Job ID = 10194780 sra ファイルのダウンロード中... Completed: 447638K bytes transferred in 5 seconds (635295K 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 19222402 spots for /home/okishinya/chipatlas/results/rn6/SRX1774912/SRR3544943.sra Written 19222402 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: 00:14:12 19222402 reads; of these: 19222402 (100.00%) were unpaired; of these: 654375 (3.40%) aligned 0 times 14153206 (73.63%) aligned exactly 1 time 4414821 (22.97%) aligned >1 times 96.60% overall alignment rate Time searching: 00:14:14 Overall time: 00:14:14 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] 2438031 / 18568027 = 0.1313 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 17:11:33: # Command line: callpeak -t SRX1774912.bam -f BAM -g 2.15e9 -n SRX1774912.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1774912.10 # format = BAM # ChIP-seq file = ['SRX1774912.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 17:11:33: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:11:33: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:11:33: # Command line: callpeak -t SRX1774912.bam -f BAM -g 2.15e9 -n SRX1774912.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1774912.05 # format = BAM # ChIP-seq file = ['SRX1774912.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 17:11:33: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:11:33: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:11:33: # Command line: callpeak -t SRX1774912.bam -f BAM -g 2.15e9 -n SRX1774912.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1774912.20 # format = BAM # ChIP-seq file = ['SRX1774912.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 17:11:33: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:11:33: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:11:41: 1000000 INFO @ Fri, 10 Nov 2017 17:11:41: 1000000 INFO @ Fri, 10 Nov 2017 17:11:41: 1000000 INFO @ Fri, 10 Nov 2017 17:11:48: 2000000 INFO @ Fri, 10 Nov 2017 17:11:49: 2000000 INFO @ Fri, 10 Nov 2017 17:11:49: 2000000 INFO @ Fri, 10 Nov 2017 17:11:56: 3000000 INFO @ Fri, 10 Nov 2017 17:11:56: 3000000 INFO @ Fri, 10 Nov 2017 17:11:56: 3000000 INFO @ Fri, 10 Nov 2017 17:12:03: 4000000 INFO @ Fri, 10 Nov 2017 17:12:04: 4000000 INFO @ Fri, 10 Nov 2017 17:12:04: 4000000 INFO @ Fri, 10 Nov 2017 17:12:10: 5000000 INFO @ Fri, 10 Nov 2017 17:12:12: 5000000 INFO @ Fri, 10 Nov 2017 17:12:12: 5000000 INFO @ Fri, 10 Nov 2017 17:12:18: 6000000 INFO @ Fri, 10 Nov 2017 17:12:19: 6000000 INFO @ Fri, 10 Nov 2017 17:12:20: 6000000 INFO @ Fri, 10 Nov 2017 17:12:26: 7000000 INFO @ Fri, 10 Nov 2017 17:12:27: 7000000 INFO @ Fri, 10 Nov 2017 17:12:27: 7000000 INFO @ Fri, 10 Nov 2017 17:12:33: 8000000 INFO @ Fri, 10 Nov 2017 17:12:34: 8000000 INFO @ Fri, 10 Nov 2017 17:12:35: 8000000 INFO @ Fri, 10 Nov 2017 17:12:41: 9000000 INFO @ Fri, 10 Nov 2017 17:12:42: 9000000 INFO @ Fri, 10 Nov 2017 17:12:43: 9000000 INFO @ Fri, 10 Nov 2017 17:12:49: 10000000 INFO @ Fri, 10 Nov 2017 17:12:49: 10000000 INFO @ Fri, 10 Nov 2017 17:12:51: 10000000 INFO @ Fri, 10 Nov 2017 17:12:57: 11000000 INFO @ Fri, 10 Nov 2017 17:12:57: 11000000 INFO @ Fri, 10 Nov 2017 17:12:58: 11000000 INFO @ Fri, 10 Nov 2017 17:13:04: 12000000 INFO @ Fri, 10 Nov 2017 17:13:05: 12000000 INFO @ Fri, 10 Nov 2017 17:13:07: 12000000 INFO @ Fri, 10 Nov 2017 17:13:11: 13000000 INFO @ Fri, 10 Nov 2017 17:13:13: 13000000 INFO @ Fri, 10 Nov 2017 17:13:15: 13000000 INFO @ Fri, 10 Nov 2017 17:13:18: 14000000 INFO @ Fri, 10 Nov 2017 17:13:21: 14000000 INFO @ Fri, 10 Nov 2017 17:13:23: 14000000 INFO @ Fri, 10 Nov 2017 17:13:26: 15000000 INFO @ Fri, 10 Nov 2017 17:13:29: 15000000 INFO @ Fri, 10 Nov 2017 17:13:32: 15000000 INFO @ Fri, 10 Nov 2017 17:13:33: 16000000 INFO @ Fri, 10 Nov 2017 17:13:34: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:13:34: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:13:34: #1 total tags in treatment: 16129996 INFO @ Fri, 10 Nov 2017 17:13:34: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:13:34: #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 17:13:35: #1 tags after filtering in treatment: 16129813 INFO @ Fri, 10 Nov 2017 17:13:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:13:35: #1 finished! INFO @ Fri, 10 Nov 2017 17:13:35: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:13:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:13:38: #2 number of paired peaks: 34562 INFO @ Fri, 10 Nov 2017 17:13:38: start model_add_line... INFO @ Fri, 10 Nov 2017 17:13:38: 16000000 INFO @ Fri, 10 Nov 2017 17:13:38: start X-correlation... INFO @ Fri, 10 Nov 2017 17:13:38: end of X-cor INFO @ Fri, 10 Nov 2017 17:13:38: #2 finished! INFO @ Fri, 10 Nov 2017 17:13:38: #2 predicted fragment length is 176 bps INFO @ Fri, 10 Nov 2017 17:13:38: #2 alternative fragment length(s) may be 176 bps INFO @ Fri, 10 Nov 2017 17:13:38: #2.2 Generate R script for model : SRX1774912.20_model.r INFO @ Fri, 10 Nov 2017 17:13:38: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:13:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:13:39: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:13:39: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:13:39: #1 total tags in treatment: 16129996 INFO @ Fri, 10 Nov 2017 17:13:39: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:13:39: #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 17:13:39: #1 tags after filtering in treatment: 16129813 INFO @ Fri, 10 Nov 2017 17:13:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:13:39: #1 finished! INFO @ Fri, 10 Nov 2017 17:13:39: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:13:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:13:40: 16000000 INFO @ Fri, 10 Nov 2017 17:13:41: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:13:41: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:13:41: #1 total tags in treatment: 16129996 INFO @ Fri, 10 Nov 2017 17:13:41: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:13:41: #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 17:13:41: #1 tags after filtering in treatment: 16129813 INFO @ Fri, 10 Nov 2017 17:13:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:13:41: #1 finished! INFO @ Fri, 10 Nov 2017 17:13:41: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:13:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:13:42: #2 number of paired peaks: 34562 INFO @ Fri, 10 Nov 2017 17:13:42: start model_add_line... INFO @ Fri, 10 Nov 2017 17:13:42: start X-correlation... INFO @ Fri, 10 Nov 2017 17:13:42: end of X-cor INFO @ Fri, 10 Nov 2017 17:13:42: #2 finished! INFO @ Fri, 10 Nov 2017 17:13:42: #2 predicted fragment length is 176 bps INFO @ Fri, 10 Nov 2017 17:13:42: #2 alternative fragment length(s) may be 176 bps INFO @ Fri, 10 Nov 2017 17:13:42: #2.2 Generate R script for model : SRX1774912.05_model.r INFO @ Fri, 10 Nov 2017 17:13:42: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:13:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:13:44: #2 number of paired peaks: 34562 INFO @ Fri, 10 Nov 2017 17:13:44: start model_add_line... INFO @ Fri, 10 Nov 2017 17:13:44: start X-correlation... INFO @ Fri, 10 Nov 2017 17:13:44: end of X-cor INFO @ Fri, 10 Nov 2017 17:13:44: #2 finished! INFO @ Fri, 10 Nov 2017 17:13:44: #2 predicted fragment length is 176 bps INFO @ Fri, 10 Nov 2017 17:13:44: #2 alternative fragment length(s) may be 176 bps INFO @ Fri, 10 Nov 2017 17:13:44: #2.2 Generate R script for model : SRX1774912.10_model.r INFO @ Fri, 10 Nov 2017 17:13:44: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:13:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:14:18: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:14:22: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:14:25: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:14:41: #4 Write output xls file... SRX1774912.20_peaks.xls INFO @ Fri, 10 Nov 2017 17:14:41: #4 Write peak in narrowPeak format file... SRX1774912.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:14:41: #4 Write summits bed file... SRX1774912.20_summits.bed INFO @ Fri, 10 Nov 2017 17:14:41: Done! pass1 - making usageList (33 chroms): 1 millis pass2 - checking and writing primary data (1605 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:14:48: #4 Write output xls file... SRX1774912.05_peaks.xls INFO @ Fri, 10 Nov 2017 17:14:48: #4 Write peak in narrowPeak format file... SRX1774912.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:14:48: #4 Write summits bed file... SRX1774912.05_summits.bed INFO @ Fri, 10 Nov 2017 17:14:48: Done! pass1 - making usageList (60 chroms): 3 millis pass2 - checking and writing primary data (12334 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:14:50: #4 Write output xls file... SRX1774912.10_peaks.xls INFO @ Fri, 10 Nov 2017 17:14:50: #4 Write peak in narrowPeak format file... SRX1774912.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:14:50: #4 Write summits bed file... SRX1774912.10_summits.bed INFO @ Fri, 10 Nov 2017 17:14:50: Done! pass1 - making usageList (42 chroms): 2 millis pass2 - checking and writing primary data (5157 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。