Job ID = 11632676 sra ファイルのダウンロード中... Completed: 875614K bytes transferred in 20 seconds (358335K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Read 50386893 spots for /home/okishinya/chipatlas/results/rn6/SRX3360114/SRR6253220.sra Written 50386893 spots for /home/okishinya/chipatlas/results/rn6/SRX3360114/SRR6253220.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:00:01 Multiseed full-index search: 00:30:22 50386893 reads; of these: 50386893 (100.00%) were unpaired; of these: 9400435 (18.66%) aligned 0 times 30325344 (60.18%) aligned exactly 1 time 10661114 (21.16%) aligned >1 times 81.34% overall alignment rate Time searching: 00:30:26 Overall time: 00:30:26 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 20 files... [bam_rmdupse_core] 5320698 / 40986458 = 0.1298 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, 15 Feb 2019 06:12:46: # Command line: callpeak -t SRX3360114.bam -f BAM -g 2.15e9 -n SRX3360114.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3360114.20 # format = BAM # ChIP-seq file = ['SRX3360114.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, 15 Feb 2019 06:12:46: # Command line: callpeak -t SRX3360114.bam -f BAM -g 2.15e9 -n SRX3360114.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3360114.10 # format = BAM # ChIP-seq file = ['SRX3360114.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, 15 Feb 2019 06:12:46: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:12:46: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:12:46: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:12:46: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:12:46: # Command line: callpeak -t SRX3360114.bam -f BAM -g 2.15e9 -n SRX3360114.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3360114.05 # format = BAM # ChIP-seq file = ['SRX3360114.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, 15 Feb 2019 06:12:46: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:12:46: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:12:53: 1000000 INFO @ Fri, 15 Feb 2019 06:12:53: 1000000 INFO @ Fri, 15 Feb 2019 06:12:53: 1000000 INFO @ Fri, 15 Feb 2019 06:13:00: 2000000 INFO @ Fri, 15 Feb 2019 06:13:00: 2000000 INFO @ Fri, 15 Feb 2019 06:13:01: 2000000 INFO @ Fri, 15 Feb 2019 06:13:07: 3000000 INFO @ Fri, 15 Feb 2019 06:13:07: 3000000 INFO @ Fri, 15 Feb 2019 06:13:08: 3000000 INFO @ Fri, 15 Feb 2019 06:13:13: 4000000 INFO @ Fri, 15 Feb 2019 06:13:13: 4000000 INFO @ Fri, 15 Feb 2019 06:13:14: 4000000 INFO @ Fri, 15 Feb 2019 06:13:20: 5000000 INFO @ Fri, 15 Feb 2019 06:13:20: 5000000 INFO @ Fri, 15 Feb 2019 06:13:21: 5000000 INFO @ Fri, 15 Feb 2019 06:13:27: 6000000 INFO @ Fri, 15 Feb 2019 06:13:27: 6000000 INFO @ Fri, 15 Feb 2019 06:13:28: 6000000 INFO @ Fri, 15 Feb 2019 06:13:34: 7000000 INFO @ Fri, 15 Feb 2019 06:13:34: 7000000 INFO @ Fri, 15 Feb 2019 06:13:35: 7000000 INFO @ Fri, 15 Feb 2019 06:13:41: 8000000 INFO @ Fri, 15 Feb 2019 06:13:41: 8000000 INFO @ Fri, 15 Feb 2019 06:13:42: 8000000 INFO @ Fri, 15 Feb 2019 06:13:48: 9000000 INFO @ Fri, 15 Feb 2019 06:13:48: 9000000 INFO @ Fri, 15 Feb 2019 06:13:49: 9000000 INFO @ Fri, 15 Feb 2019 06:13:55: 10000000 INFO @ Fri, 15 Feb 2019 06:13:55: 10000000 INFO @ Fri, 15 Feb 2019 06:13:56: 10000000 INFO @ Fri, 15 Feb 2019 06:14:02: 11000000 INFO @ Fri, 15 Feb 2019 06:14:02: 11000000 INFO @ Fri, 15 Feb 2019 06:14:03: 11000000 INFO @ Fri, 15 Feb 2019 06:14:09: 12000000 INFO @ Fri, 15 Feb 2019 06:14:09: 12000000 INFO @ Fri, 15 Feb 2019 06:14:10: 12000000 INFO @ Fri, 15 Feb 2019 06:14:16: 13000000 INFO @ Fri, 15 Feb 2019 06:14:16: 13000000 INFO @ Fri, 15 Feb 2019 06:14:16: 13000000 INFO @ Fri, 15 Feb 2019 06:14:23: 14000000 INFO @ Fri, 15 Feb 2019 06:14:23: 14000000 INFO @ Fri, 15 Feb 2019 06:14:23: 14000000 INFO @ Fri, 15 Feb 2019 06:14:29: 15000000 INFO @ Fri, 15 Feb 2019 06:14:29: 15000000 INFO @ Fri, 15 Feb 2019 06:14:31: 15000000 INFO @ Fri, 15 Feb 2019 06:14:37: 16000000 INFO @ Fri, 15 Feb 2019 06:14:37: 16000000 INFO @ Fri, 15 Feb 2019 06:14:38: 16000000 INFO @ Fri, 15 Feb 2019 06:14:43: 17000000 INFO @ Fri, 15 Feb 2019 06:14:43: 17000000 INFO @ Fri, 15 Feb 2019 06:14:46: 17000000 INFO @ Fri, 15 Feb 2019 06:14:50: 18000000 INFO @ Fri, 15 Feb 2019 06:14:50: 18000000 INFO @ Fri, 15 Feb 2019 06:14:54: 18000000 INFO @ Fri, 15 Feb 2019 06:14:57: 19000000 INFO @ Fri, 15 Feb 2019 06:14:57: 19000000 INFO @ Fri, 15 Feb 2019 06:15:01: 19000000 INFO @ Fri, 15 Feb 2019 06:15:04: 20000000 INFO @ Fri, 15 Feb 2019 06:15:04: 20000000 INFO @ Fri, 15 Feb 2019 06:15:08: 20000000 INFO @ Fri, 15 Feb 2019 06:15:11: 21000000 INFO @ Fri, 15 Feb 2019 06:15:11: 21000000 INFO @ Fri, 15 Feb 2019 06:15:14: 21000000 INFO @ Fri, 15 Feb 2019 06:15:18: 22000000 INFO @ Fri, 15 Feb 2019 06:15:18: 22000000 INFO @ Fri, 15 Feb 2019 06:15:21: 22000000 INFO @ Fri, 15 Feb 2019 06:15:25: 23000000 INFO @ Fri, 15 Feb 2019 06:15:25: 23000000 INFO @ Fri, 15 Feb 2019 06:15:28: 23000000 INFO @ Fri, 15 Feb 2019 06:15:32: 24000000 INFO @ Fri, 15 Feb 2019 06:15:32: 24000000 INFO @ Fri, 15 Feb 2019 06:15:35: 24000000 INFO @ Fri, 15 Feb 2019 06:15:39: 25000000 INFO @ Fri, 15 Feb 2019 06:15:39: 25000000 INFO @ Fri, 15 Feb 2019 06:15:42: 25000000 INFO @ Fri, 15 Feb 2019 06:15:46: 26000000 INFO @ Fri, 15 Feb 2019 06:15:46: 26000000 INFO @ Fri, 15 Feb 2019 06:15:49: 26000000 INFO @ Fri, 15 Feb 2019 06:15:53: 27000000 INFO @ Fri, 15 Feb 2019 06:15:53: 27000000 INFO @ Fri, 15 Feb 2019 06:15:55: 27000000 INFO @ Fri, 15 Feb 2019 06:16:00: 28000000 INFO @ Fri, 15 Feb 2019 06:16:00: 28000000 INFO @ Fri, 15 Feb 2019 06:16:02: 28000000 INFO @ Fri, 15 Feb 2019 06:16:07: 29000000 INFO @ Fri, 15 Feb 2019 06:16:07: 29000000 INFO @ Fri, 15 Feb 2019 06:16:09: 29000000 INFO @ Fri, 15 Feb 2019 06:16:14: 30000000 INFO @ Fri, 15 Feb 2019 06:16:14: 30000000 INFO @ Fri, 15 Feb 2019 06:16:15: 30000000 INFO @ Fri, 15 Feb 2019 06:16:21: 31000000 INFO @ Fri, 15 Feb 2019 06:16:21: 31000000 INFO @ Fri, 15 Feb 2019 06:16:23: 31000000 INFO @ Fri, 15 Feb 2019 06:16:28: 32000000 INFO @ Fri, 15 Feb 2019 06:16:28: 32000000 INFO @ Fri, 15 Feb 2019 06:16:30: 32000000 INFO @ Fri, 15 Feb 2019 06:16:35: 33000000 INFO @ Fri, 15 Feb 2019 06:16:35: 33000000 INFO @ Fri, 15 Feb 2019 06:16:37: 33000000 INFO @ Fri, 15 Feb 2019 06:16:41: 34000000 INFO @ Fri, 15 Feb 2019 06:16:41: 34000000 INFO @ Fri, 15 Feb 2019 06:16:44: 34000000 INFO @ Fri, 15 Feb 2019 06:16:49: 35000000 INFO @ Fri, 15 Feb 2019 06:16:49: 35000000 INFO @ Fri, 15 Feb 2019 06:16:51: 35000000 INFO @ Fri, 15 Feb 2019 06:16:54: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 06:16:54: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 06:16:54: #1 total tags in treatment: 35665760 INFO @ Fri, 15 Feb 2019 06:16:54: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:16:54: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 06:16:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 06:16:54: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 06:16:54: #1 total tags in treatment: 35665760 INFO @ Fri, 15 Feb 2019 06:16:54: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:16:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 06:16:55: #1 tags after filtering in treatment: 35665668 INFO @ Fri, 15 Feb 2019 06:16:55: #1 tags after filtering in treatment: 35665668 INFO @ Fri, 15 Feb 2019 06:16:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:16:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:16:55: #1 finished! INFO @ Fri, 15 Feb 2019 06:16:55: #1 finished! INFO @ Fri, 15 Feb 2019 06:16:55: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:16:55: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:16:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:16:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:16:56: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 06:16:56: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 06:16:56: #1 total tags in treatment: 35665760 INFO @ Fri, 15 Feb 2019 06:16:56: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:16:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 06:16:57: #1 tags after filtering in treatment: 35665668 INFO @ Fri, 15 Feb 2019 06:16:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:16:57: #1 finished! INFO @ Fri, 15 Feb 2019 06:16:57: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:16:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:17:00: #2 number of paired peaks: 42081 INFO @ Fri, 15 Feb 2019 06:17:00: start model_add_line... INFO @ Fri, 15 Feb 2019 06:17:00: #2 number of paired peaks: 42081 INFO @ Fri, 15 Feb 2019 06:17:00: start model_add_line... INFO @ Fri, 15 Feb 2019 06:17:00: start X-correlation... INFO @ Fri, 15 Feb 2019 06:17:00: end of X-cor INFO @ Fri, 15 Feb 2019 06:17:00: #2 finished! INFO @ Fri, 15 Feb 2019 06:17:00: #2 predicted fragment length is 158 bps INFO @ Fri, 15 Feb 2019 06:17:00: #2 alternative fragment length(s) may be 158 bps INFO @ Fri, 15 Feb 2019 06:17:00: #2.2 Generate R script for model : SRX3360114.05_model.r INFO @ Fri, 15 Feb 2019 06:17:00: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:17:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:17:01: start X-correlation... INFO @ Fri, 15 Feb 2019 06:17:01: end of X-cor INFO @ Fri, 15 Feb 2019 06:17:01: #2 finished! INFO @ Fri, 15 Feb 2019 06:17:01: #2 predicted fragment length is 158 bps INFO @ Fri, 15 Feb 2019 06:17:01: #2 alternative fragment length(s) may be 158 bps INFO @ Fri, 15 Feb 2019 06:17:01: #2.2 Generate R script for model : SRX3360114.20_model.r INFO @ Fri, 15 Feb 2019 06:17:01: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:17:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:17:02: #2 number of paired peaks: 42081 INFO @ Fri, 15 Feb 2019 06:17:02: start model_add_line... INFO @ Fri, 15 Feb 2019 06:17:03: start X-correlation... INFO @ Fri, 15 Feb 2019 06:17:03: end of X-cor INFO @ Fri, 15 Feb 2019 06:17:03: #2 finished! INFO @ Fri, 15 Feb 2019 06:17:03: #2 predicted fragment length is 158 bps INFO @ Fri, 15 Feb 2019 06:17:03: #2 alternative fragment length(s) may be 158 bps INFO @ Fri, 15 Feb 2019 06:17:03: #2.2 Generate R script for model : SRX3360114.10_model.r INFO @ Fri, 15 Feb 2019 06:17:03: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:17:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:18:28: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:18:28: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:18:31: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:19:18: #4 Write output xls file... SRX3360114.10_peaks.xls INFO @ Fri, 15 Feb 2019 06:19:18: #4 Write peak in narrowPeak format file... SRX3360114.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:19:19: #4 Write summits bed file... SRX3360114.10_summits.bed INFO @ Fri, 15 Feb 2019 06:19:19: Done! pass1 - making usageList (97 chroms): 5 millis pass2 - checking and writing primary data (19496 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 06:19:21: #4 Write output xls file... SRX3360114.20_peaks.xls INFO @ Fri, 15 Feb 2019 06:19:21: #4 Write peak in narrowPeak format file... SRX3360114.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:19:21: #4 Write summits bed file... SRX3360114.20_summits.bed INFO @ Fri, 15 Feb 2019 06:19:21: Done! pass1 - making usageList (79 chroms): 3 millis pass2 - checking and writing primary data (13258 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 06:19:23: #4 Write output xls file... SRX3360114.05_peaks.xls INFO @ Fri, 15 Feb 2019 06:19:23: #4 Write peak in narrowPeak format file... SRX3360114.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:19:23: #4 Write summits bed file... SRX3360114.05_summits.bed INFO @ Fri, 15 Feb 2019 06:19:23: Done! pass1 - making usageList (128 chroms): 6 millis pass2 - checking and writing primary data (24158 records, 4 fields): 36 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。