Job ID = 11192554 sra ファイルのダウンロード中... Completed: 964011K bytes transferred in 12 seconds (627676K 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 30285484 spots for /home/okishinya/chipatlas/results/rn6/SRX2226568/SRR4374818.sra Written 30285484 spots for /home/okishinya/chipatlas/results/rn6/SRX2226568/SRR4374818.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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:18:24 30285484 reads; of these: 30285484 (100.00%) were unpaired; of these: 3615823 (11.94%) aligned 0 times 21738289 (71.78%) aligned exactly 1 time 4931372 (16.28%) aligned >1 times 88.06% overall alignment rate Time searching: 00:18:27 Overall time: 00:18:27 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] 13176604 / 26669661 = 0.4941 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 @ Sat, 15 Sep 2018 09:07:55: # Command line: callpeak -t SRX2226568.bam -f BAM -g 2.15e9 -n SRX2226568.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2226568.20 # format = BAM # ChIP-seq file = ['SRX2226568.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, 15 Sep 2018 09:07:55: # Command line: callpeak -t SRX2226568.bam -f BAM -g 2.15e9 -n SRX2226568.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2226568.05 # format = BAM # ChIP-seq file = ['SRX2226568.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, 15 Sep 2018 09:07:55: # Command line: callpeak -t SRX2226568.bam -f BAM -g 2.15e9 -n SRX2226568.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2226568.10 # format = BAM # ChIP-seq file = ['SRX2226568.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, 15 Sep 2018 09:07:55: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:07:55: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:07:55: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:07:55: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:07:55: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:07:55: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:08:01: 1000000 INFO @ Sat, 15 Sep 2018 09:08:01: 1000000 INFO @ Sat, 15 Sep 2018 09:08:01: 1000000 INFO @ Sat, 15 Sep 2018 09:08:07: 2000000 INFO @ Sat, 15 Sep 2018 09:08:07: 2000000 INFO @ Sat, 15 Sep 2018 09:08:07: 2000000 INFO @ Sat, 15 Sep 2018 09:08:13: 3000000 INFO @ Sat, 15 Sep 2018 09:08:13: 3000000 INFO @ Sat, 15 Sep 2018 09:08:14: 3000000 INFO @ Sat, 15 Sep 2018 09:08:19: 4000000 INFO @ Sat, 15 Sep 2018 09:08:19: 4000000 INFO @ Sat, 15 Sep 2018 09:08:20: 4000000 INFO @ Sat, 15 Sep 2018 09:08:25: 5000000 INFO @ Sat, 15 Sep 2018 09:08:25: 5000000 INFO @ Sat, 15 Sep 2018 09:08:26: 5000000 INFO @ Sat, 15 Sep 2018 09:08:31: 6000000 INFO @ Sat, 15 Sep 2018 09:08:31: 6000000 INFO @ Sat, 15 Sep 2018 09:08:33: 6000000 INFO @ Sat, 15 Sep 2018 09:08:37: 7000000 INFO @ Sat, 15 Sep 2018 09:08:37: 7000000 INFO @ Sat, 15 Sep 2018 09:08:39: 7000000 INFO @ Sat, 15 Sep 2018 09:08:43: 8000000 INFO @ Sat, 15 Sep 2018 09:08:43: 8000000 INFO @ Sat, 15 Sep 2018 09:08:45: 8000000 INFO @ Sat, 15 Sep 2018 09:08:49: 9000000 INFO @ Sat, 15 Sep 2018 09:08:49: 9000000 INFO @ Sat, 15 Sep 2018 09:08:52: 9000000 INFO @ Sat, 15 Sep 2018 09:08:56: 10000000 INFO @ Sat, 15 Sep 2018 09:08:56: 10000000 INFO @ Sat, 15 Sep 2018 09:08:58: 10000000 INFO @ Sat, 15 Sep 2018 09:09:02: 11000000 INFO @ Sat, 15 Sep 2018 09:09:02: 11000000 INFO @ Sat, 15 Sep 2018 09:09:04: 11000000 INFO @ Sat, 15 Sep 2018 09:09:08: 12000000 INFO @ Sat, 15 Sep 2018 09:09:08: 12000000 INFO @ Sat, 15 Sep 2018 09:09:11: 12000000 INFO @ Sat, 15 Sep 2018 09:09:14: 13000000 INFO @ Sat, 15 Sep 2018 09:09:14: 13000000 INFO @ Sat, 15 Sep 2018 09:09:17: 13000000 INFO @ Sat, 15 Sep 2018 09:09:17: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:09:17: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:09:17: #1 total tags in treatment: 13493057 INFO @ Sat, 15 Sep 2018 09:09:17: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:09:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:09:17: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:09:17: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:09:17: #1 total tags in treatment: 13493057 INFO @ Sat, 15 Sep 2018 09:09:17: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:09:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:09:18: #1 tags after filtering in treatment: 13492876 INFO @ Sat, 15 Sep 2018 09:09:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:09:18: #1 finished! INFO @ Sat, 15 Sep 2018 09:09:18: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:09:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:09:18: #1 tags after filtering in treatment: 13492876 INFO @ Sat, 15 Sep 2018 09:09:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:09:18: #1 finished! INFO @ Sat, 15 Sep 2018 09:09:18: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:09:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:09:20: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:09:20: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:09:20: #1 total tags in treatment: 13493057 INFO @ Sat, 15 Sep 2018 09:09:20: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:09:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:09:21: #1 tags after filtering in treatment: 13492876 INFO @ Sat, 15 Sep 2018 09:09:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:09:21: #1 finished! INFO @ Sat, 15 Sep 2018 09:09:21: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:09:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:09:21: #2 number of paired peaks: 77393 INFO @ Sat, 15 Sep 2018 09:09:21: start model_add_line... INFO @ Sat, 15 Sep 2018 09:09:21: #2 number of paired peaks: 77393 INFO @ Sat, 15 Sep 2018 09:09:21: start model_add_line... INFO @ Sat, 15 Sep 2018 09:09:22: start X-correlation... INFO @ Sat, 15 Sep 2018 09:09:22: end of X-cor INFO @ Sat, 15 Sep 2018 09:09:22: #2 finished! INFO @ Sat, 15 Sep 2018 09:09:22: #2 predicted fragment length is 247 bps INFO @ Sat, 15 Sep 2018 09:09:22: #2 alternative fragment length(s) may be 247 bps INFO @ Sat, 15 Sep 2018 09:09:22: #2.2 Generate R script for model : SRX2226568.10_model.r INFO @ Sat, 15 Sep 2018 09:09:22: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:09:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:09:22: start X-correlation... INFO @ Sat, 15 Sep 2018 09:09:22: end of X-cor INFO @ Sat, 15 Sep 2018 09:09:22: #2 finished! INFO @ Sat, 15 Sep 2018 09:09:22: #2 predicted fragment length is 247 bps INFO @ Sat, 15 Sep 2018 09:09:22: #2 alternative fragment length(s) may be 247 bps INFO @ Sat, 15 Sep 2018 09:09:22: #2.2 Generate R script for model : SRX2226568.20_model.r INFO @ Sat, 15 Sep 2018 09:09:22: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:09:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:09:24: #2 number of paired peaks: 77393 INFO @ Sat, 15 Sep 2018 09:09:24: start model_add_line... INFO @ Sat, 15 Sep 2018 09:09:25: start X-correlation... INFO @ Sat, 15 Sep 2018 09:09:25: end of X-cor INFO @ Sat, 15 Sep 2018 09:09:25: #2 finished! INFO @ Sat, 15 Sep 2018 09:09:25: #2 predicted fragment length is 247 bps INFO @ Sat, 15 Sep 2018 09:09:25: #2 alternative fragment length(s) may be 247 bps INFO @ Sat, 15 Sep 2018 09:09:25: #2.2 Generate R script for model : SRX2226568.05_model.r INFO @ Sat, 15 Sep 2018 09:09:25: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:09:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:09:55: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:09:58: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:10:00: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:10:16: #4 Write output xls file... SRX2226568.10_peaks.xls INFO @ Sat, 15 Sep 2018 09:10:17: #4 Write peak in narrowPeak format file... SRX2226568.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:10:17: #4 Write summits bed file... SRX2226568.10_summits.bed INFO @ Sat, 15 Sep 2018 09:10:17: Done! pass1 - making usageList (75 chroms): 3 millis pass2 - checking and writing primary data (11906 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:10:18: #4 Write output xls file... SRX2226568.20_peaks.xls INFO @ Sat, 15 Sep 2018 09:10:18: #4 Write peak in narrowPeak format file... SRX2226568.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:10:18: #4 Write summits bed file... SRX2226568.20_summits.bed INFO @ Sat, 15 Sep 2018 09:10:18: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (4278 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:10:20: #4 Write output xls file... SRX2226568.05_peaks.xls INFO @ Sat, 15 Sep 2018 09:10:20: #4 Write peak in narrowPeak format file... SRX2226568.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:10:20: #4 Write summits bed file... SRX2226568.05_summits.bed INFO @ Sat, 15 Sep 2018 09:10:20: Done! pass1 - making usageList (116 chroms): 5 millis pass2 - checking and writing primary data (23980 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。