Job ID = 2001614 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 31,703,216 reads read : 31,703,216 reads written : 31,703,216 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: 00:13:50 31703216 reads; of these: 31703216 (100.00%) were unpaired; of these: 727151 (2.29%) aligned 0 times 23764245 (74.96%) aligned exactly 1 time 7211820 (22.75%) aligned >1 times 97.71% overall alignment rate Time searching: 00:13:53 Overall time: 00:13:53 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] 3049762 / 30976065 = 0.0985 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 06:42:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101937/ERX101937.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101937/ERX101937.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101937/ERX101937.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101937/ERX101937.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 06:42:28: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:42:28: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:42:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101937/ERX101937.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101937/ERX101937.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101937/ERX101937.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101937/ERX101937.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 06:42:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:42:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:42:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101937/ERX101937.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101937/ERX101937.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101937/ERX101937.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101937/ERX101937.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 06:42:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:42:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:42:38: 1000000 INFO @ Fri, 05 Jul 2019 06:42:39: 1000000 INFO @ Fri, 05 Jul 2019 06:42:41: 1000000 INFO @ Fri, 05 Jul 2019 06:42:48: 2000000 INFO @ Fri, 05 Jul 2019 06:42:48: 2000000 INFO @ Fri, 05 Jul 2019 06:42:50: 2000000 INFO @ Fri, 05 Jul 2019 06:42:57: 3000000 INFO @ Fri, 05 Jul 2019 06:42:58: 3000000 INFO @ Fri, 05 Jul 2019 06:42:59: 3000000 INFO @ Fri, 05 Jul 2019 06:43:06: 4000000 INFO @ Fri, 05 Jul 2019 06:43:07: 4000000 INFO @ Fri, 05 Jul 2019 06:43:09: 4000000 INFO @ Fri, 05 Jul 2019 06:43:15: 5000000 INFO @ Fri, 05 Jul 2019 06:43:16: 5000000 INFO @ Fri, 05 Jul 2019 06:43:18: 5000000 INFO @ Fri, 05 Jul 2019 06:43:24: 6000000 INFO @ Fri, 05 Jul 2019 06:43:25: 6000000 INFO @ Fri, 05 Jul 2019 06:43:28: 6000000 INFO @ Fri, 05 Jul 2019 06:43:33: 7000000 INFO @ Fri, 05 Jul 2019 06:43:33: 7000000 INFO @ Fri, 05 Jul 2019 06:43:37: 7000000 INFO @ Fri, 05 Jul 2019 06:43:42: 8000000 INFO @ Fri, 05 Jul 2019 06:43:42: 8000000 INFO @ Fri, 05 Jul 2019 06:43:47: 8000000 INFO @ Fri, 05 Jul 2019 06:43:51: 9000000 INFO @ Fri, 05 Jul 2019 06:43:51: 9000000 INFO @ Fri, 05 Jul 2019 06:43:56: 9000000 INFO @ Fri, 05 Jul 2019 06:43:59: 10000000 INFO @ Fri, 05 Jul 2019 06:44:00: 10000000 INFO @ Fri, 05 Jul 2019 06:44:05: 10000000 INFO @ Fri, 05 Jul 2019 06:44:08: 11000000 INFO @ Fri, 05 Jul 2019 06:44:09: 11000000 INFO @ Fri, 05 Jul 2019 06:44:15: 11000000 INFO @ Fri, 05 Jul 2019 06:44:17: 12000000 INFO @ Fri, 05 Jul 2019 06:44:19: 12000000 INFO @ Fri, 05 Jul 2019 06:44:24: 12000000 INFO @ Fri, 05 Jul 2019 06:44:26: 13000000 INFO @ Fri, 05 Jul 2019 06:44:28: 13000000 INFO @ Fri, 05 Jul 2019 06:44:34: 13000000 INFO @ Fri, 05 Jul 2019 06:44:35: 14000000 INFO @ Fri, 05 Jul 2019 06:44:37: 14000000 INFO @ Fri, 05 Jul 2019 06:44:43: 14000000 INFO @ Fri, 05 Jul 2019 06:44:44: 15000000 INFO @ Fri, 05 Jul 2019 06:44:46: 15000000 INFO @ Fri, 05 Jul 2019 06:44:52: 15000000 INFO @ Fri, 05 Jul 2019 06:44:52: 16000000 INFO @ Fri, 05 Jul 2019 06:44:56: 16000000 INFO @ Fri, 05 Jul 2019 06:45:01: 17000000 INFO @ Fri, 05 Jul 2019 06:45:01: 16000000 INFO @ Fri, 05 Jul 2019 06:45:05: 17000000 INFO @ Fri, 05 Jul 2019 06:45:10: 17000000 INFO @ Fri, 05 Jul 2019 06:45:11: 18000000 INFO @ Fri, 05 Jul 2019 06:45:15: 18000000 INFO @ Fri, 05 Jul 2019 06:45:19: 18000000 INFO @ Fri, 05 Jul 2019 06:45:20: 19000000 INFO @ Fri, 05 Jul 2019 06:45:23: 19000000 INFO @ Fri, 05 Jul 2019 06:45:28: 20000000 INFO @ Fri, 05 Jul 2019 06:45:29: 19000000 INFO @ Fri, 05 Jul 2019 06:45:32: 20000000 INFO @ Fri, 05 Jul 2019 06:45:38: 21000000 INFO @ Fri, 05 Jul 2019 06:45:38: 20000000 INFO @ Fri, 05 Jul 2019 06:45:41: 21000000 INFO @ Fri, 05 Jul 2019 06:45:46: 22000000 INFO @ Fri, 05 Jul 2019 06:45:47: 21000000 INFO @ Fri, 05 Jul 2019 06:45:49: 22000000 INFO @ Fri, 05 Jul 2019 06:45:55: 23000000 INFO @ Fri, 05 Jul 2019 06:45:56: 22000000 INFO @ Fri, 05 Jul 2019 06:45:57: 23000000 INFO @ Fri, 05 Jul 2019 06:46:04: 24000000 INFO @ Fri, 05 Jul 2019 06:46:05: 23000000 INFO @ Fri, 05 Jul 2019 06:46:06: 24000000 INFO @ Fri, 05 Jul 2019 06:46:13: 24000000 INFO @ Fri, 05 Jul 2019 06:46:14: 25000000 INFO @ Fri, 05 Jul 2019 06:46:14: 25000000 INFO @ Fri, 05 Jul 2019 06:46:23: 25000000 INFO @ Fri, 05 Jul 2019 06:46:23: 26000000 INFO @ Fri, 05 Jul 2019 06:46:23: 26000000 INFO @ Fri, 05 Jul 2019 06:46:32: 26000000 INFO @ Fri, 05 Jul 2019 06:46:32: 27000000 INFO @ Fri, 05 Jul 2019 06:46:32: 27000000 INFO @ Fri, 05 Jul 2019 06:46:40: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 06:46:40: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 06:46:40: #1 total tags in treatment: 27926303 INFO @ Fri, 05 Jul 2019 06:46:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:46:40: #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 06:46:41: 27000000 INFO @ Fri, 05 Jul 2019 06:46:41: #1 tags after filtering in treatment: 27926137 INFO @ Fri, 05 Jul 2019 06:46:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:46:41: #1 finished! INFO @ Fri, 05 Jul 2019 06:46:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:46:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:46:41: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 06:46:41: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 06:46:41: #1 total tags in treatment: 27926303 INFO @ Fri, 05 Jul 2019 06:46:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:46:41: #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 06:46:42: #1 tags after filtering in treatment: 27926137 INFO @ Fri, 05 Jul 2019 06:46:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:46:42: #1 finished! INFO @ Fri, 05 Jul 2019 06:46:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:46:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:46:48: #2 number of paired peaks: 76718 INFO @ Fri, 05 Jul 2019 06:46:48: start model_add_line... INFO @ Fri, 05 Jul 2019 06:46:48: start X-correlation... INFO @ Fri, 05 Jul 2019 06:46:48: end of X-cor INFO @ Fri, 05 Jul 2019 06:46:48: #2 finished! INFO @ Fri, 05 Jul 2019 06:46:48: #2 predicted fragment length is 133 bps INFO @ Fri, 05 Jul 2019 06:46:48: #2 alternative fragment length(s) may be 4,133,506 bps INFO @ Fri, 05 Jul 2019 06:46:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101937/ERX101937.05_model.r INFO @ Fri, 05 Jul 2019 06:46:48: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:46:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:46:49: #2 number of paired peaks: 76718 INFO @ Fri, 05 Jul 2019 06:46:49: start model_add_line... INFO @ Fri, 05 Jul 2019 06:46:49: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 06:46:49: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 06:46:49: #1 total tags in treatment: 27926303 INFO @ Fri, 05 Jul 2019 06:46:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:46:49: #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 06:46:49: start X-correlation... INFO @ Fri, 05 Jul 2019 06:46:49: end of X-cor INFO @ Fri, 05 Jul 2019 06:46:49: #2 finished! INFO @ Fri, 05 Jul 2019 06:46:49: #2 predicted fragment length is 133 bps INFO @ Fri, 05 Jul 2019 06:46:49: #2 alternative fragment length(s) may be 4,133,506 bps INFO @ Fri, 05 Jul 2019 06:46:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101937/ERX101937.10_model.r INFO @ Fri, 05 Jul 2019 06:46:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:46:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:46:50: #1 tags after filtering in treatment: 27926137 INFO @ Fri, 05 Jul 2019 06:46:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:46:50: #1 finished! INFO @ Fri, 05 Jul 2019 06:46:50: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:46:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:46:56: #2 number of paired peaks: 76718 INFO @ Fri, 05 Jul 2019 06:46:56: start model_add_line... INFO @ Fri, 05 Jul 2019 06:46:57: start X-correlation... INFO @ Fri, 05 Jul 2019 06:46:57: end of X-cor INFO @ Fri, 05 Jul 2019 06:46:57: #2 finished! INFO @ Fri, 05 Jul 2019 06:46:57: #2 predicted fragment length is 133 bps INFO @ Fri, 05 Jul 2019 06:46:57: #2 alternative fragment length(s) may be 4,133,506 bps INFO @ Fri, 05 Jul 2019 06:46:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101937/ERX101937.20_model.r INFO @ Fri, 05 Jul 2019 06:46:57: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:46:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:48:27: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:48:29: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:48:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:49:21: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101937/ERX101937.05_peaks.xls INFO @ Fri, 05 Jul 2019 06:49:21: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101937/ERX101937.10_peaks.xls INFO @ Fri, 05 Jul 2019 06:49:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101937/ERX101937.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:49:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101937/ERX101937.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:49:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101937/ERX101937.10_summits.bed INFO @ Fri, 05 Jul 2019 06:49:21: Done! INFO @ Fri, 05 Jul 2019 06:49:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101937/ERX101937.05_summits.bed INFO @ Fri, 05 Jul 2019 06:49:21: Done! pass1 - making usageList (52 chroms): 3 millis pass2 - checking and writing primary data (3485 records, 4 fields): 11 millis CompletedMACS2peakCalling pass1 - making usageList (97 chroms): 4 millis pass2 - checking and writing primary data (11783 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 06:49:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101937/ERX101937.20_peaks.xls INFO @ Fri, 05 Jul 2019 06:49:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101937/ERX101937.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:49:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101937/ERX101937.20_summits.bed INFO @ Fri, 05 Jul 2019 06:49:31: Done! pass1 - making usageList (32 chroms): 2 millis pass2 - checking and writing primary data (520 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。