Job ID = 10194741 sra ファイルのダウンロード中... Completed: 595781K bytes transferred in 7 seconds (612196K 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 22904684 spots for /home/okishinya/chipatlas/results/rn6/SRX1068230/SRR2073189.sra Written 22904684 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: 00:20:49 22904684 reads; of these: 22904684 (100.00%) were unpaired; of these: 590224 (2.58%) aligned 0 times 19713915 (86.07%) aligned exactly 1 time 2600545 (11.35%) aligned >1 times 97.42% overall alignment rate Time searching: 00:20:51 Overall time: 00:20:51 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] 3199604 / 22314460 = 0.1434 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 23:51:10: # Command line: callpeak -t SRX1068230.bam -f BAM -g 2.15e9 -n SRX1068230.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1068230.20 # format = BAM # ChIP-seq file = ['SRX1068230.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 23:51:10: # Command line: callpeak -t SRX1068230.bam -f BAM -g 2.15e9 -n SRX1068230.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1068230.05 # format = BAM # ChIP-seq file = ['SRX1068230.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 23:51:10: # Command line: callpeak -t SRX1068230.bam -f BAM -g 2.15e9 -n SRX1068230.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1068230.10 # format = BAM # ChIP-seq file = ['SRX1068230.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 23:51:10: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:51:10: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:51:10: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:51:10: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:51:10: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:51:10: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:51:17: 1000000 INFO @ Fri, 10 Nov 2017 23:51:17: 1000000 INFO @ Fri, 10 Nov 2017 23:51:17: 1000000 INFO @ Fri, 10 Nov 2017 23:51:24: 2000000 INFO @ Fri, 10 Nov 2017 23:51:24: 2000000 INFO @ Fri, 10 Nov 2017 23:51:24: 2000000 INFO @ Fri, 10 Nov 2017 23:51:31: 3000000 INFO @ Fri, 10 Nov 2017 23:51:31: 3000000 INFO @ Fri, 10 Nov 2017 23:51:31: 3000000 INFO @ Fri, 10 Nov 2017 23:51:38: 4000000 INFO @ Fri, 10 Nov 2017 23:51:38: 4000000 INFO @ Fri, 10 Nov 2017 23:51:39: 4000000 INFO @ Fri, 10 Nov 2017 23:51:45: 5000000 INFO @ Fri, 10 Nov 2017 23:51:45: 5000000 INFO @ Fri, 10 Nov 2017 23:51:46: 5000000 INFO @ Fri, 10 Nov 2017 23:51:53: 6000000 INFO @ Fri, 10 Nov 2017 23:51:53: 6000000 INFO @ Fri, 10 Nov 2017 23:51:53: 6000000 INFO @ Fri, 10 Nov 2017 23:52:00: 7000000 INFO @ Fri, 10 Nov 2017 23:52:00: 7000000 INFO @ Fri, 10 Nov 2017 23:52:00: 7000000 INFO @ Fri, 10 Nov 2017 23:52:07: 8000000 INFO @ Fri, 10 Nov 2017 23:52:07: 8000000 INFO @ Fri, 10 Nov 2017 23:52:07: 8000000 INFO @ Fri, 10 Nov 2017 23:52:14: 9000000 INFO @ Fri, 10 Nov 2017 23:52:14: 9000000 INFO @ Fri, 10 Nov 2017 23:52:15: 9000000 INFO @ Fri, 10 Nov 2017 23:52:21: 10000000 INFO @ Fri, 10 Nov 2017 23:52:21: 10000000 INFO @ Fri, 10 Nov 2017 23:52:22: 10000000 INFO @ Fri, 10 Nov 2017 23:52:29: 11000000 INFO @ Fri, 10 Nov 2017 23:52:29: 11000000 INFO @ Fri, 10 Nov 2017 23:52:29: 11000000 INFO @ Fri, 10 Nov 2017 23:52:36: 12000000 INFO @ Fri, 10 Nov 2017 23:52:36: 12000000 INFO @ Fri, 10 Nov 2017 23:52:37: 12000000 INFO @ Fri, 10 Nov 2017 23:52:43: 13000000 INFO @ Fri, 10 Nov 2017 23:52:43: 13000000 INFO @ Fri, 10 Nov 2017 23:52:44: 13000000 INFO @ Fri, 10 Nov 2017 23:52:50: 14000000 INFO @ Fri, 10 Nov 2017 23:52:50: 14000000 INFO @ Fri, 10 Nov 2017 23:52:51: 14000000 INFO @ Fri, 10 Nov 2017 23:52:57: 15000000 INFO @ Fri, 10 Nov 2017 23:52:57: 15000000 INFO @ Fri, 10 Nov 2017 23:52:58: 15000000 INFO @ Fri, 10 Nov 2017 23:53:04: 16000000 INFO @ Fri, 10 Nov 2017 23:53:04: 16000000 INFO @ Fri, 10 Nov 2017 23:53:05: 16000000 INFO @ Fri, 10 Nov 2017 23:53:11: 17000000 INFO @ Fri, 10 Nov 2017 23:53:12: 17000000 INFO @ Fri, 10 Nov 2017 23:53:13: 17000000 INFO @ Fri, 10 Nov 2017 23:53:19: 18000000 INFO @ Fri, 10 Nov 2017 23:53:19: 18000000 INFO @ Fri, 10 Nov 2017 23:53:20: 18000000 INFO @ Fri, 10 Nov 2017 23:53:26: 19000000 INFO @ Fri, 10 Nov 2017 23:53:26: 19000000 INFO @ Fri, 10 Nov 2017 23:53:27: #1 tag size is determined as 64 bps INFO @ Fri, 10 Nov 2017 23:53:27: #1 tag size = 64 INFO @ Fri, 10 Nov 2017 23:53:27: #1 total tags in treatment: 19114856 INFO @ Fri, 10 Nov 2017 23:53:27: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:53:27: #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 23:53:27: #1 tag size is determined as 64 bps INFO @ Fri, 10 Nov 2017 23:53:27: #1 tag size = 64 INFO @ Fri, 10 Nov 2017 23:53:27: #1 total tags in treatment: 19114856 INFO @ Fri, 10 Nov 2017 23:53:27: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:53:27: #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 23:53:27: 19000000 INFO @ Fri, 10 Nov 2017 23:53:27: #1 tags after filtering in treatment: 19114587 INFO @ Fri, 10 Nov 2017 23:53:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:53:27: #1 finished! INFO @ Fri, 10 Nov 2017 23:53:27: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:53:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:53:27: #1 tags after filtering in treatment: 19114587 INFO @ Fri, 10 Nov 2017 23:53:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:53:27: #1 finished! INFO @ Fri, 10 Nov 2017 23:53:27: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:53:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:53:28: #1 tag size is determined as 64 bps INFO @ Fri, 10 Nov 2017 23:53:28: #1 tag size = 64 INFO @ Fri, 10 Nov 2017 23:53:28: #1 total tags in treatment: 19114856 INFO @ Fri, 10 Nov 2017 23:53:28: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:53:28: #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 23:53:29: #1 tags after filtering in treatment: 19114587 INFO @ Fri, 10 Nov 2017 23:53:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:53:29: #1 finished! INFO @ Fri, 10 Nov 2017 23:53:29: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:53:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:53:32: #2 number of paired peaks: 76511 INFO @ Fri, 10 Nov 2017 23:53:32: start model_add_line... INFO @ Fri, 10 Nov 2017 23:53:32: #2 number of paired peaks: 76511 INFO @ Fri, 10 Nov 2017 23:53:32: start model_add_line... INFO @ Fri, 10 Nov 2017 23:53:33: start X-correlation... INFO @ Fri, 10 Nov 2017 23:53:33: end of X-cor INFO @ Fri, 10 Nov 2017 23:53:33: #2 finished! INFO @ Fri, 10 Nov 2017 23:53:33: #2 predicted fragment length is 241 bps INFO @ Fri, 10 Nov 2017 23:53:33: #2 alternative fragment length(s) may be 241 bps INFO @ Fri, 10 Nov 2017 23:53:33: #2.2 Generate R script for model : SRX1068230.10_model.r INFO @ Fri, 10 Nov 2017 23:53:33: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:53:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:53:33: start X-correlation... INFO @ Fri, 10 Nov 2017 23:53:33: end of X-cor INFO @ Fri, 10 Nov 2017 23:53:33: #2 finished! INFO @ Fri, 10 Nov 2017 23:53:33: #2 predicted fragment length is 241 bps INFO @ Fri, 10 Nov 2017 23:53:33: #2 alternative fragment length(s) may be 241 bps INFO @ Fri, 10 Nov 2017 23:53:33: #2.2 Generate R script for model : SRX1068230.05_model.r INFO @ Fri, 10 Nov 2017 23:53:33: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:53:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:53:34: #2 number of paired peaks: 76511 INFO @ Fri, 10 Nov 2017 23:53:34: start model_add_line... INFO @ Fri, 10 Nov 2017 23:53:34: start X-correlation... INFO @ Fri, 10 Nov 2017 23:53:34: end of X-cor INFO @ Fri, 10 Nov 2017 23:53:34: #2 finished! INFO @ Fri, 10 Nov 2017 23:53:34: #2 predicted fragment length is 241 bps INFO @ Fri, 10 Nov 2017 23:53:34: #2 alternative fragment length(s) may be 241 bps INFO @ Fri, 10 Nov 2017 23:53:34: #2.2 Generate R script for model : SRX1068230.20_model.r INFO @ Fri, 10 Nov 2017 23:53:34: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:53:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:54:34: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:54:37: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:54:39: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:55:07: #4 Write output xls file... SRX1068230.20_peaks.xls INFO @ Fri, 10 Nov 2017 23:55:07: #4 Write peak in narrowPeak format file... SRX1068230.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:55:07: #4 Write summits bed file... SRX1068230.20_summits.bed INFO @ Fri, 10 Nov 2017 23:55:08: Done! pass1 - making usageList (76 chroms): 4 millis pass2 - checking and writing primary data (19893 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:55:10: #4 Write output xls file... SRX1068230.05_peaks.xls INFO @ Fri, 10 Nov 2017 23:55:10: #4 Write peak in narrowPeak format file... SRX1068230.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:55:10: #4 Write summits bed file... SRX1068230.05_summits.bed INFO @ Fri, 10 Nov 2017 23:55:10: Done! pass1 - making usageList (114 chroms): 7 millis pass2 - checking and writing primary data (36282 records, 4 fields): 47 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:55:13: #4 Write output xls file... SRX1068230.10_peaks.xls INFO @ Fri, 10 Nov 2017 23:55:13: #4 Write peak in narrowPeak format file... SRX1068230.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:55:13: #4 Write summits bed file... SRX1068230.10_summits.bed INFO @ Fri, 10 Nov 2017 23:55:13: Done! pass1 - making usageList (95 chroms): 5 millis pass2 - checking and writing primary data (28554 records, 4 fields): 37 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。