fragment length is 156 bps INFO @ Fri, 05 Jul 2019 15:54:27: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 05 Jul 2019 15:54:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4370838/SRX4370838.20_model.r INFO @ Fri, 05 Jul 2019 15:54:27: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:54:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:54:28: 22000000 INFO @ Fri, 05 Jul 2019 15:54:41: 23000000 INFO @ Fri, 05 Jul 2019 15:54:54: 24000000 INFO @ Fri, 05 Jul 2019 15:55:06: 25000000 INFO @ Fri, 05 Jul 2019 15:55:20: 26000000 INFO @ Fri, 05 Jul 2019 15:55:26: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:55:30: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:55:32: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:55:32: #1 total tags in treatment: 26860024 INFO @ Fri, 05 Jul 2019 15:55:32: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:55:32: #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 15:55:33: #1 tags after filtering in treatment: 26859945 INFO @ Fri, 05 Jul 2019 15:55:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:55:33: #1 finished! INFO @ Fri, 05 Jul 2019 15:55:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:55:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:55:37: #2 number of paired peaks: 23400 INFO @ Fri, 05 Jul 2019 15:55:38: start model_add_line... INFO @ Fri, 05 Jul 2019 15:55:38: start X-correlation... INFO @ Fri, 05 Jul 2019 15:55:39: end of X-cor INFO @ Fri, 05 Jul 2019 15:55:39: #2 finished! INFO @ Fri, 05 Jul 2019 15:55:39: #2 predicted fragment length is 156 bps INFO @ Fri, 05 Jul 2019 15:55:39: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 05 Jul 2019 15:55:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4370838/SRX4370838.05_model.r INFO @ Fri, 05 Jul 2019 15:55:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:55:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:55:55: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:56:11: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4370838/SRX4370838.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:56:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4370838/SRX4370838.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:56:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4370838/SRX4370838.10_summits.bed INFO @ Fri, 05 Jul 2019 15:56:13: Done! pass1 - making usageList (86 chroms): 4 millis pass2 - checking and writing primary data (4561 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 15:56:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4370838/SRX4370838.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:56:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4370838/SRX4370838.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:56:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4370838/SRX4370838.20_summits.bed INFO @ Fri, 05 Jul 2019 15:56:40: Done! pass1 - making usageList (47 chroms): 2 millis pass2 - checking and writing primary data (1107 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 15:57:08: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:57:53: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4370838/SRX4370838.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:57:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4370838/SRX4370838.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:57:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4370838/SRX4370838.05_summits.bed INFO @ Fri, 05 Jul 2019 15:57:53: Done! pass1 - making usageList (144 chroms): 7 millis pass2 - checking and writing primary data (18223 records, 4 fields): 31 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。