Job ID = 10194783 sra ファイルのダウンロード中... Completed: 621983K bytes transferred in 9 seconds (510689K 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 26437851 spots for /home/okishinya/chipatlas/results/rn6/SRX1774915/SRR3544948.sra Written 26437851 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: 00:22:22 26437851 reads; of these: 26437851 (100.00%) were unpaired; of these: 731070 (2.77%) aligned 0 times 20638171 (78.06%) aligned exactly 1 time 5068610 (19.17%) aligned >1 times 97.23% overall alignment rate Time searching: 00:22:24 Overall time: 00:22:24 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] 9375677 / 25706781 = 0.3647 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 17:25:59: # Command line: callpeak -t SRX1774915.bam -f BAM -g 2.15e9 -n SRX1774915.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1774915.20 # format = BAM # ChIP-seq file = ['SRX1774915.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 17:25:59: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:25:59: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:25:59: # Command line: callpeak -t SRX1774915.bam -f BAM -g 2.15e9 -n SRX1774915.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1774915.05 # format = BAM # ChIP-seq file = ['SRX1774915.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 17:25:59: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:25:59: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:25:59: # Command line: callpeak -t SRX1774915.bam -f BAM -g 2.15e9 -n SRX1774915.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1774915.10 # format = BAM # ChIP-seq file = ['SRX1774915.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 17:25:59: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:25:59: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:26:05: 1000000 INFO @ Fri, 10 Nov 2017 17:26:05: 1000000 INFO @ Fri, 10 Nov 2017 17:26:05: 1000000 INFO @ Fri, 10 Nov 2017 17:26:12: 2000000 INFO @ Fri, 10 Nov 2017 17:26:12: 2000000 INFO @ Fri, 10 Nov 2017 17:26:12: 2000000 INFO @ Fri, 10 Nov 2017 17:26:18: 3000000 INFO @ Fri, 10 Nov 2017 17:26:19: 3000000 INFO @ Fri, 10 Nov 2017 17:26:19: 3000000 INFO @ Fri, 10 Nov 2017 17:26:25: 4000000 INFO @ Fri, 10 Nov 2017 17:26:25: 4000000 INFO @ Fri, 10 Nov 2017 17:26:27: 4000000 INFO @ Fri, 10 Nov 2017 17:26:32: 5000000 INFO @ Fri, 10 Nov 2017 17:26:32: 5000000 INFO @ Fri, 10 Nov 2017 17:26:34: 5000000 INFO @ Fri, 10 Nov 2017 17:26:39: 6000000 INFO @ Fri, 10 Nov 2017 17:26:39: 6000000 INFO @ Fri, 10 Nov 2017 17:26:41: 6000000 INFO @ Fri, 10 Nov 2017 17:26:45: 7000000 INFO @ Fri, 10 Nov 2017 17:26:45: 7000000 INFO @ Fri, 10 Nov 2017 17:26:48: 7000000 INFO @ Fri, 10 Nov 2017 17:26:52: 8000000 INFO @ Fri, 10 Nov 2017 17:26:52: 8000000 INFO @ Fri, 10 Nov 2017 17:26:55: 8000000 INFO @ Fri, 10 Nov 2017 17:26:59: 9000000 INFO @ Fri, 10 Nov 2017 17:26:59: 9000000 INFO @ Fri, 10 Nov 2017 17:27:03: 9000000 INFO @ Fri, 10 Nov 2017 17:27:05: 10000000 INFO @ Fri, 10 Nov 2017 17:27:06: 10000000 INFO @ Fri, 10 Nov 2017 17:27:10: 10000000 INFO @ Fri, 10 Nov 2017 17:27:12: 11000000 INFO @ Fri, 10 Nov 2017 17:27:13: 11000000 INFO @ Fri, 10 Nov 2017 17:27:17: 11000000 INFO @ Fri, 10 Nov 2017 17:27:19: 12000000 INFO @ Fri, 10 Nov 2017 17:27:19: 12000000 INFO @ Fri, 10 Nov 2017 17:27:24: 12000000 INFO @ Fri, 10 Nov 2017 17:27:25: 13000000 INFO @ Fri, 10 Nov 2017 17:27:26: 13000000 INFO @ Fri, 10 Nov 2017 17:27:31: 13000000 INFO @ Fri, 10 Nov 2017 17:27:32: 14000000 INFO @ Fri, 10 Nov 2017 17:27:33: 14000000 INFO @ Fri, 10 Nov 2017 17:27:39: 14000000 INFO @ Fri, 10 Nov 2017 17:27:39: 15000000 INFO @ Fri, 10 Nov 2017 17:27:40: 15000000 INFO @ Fri, 10 Nov 2017 17:27:46: 16000000 INFO @ Fri, 10 Nov 2017 17:27:46: 15000000 INFO @ Fri, 10 Nov 2017 17:27:47: 16000000 INFO @ Fri, 10 Nov 2017 17:27:48: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:27:48: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:27:48: #1 total tags in treatment: 16331104 INFO @ Fri, 10 Nov 2017 17:27:48: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:27:48: #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 17:27:48: #1 tags after filtering in treatment: 16330937 INFO @ Fri, 10 Nov 2017 17:27:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:27:48: #1 finished! INFO @ Fri, 10 Nov 2017 17:27:48: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:27:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:27:49: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:27:49: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:27:49: #1 total tags in treatment: 16331104 INFO @ Fri, 10 Nov 2017 17:27:49: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:27:49: #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 17:27:49: #1 tags after filtering in treatment: 16330937 INFO @ Fri, 10 Nov 2017 17:27:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:27:49: #1 finished! INFO @ Fri, 10 Nov 2017 17:27:49: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:27:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:27:51: #2 number of paired peaks: 40780 INFO @ Fri, 10 Nov 2017 17:27:51: start model_add_line... INFO @ Fri, 10 Nov 2017 17:27:52: start X-correlation... INFO @ Fri, 10 Nov 2017 17:27:52: end of X-cor INFO @ Fri, 10 Nov 2017 17:27:52: #2 finished! INFO @ Fri, 10 Nov 2017 17:27:52: #2 predicted fragment length is 181 bps INFO @ Fri, 10 Nov 2017 17:27:52: #2 alternative fragment length(s) may be 181 bps INFO @ Fri, 10 Nov 2017 17:27:52: #2.2 Generate R script for model : SRX1774915.05_model.r INFO @ Fri, 10 Nov 2017 17:27:52: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:27:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:27:53: #2 number of paired peaks: 40780 INFO @ Fri, 10 Nov 2017 17:27:53: start model_add_line... INFO @ Fri, 10 Nov 2017 17:27:53: 16000000 INFO @ Fri, 10 Nov 2017 17:27:53: start X-correlation... INFO @ Fri, 10 Nov 2017 17:27:53: end of X-cor INFO @ Fri, 10 Nov 2017 17:27:53: #2 finished! INFO @ Fri, 10 Nov 2017 17:27:53: #2 predicted fragment length is 181 bps INFO @ Fri, 10 Nov 2017 17:27:53: #2 alternative fragment length(s) may be 181 bps INFO @ Fri, 10 Nov 2017 17:27:53: #2.2 Generate R script for model : SRX1774915.20_model.r INFO @ Fri, 10 Nov 2017 17:27:53: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:27:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:27:55: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:27:55: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:27:55: #1 total tags in treatment: 16331104 INFO @ Fri, 10 Nov 2017 17:27:55: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:27:55: #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 17:27:55: #1 tags after filtering in treatment: 16330937 INFO @ Fri, 10 Nov 2017 17:27:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:27:55: #1 finished! INFO @ Fri, 10 Nov 2017 17:27:55: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:27:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:27:58: #2 number of paired peaks: 40780 INFO @ Fri, 10 Nov 2017 17:27:58: start model_add_line... INFO @ Fri, 10 Nov 2017 17:27:59: start X-correlation... INFO @ Fri, 10 Nov 2017 17:27:59: end of X-cor INFO @ Fri, 10 Nov 2017 17:27:59: #2 finished! INFO @ Fri, 10 Nov 2017 17:27:59: #2 predicted fragment length is 181 bps INFO @ Fri, 10 Nov 2017 17:27:59: #2 alternative fragment length(s) may be 181 bps INFO @ Fri, 10 Nov 2017 17:27:59: #2.2 Generate R script for model : SRX1774915.10_model.r INFO @ Fri, 10 Nov 2017 17:27:59: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:27:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:28:36: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:28:37: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:28:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:29:00: #4 Write output xls file... SRX1774915.05_peaks.xls INFO @ Fri, 10 Nov 2017 17:29:01: #4 Write peak in narrowPeak format file... SRX1774915.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:29:01: #4 Write summits bed file... SRX1774915.05_summits.bed INFO @ Fri, 10 Nov 2017 17:29:01: Done! INFO @ Fri, 10 Nov 2017 17:29:01: #4 Write output xls file... SRX1774915.20_peaks.xls pass1 - making usageList (94 chroms): 5 millis INFO @ Fri, 10 Nov 2017 17:29:01: #4 Write peak in narrowPeak format file... SRX1774915.20_peaks.narrowPeak pass2 - checking and writing primary data (20541 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:29:01: #4 Write summits bed file... SRX1774915.20_summits.bed INFO @ Fri, 10 Nov 2017 17:29:01: Done! pass1 - making usageList (43 chroms): 2 millis pass2 - checking and writing primary data (7520 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:29:08: #4 Write output xls file... SRX1774915.10_peaks.xls INFO @ Fri, 10 Nov 2017 17:29:08: #4 Write peak in narrowPeak format file... SRX1774915.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:29:08: #4 Write summits bed file... SRX1774915.10_summits.bed INFO @ Fri, 10 Nov 2017 17:29:08: Done! pass1 - making usageList (67 chroms): 3 millis pass2 - checking and writing primary data (12949 records, 4 fields): 19 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。