Job ID = 10194785 sra ファイルのダウンロード中... Completed: 551233K bytes transferred in 7 seconds (620982K 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... Written 23571510 spots for /home/okishinya/chipatlas/results/rn6/SRX1774917/SRR3544951.sra Written 23571510 spots total 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: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:18:58 23571510 reads; of these: 23571510 (100.00%) were unpaired; of these: 646019 (2.74%) aligned 0 times 18274659 (77.53%) aligned exactly 1 time 4650832 (19.73%) aligned >1 times 97.26% overall alignment rate Time searching: 00:19:00 Overall time: 00:19:00 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] 8491640 / 22925491 = 0.3704 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, 10 Nov 2017 17:29:48: # Command line: callpeak -t SRX1774917.bam -f BAM -g 2.15e9 -n SRX1774917.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1774917.10 # format = BAM # ChIP-seq file = ['SRX1774917.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, 10 Nov 2017 17:29:48: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:29:48: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:29:48: # Command line: callpeak -t SRX1774917.bam -f BAM -g 2.15e9 -n SRX1774917.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1774917.05 # format = BAM # ChIP-seq file = ['SRX1774917.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, 10 Nov 2017 17:29:48: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:29:48: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:29:48: # Command line: callpeak -t SRX1774917.bam -f BAM -g 2.15e9 -n SRX1774917.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1774917.20 # format = BAM # ChIP-seq file = ['SRX1774917.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, 10 Nov 2017 17:29:48: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:29:48: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:29:55: 1000000 INFO @ Fri, 10 Nov 2017 17:29:55: 1000000 INFO @ Fri, 10 Nov 2017 17:29:55: 1000000 INFO @ Fri, 10 Nov 2017 17:30:01: 2000000 INFO @ Fri, 10 Nov 2017 17:30:02: 2000000 INFO @ Fri, 10 Nov 2017 17:30:02: 2000000 INFO @ Fri, 10 Nov 2017 17:30:07: 3000000 INFO @ Fri, 10 Nov 2017 17:30:08: 3000000 INFO @ Fri, 10 Nov 2017 17:30:08: 3000000 INFO @ Fri, 10 Nov 2017 17:30:13: 4000000 INFO @ Fri, 10 Nov 2017 17:30:14: 4000000 INFO @ Fri, 10 Nov 2017 17:30:14: 4000000 INFO @ Fri, 10 Nov 2017 17:30:19: 5000000 INFO @ Fri, 10 Nov 2017 17:30:20: 5000000 INFO @ Fri, 10 Nov 2017 17:30:21: 5000000 INFO @ Fri, 10 Nov 2017 17:30:26: 6000000 INFO @ Fri, 10 Nov 2017 17:30:27: 6000000 INFO @ Fri, 10 Nov 2017 17:30:27: 6000000 INFO @ Fri, 10 Nov 2017 17:30:33: 7000000 INFO @ Fri, 10 Nov 2017 17:30:34: 7000000 INFO @ Fri, 10 Nov 2017 17:30:35: 7000000 INFO @ Fri, 10 Nov 2017 17:30:40: 8000000 INFO @ Fri, 10 Nov 2017 17:30:42: 8000000 INFO @ Fri, 10 Nov 2017 17:30:42: 8000000 INFO @ Fri, 10 Nov 2017 17:30:48: 9000000 INFO @ Fri, 10 Nov 2017 17:30:49: 9000000 INFO @ Fri, 10 Nov 2017 17:30:49: 9000000 INFO @ Fri, 10 Nov 2017 17:30:55: 10000000 INFO @ Fri, 10 Nov 2017 17:30:57: 10000000 INFO @ Fri, 10 Nov 2017 17:30:57: 10000000 INFO @ Fri, 10 Nov 2017 17:31:03: 11000000 INFO @ Fri, 10 Nov 2017 17:31:04: 11000000 INFO @ Fri, 10 Nov 2017 17:31:05: 11000000 INFO @ Fri, 10 Nov 2017 17:31:10: 12000000 INFO @ Fri, 10 Nov 2017 17:31:12: 12000000 INFO @ Fri, 10 Nov 2017 17:31:12: 12000000 INFO @ Fri, 10 Nov 2017 17:31:18: 13000000 INFO @ Fri, 10 Nov 2017 17:31:20: 13000000 INFO @ Fri, 10 Nov 2017 17:31:20: 13000000 INFO @ Fri, 10 Nov 2017 17:31:25: 14000000 INFO @ Fri, 10 Nov 2017 17:31:27: 14000000 INFO @ Fri, 10 Nov 2017 17:31:28: 14000000 INFO @ Fri, 10 Nov 2017 17:31:29: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:31:29: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:31:29: #1 total tags in treatment: 14433851 INFO @ Fri, 10 Nov 2017 17:31:29: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:31:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 17:31:29: #1 tags after filtering in treatment: 14433677 INFO @ Fri, 10 Nov 2017 17:31:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:31:29: #1 finished! INFO @ Fri, 10 Nov 2017 17:31:29: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:31:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:31:31: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:31:31: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:31:31: #1 total tags in treatment: 14433851 INFO @ Fri, 10 Nov 2017 17:31:31: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:31:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 17:31:31: #1 tags after filtering in treatment: 14433677 INFO @ Fri, 10 Nov 2017 17:31:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:31:31: #1 finished! INFO @ Fri, 10 Nov 2017 17:31:31: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:31:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:31:31: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:31:31: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:31:31: #1 total tags in treatment: 14433851 INFO @ Fri, 10 Nov 2017 17:31:31: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:31:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 17:31:32: #2 number of paired peaks: 37132 INFO @ Fri, 10 Nov 2017 17:31:32: start model_add_line... INFO @ Fri, 10 Nov 2017 17:31:32: #1 tags after filtering in treatment: 14433677 INFO @ Fri, 10 Nov 2017 17:31:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:31:32: #1 finished! INFO @ Fri, 10 Nov 2017 17:31:32: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:31:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:31:32: start X-correlation... INFO @ Fri, 10 Nov 2017 17:31:32: end of X-cor INFO @ Fri, 10 Nov 2017 17:31:32: #2 finished! INFO @ Fri, 10 Nov 2017 17:31:32: #2 predicted fragment length is 183 bps INFO @ Fri, 10 Nov 2017 17:31:32: #2 alternative fragment length(s) may be 183 bps INFO @ Fri, 10 Nov 2017 17:31:32: #2.2 Generate R script for model : SRX1774917.05_model.r INFO @ Fri, 10 Nov 2017 17:31:32: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:31:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:31:34: #2 number of paired peaks: 37132 INFO @ Fri, 10 Nov 2017 17:31:34: start model_add_line... INFO @ Fri, 10 Nov 2017 17:31:34: start X-correlation... INFO @ Fri, 10 Nov 2017 17:31:34: end of X-cor INFO @ Fri, 10 Nov 2017 17:31:34: #2 finished! INFO @ Fri, 10 Nov 2017 17:31:34: #2 predicted fragment length is 183 bps INFO @ Fri, 10 Nov 2017 17:31:34: #2 alternative fragment length(s) may be 183 bps INFO @ Fri, 10 Nov 2017 17:31:34: #2.2 Generate R script for model : SRX1774917.10_model.r INFO @ Fri, 10 Nov 2017 17:31:34: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:31:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:31:35: #2 number of paired peaks: 37132 INFO @ Fri, 10 Nov 2017 17:31:35: start model_add_line... INFO @ Fri, 10 Nov 2017 17:31:35: start X-correlation... INFO @ Fri, 10 Nov 2017 17:31:35: end of X-cor INFO @ Fri, 10 Nov 2017 17:31:35: #2 finished! INFO @ Fri, 10 Nov 2017 17:31:35: #2 predicted fragment length is 183 bps INFO @ Fri, 10 Nov 2017 17:31:35: #2 alternative fragment length(s) may be 183 bps INFO @ Fri, 10 Nov 2017 17:31:35: #2.2 Generate R script for model : SRX1774917.20_model.r INFO @ Fri, 10 Nov 2017 17:31:35: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:31:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:32:09: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:32:11: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:32:15: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:32:33: #4 Write output xls file... SRX1774917.05_peaks.xls INFO @ Fri, 10 Nov 2017 17:32:33: #4 Write peak in narrowPeak format file... SRX1774917.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:32:33: #4 Write summits bed file... SRX1774917.05_summits.bed INFO @ Fri, 10 Nov 2017 17:32:33: Done! INFO @ Fri, 10 Nov 2017 17:32:34: #4 Write output xls file... SRX1774917.20_peaks.xls INFO @ Fri, 10 Nov 2017 17:32:34: #4 Write peak in narrowPeak format file... SRX1774917.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:32:34: #4 Write summits bed file... SRX1774917.20_summits.bed pass1 - making usageList (91 chroms): 5 millis pass2 - checking and writing primary data (22088 records, 4 fields): 29 millis INFO @ Fri, 10 Nov 2017 17:32:34: Done! CompletedMACS2peakCalling pass1 - making usageList (47 chroms): 2 millis pass2 - checking and writing primary data (8371 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:32:37: #4 Write output xls file... SRX1774917.10_peaks.xls INFO @ Fri, 10 Nov 2017 17:32:37: #4 Write peak in narrowPeak format file... SRX1774917.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:32:37: #4 Write summits bed file... SRX1774917.10_summits.bed INFO @ Fri, 10 Nov 2017 17:32:37: Done! pass1 - making usageList (69 chroms): 3 millis pass2 - checking and writing primary data (14299 records, 4 fields): 20 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。