Job ID = 2001575 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,504,098 reads read : 27,504,098 reads written : 27,504,098 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: 00:10:56 27504098 reads; of these: 27504098 (100.00%) were unpaired; of these: 701739 (2.55%) aligned 0 times 20490094 (74.50%) aligned exactly 1 time 6312265 (22.95%) aligned >1 times 97.45% overall alignment rate Time searching: 00:10:59 Overall time: 00:10:59 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] 1860386 / 26802359 = 0.0694 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 05:44:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101918/ERX101918.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101918/ERX101918.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101918/ERX101918.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101918/ERX101918.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 05:44:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:44:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:44:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101918/ERX101918.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101918/ERX101918.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101918/ERX101918.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101918/ERX101918.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 05:44:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:44:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:44:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101918/ERX101918.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101918/ERX101918.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101918/ERX101918.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101918/ERX101918.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 05:44:43: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:44:43: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:44:50: 1000000 INFO @ Fri, 05 Jul 2019 05:44:51: 1000000 INFO @ Fri, 05 Jul 2019 05:44:52: 1000000 INFO @ Fri, 05 Jul 2019 05:44:57: 2000000 INFO @ Fri, 05 Jul 2019 05:44:59: 2000000 INFO @ Fri, 05 Jul 2019 05:45:01: 2000000 INFO @ Fri, 05 Jul 2019 05:45:04: 3000000 INFO @ Fri, 05 Jul 2019 05:45:08: 3000000 INFO @ Fri, 05 Jul 2019 05:45:10: 3000000 INFO @ Fri, 05 Jul 2019 05:45:12: 4000000 INFO @ Fri, 05 Jul 2019 05:45:16: 4000000 INFO @ Fri, 05 Jul 2019 05:45:19: 4000000 INFO @ Fri, 05 Jul 2019 05:45:19: 5000000 INFO @ Fri, 05 Jul 2019 05:45:25: 5000000 INFO @ Fri, 05 Jul 2019 05:45:27: 6000000 INFO @ Fri, 05 Jul 2019 05:45:28: 5000000 INFO @ Fri, 05 Jul 2019 05:45:33: 7000000 INFO @ Fri, 05 Jul 2019 05:45:34: 6000000 INFO @ Fri, 05 Jul 2019 05:45:36: 6000000 INFO @ Fri, 05 Jul 2019 05:45:40: 8000000 INFO @ Fri, 05 Jul 2019 05:45:42: 7000000 INFO @ Fri, 05 Jul 2019 05:45:45: 7000000 INFO @ Fri, 05 Jul 2019 05:45:48: 9000000 INFO @ Fri, 05 Jul 2019 05:45:51: 8000000 INFO @ Fri, 05 Jul 2019 05:45:54: 8000000 INFO @ Fri, 05 Jul 2019 05:45:55: 10000000 INFO @ Fri, 05 Jul 2019 05:46:00: 9000000 INFO @ Fri, 05 Jul 2019 05:46:01: 11000000 INFO @ Fri, 05 Jul 2019 05:46:03: 9000000 INFO @ Fri, 05 Jul 2019 05:46:08: 10000000 INFO @ Fri, 05 Jul 2019 05:46:08: 12000000 INFO @ Fri, 05 Jul 2019 05:46:12: 10000000 INFO @ Fri, 05 Jul 2019 05:46:15: 13000000 INFO @ Fri, 05 Jul 2019 05:46:17: 11000000 INFO @ Fri, 05 Jul 2019 05:46:21: 11000000 INFO @ Fri, 05 Jul 2019 05:46:22: 14000000 INFO @ Fri, 05 Jul 2019 05:46:25: 12000000 INFO @ Fri, 05 Jul 2019 05:46:29: 15000000 INFO @ Fri, 05 Jul 2019 05:46:30: 12000000 INFO @ Fri, 05 Jul 2019 05:46:33: 13000000 INFO @ Fri, 05 Jul 2019 05:46:36: 16000000 INFO @ Fri, 05 Jul 2019 05:46:39: 13000000 INFO @ Fri, 05 Jul 2019 05:46:42: 14000000 INFO @ Fri, 05 Jul 2019 05:46:43: 17000000 INFO @ Fri, 05 Jul 2019 05:46:47: 14000000 INFO @ Fri, 05 Jul 2019 05:46:50: 15000000 INFO @ Fri, 05 Jul 2019 05:46:51: 18000000 INFO @ Fri, 05 Jul 2019 05:46:56: 15000000 INFO @ Fri, 05 Jul 2019 05:46:58: 19000000 INFO @ Fri, 05 Jul 2019 05:46:59: 16000000 INFO @ Fri, 05 Jul 2019 05:47:04: 16000000 INFO @ Fri, 05 Jul 2019 05:47:05: 20000000 INFO @ Fri, 05 Jul 2019 05:47:07: 17000000 INFO @ Fri, 05 Jul 2019 05:47:12: 21000000 INFO @ Fri, 05 Jul 2019 05:47:13: 17000000 INFO @ Fri, 05 Jul 2019 05:47:15: 18000000 INFO @ Fri, 05 Jul 2019 05:47:20: 22000000 INFO @ Fri, 05 Jul 2019 05:47:21: 18000000 INFO @ Fri, 05 Jul 2019 05:47:24: 19000000 INFO @ Fri, 05 Jul 2019 05:47:27: 23000000 INFO @ Fri, 05 Jul 2019 05:47:30: 19000000 INFO @ Fri, 05 Jul 2019 05:47:33: 20000000 INFO @ Fri, 05 Jul 2019 05:47:34: 24000000 INFO @ Fri, 05 Jul 2019 05:47:39: 20000000 INFO @ Fri, 05 Jul 2019 05:47:41: 21000000 INFO @ Fri, 05 Jul 2019 05:47:42: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:47:42: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:47:42: #1 total tags in treatment: 24941973 INFO @ Fri, 05 Jul 2019 05:47:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:47:42: #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 05:47:42: #1 tags after filtering in treatment: 24941825 INFO @ Fri, 05 Jul 2019 05:47:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:47:42: #1 finished! INFO @ Fri, 05 Jul 2019 05:47:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:47:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:47:48: #2 number of paired peaks: 63669 INFO @ Fri, 05 Jul 2019 05:47:48: start model_add_line... INFO @ Fri, 05 Jul 2019 05:47:48: 21000000 INFO @ Fri, 05 Jul 2019 05:47:48: start X-correlation... INFO @ Fri, 05 Jul 2019 05:47:48: end of X-cor INFO @ Fri, 05 Jul 2019 05:47:48: #2 finished! INFO @ Fri, 05 Jul 2019 05:47:48: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 05:47:48: #2 alternative fragment length(s) may be 135,299,509 bps INFO @ Fri, 05 Jul 2019 05:47:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101918/ERX101918.05_model.r INFO @ Fri, 05 Jul 2019 05:47:48: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:47:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:47:49: 22000000 INFO @ Fri, 05 Jul 2019 05:47:56: 22000000 INFO @ Fri, 05 Jul 2019 05:47:57: 23000000 INFO @ Fri, 05 Jul 2019 05:48:05: 23000000 INFO @ Fri, 05 Jul 2019 05:48:05: 24000000 INFO @ Fri, 05 Jul 2019 05:48:13: 24000000 INFO @ Fri, 05 Jul 2019 05:48:14: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:48:14: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:48:14: #1 total tags in treatment: 24941973 INFO @ Fri, 05 Jul 2019 05:48:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:48:14: #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 05:48:15: #1 tags after filtering in treatment: 24941825 INFO @ Fri, 05 Jul 2019 05:48:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:48:15: #1 finished! INFO @ Fri, 05 Jul 2019 05:48:15: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:48:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:48:20: #2 number of paired peaks: 63669 INFO @ Fri, 05 Jul 2019 05:48:20: start model_add_line... INFO @ Fri, 05 Jul 2019 05:48:21: start X-correlation... INFO @ Fri, 05 Jul 2019 05:48:21: end of X-cor INFO @ Fri, 05 Jul 2019 05:48:21: #2 finished! INFO @ Fri, 05 Jul 2019 05:48:21: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 05:48:21: #2 alternative fragment length(s) may be 135,299,509 bps INFO @ Fri, 05 Jul 2019 05:48:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101918/ERX101918.10_model.r INFO @ Fri, 05 Jul 2019 05:48:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:48:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:48:22: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:48:22: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:48:22: #1 total tags in treatment: 24941973 INFO @ Fri, 05 Jul 2019 05:48:22: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:48:22: #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 05:48:23: #1 tags after filtering in treatment: 24941825 INFO @ Fri, 05 Jul 2019 05:48:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:48:23: #1 finished! INFO @ Fri, 05 Jul 2019 05:48:23: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:48:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:48:28: #2 number of paired peaks: 63669 INFO @ Fri, 05 Jul 2019 05:48:28: start model_add_line... INFO @ Fri, 05 Jul 2019 05:48:29: start X-correlation... INFO @ Fri, 05 Jul 2019 05:48:29: end of X-cor INFO @ Fri, 05 Jul 2019 05:48:29: #2 finished! INFO @ Fri, 05 Jul 2019 05:48:29: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 05:48:29: #2 alternative fragment length(s) may be 135,299,509 bps INFO @ Fri, 05 Jul 2019 05:48:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101918/ERX101918.20_model.r INFO @ Fri, 05 Jul 2019 05:48:29: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:48:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:49:12: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:49:46: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:49:50: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:49:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101918/ERX101918.05_peaks.xls INFO @ Fri, 05 Jul 2019 05:49:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101918/ERX101918.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:49:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101918/ERX101918.05_summits.bed INFO @ Fri, 05 Jul 2019 05:49:55: Done! pass1 - making usageList (66 chroms): 3 millis pass2 - checking and writing primary data (4660 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:50:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101918/ERX101918.20_peaks.xls INFO @ Fri, 05 Jul 2019 05:50:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101918/ERX101918.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:50:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101918/ERX101918.20_summits.bed INFO @ Fri, 05 Jul 2019 05:50:33: Done! pass1 - making usageList (26 chroms): 1 millis pass2 - checking and writing primary data (105 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:50:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101918/ERX101918.10_peaks.xls INFO @ Fri, 05 Jul 2019 05:50:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101918/ERX101918.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:50:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101918/ERX101918.10_summits.bed INFO @ Fri, 05 Jul 2019 05:50:33: Done! pass1 - making usageList (41 chroms): 1 millis pass2 - checking and writing primary data (1033 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。