Job ID = 10487615 sra ファイルのダウンロード中... Completed: 854531K bytes transferred in 19 seconds (352214K 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 23243190 spots for /home/okishinya/chipatlas/results/rn6/SRX3358571/SRR6251630.sra Written 23243190 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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:32:39 23243190 reads; of these: 23243190 (100.00%) were unpaired; of these: 800199 (3.44%) aligned 0 times 20175199 (86.80%) aligned exactly 1 time 2267792 (9.76%) aligned >1 times 96.56% overall alignment rate Time searching: 00:32:44 Overall time: 00:32:44 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] 2467100 / 22442991 = 0.1099 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 @ Sun, 18 Mar 2018 10:59:17: # Command line: callpeak -t SRX3358571.bam -f BAM -g 2.15e9 -n SRX3358571.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3358571.10 # format = BAM # ChIP-seq file = ['SRX3358571.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 @ Sun, 18 Mar 2018 10:59:17: #1 read tag files... INFO @ Sun, 18 Mar 2018 10:59:17: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 10:59:17: # Command line: callpeak -t SRX3358571.bam -f BAM -g 2.15e9 -n SRX3358571.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3358571.05 # format = BAM # ChIP-seq file = ['SRX3358571.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 @ Sun, 18 Mar 2018 10:59:17: #1 read tag files... INFO @ Sun, 18 Mar 2018 10:59:17: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 10:59:17: # Command line: callpeak -t SRX3358571.bam -f BAM -g 2.15e9 -n SRX3358571.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3358571.20 # format = BAM # ChIP-seq file = ['SRX3358571.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 @ Sun, 18 Mar 2018 10:59:17: #1 read tag files... INFO @ Sun, 18 Mar 2018 10:59:17: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 10:59:27: 1000000 INFO @ Sun, 18 Mar 2018 10:59:30: 1000000 INFO @ Sun, 18 Mar 2018 10:59:30: 1000000 INFO @ Sun, 18 Mar 2018 10:59:37: 2000000 INFO @ Sun, 18 Mar 2018 10:59:42: 2000000 INFO @ Sun, 18 Mar 2018 10:59:43: 2000000 INFO @ Sun, 18 Mar 2018 10:59:48: 3000000 INFO @ Sun, 18 Mar 2018 10:59:57: 3000000 INFO @ Sun, 18 Mar 2018 10:59:57: 3000000 INFO @ Sun, 18 Mar 2018 10:59:59: 4000000 INFO @ Sun, 18 Mar 2018 11:00:08: 5000000 INFO @ Sun, 18 Mar 2018 11:00:10: 4000000 INFO @ Sun, 18 Mar 2018 11:00:11: 4000000 INFO @ Sun, 18 Mar 2018 11:00:18: 6000000 INFO @ Sun, 18 Mar 2018 11:00:23: 5000000 INFO @ Sun, 18 Mar 2018 11:00:25: 5000000 INFO @ Sun, 18 Mar 2018 11:00:27: 7000000 INFO @ Sun, 18 Mar 2018 11:00:31: 6000000 INFO @ Sun, 18 Mar 2018 11:00:38: 8000000 INFO @ Sun, 18 Mar 2018 11:00:39: 6000000 INFO @ Sun, 18 Mar 2018 11:00:42: 7000000 INFO @ Sun, 18 Mar 2018 11:00:49: 9000000 INFO @ Sun, 18 Mar 2018 11:00:50: 7000000 INFO @ Sun, 18 Mar 2018 11:00:56: 8000000 INFO @ Sun, 18 Mar 2018 11:01:02: 8000000 INFO @ Sun, 18 Mar 2018 11:01:03: 10000000 INFO @ Sun, 18 Mar 2018 11:01:10: 9000000 INFO @ Sun, 18 Mar 2018 11:01:12: 9000000 INFO @ Sun, 18 Mar 2018 11:01:13: 11000000 INFO @ Sun, 18 Mar 2018 11:01:22: 10000000 INFO @ Sun, 18 Mar 2018 11:01:24: 10000000 INFO @ Sun, 18 Mar 2018 11:01:25: 12000000 INFO @ Sun, 18 Mar 2018 11:01:33: 11000000 INFO @ Sun, 18 Mar 2018 11:01:33: 13000000 INFO @ Sun, 18 Mar 2018 11:01:37: 11000000 INFO @ Sun, 18 Mar 2018 11:01:41: 14000000 INFO @ Sun, 18 Mar 2018 11:01:45: 12000000 INFO @ Sun, 18 Mar 2018 11:01:49: 15000000 INFO @ Sun, 18 Mar 2018 11:01:50: 12000000 INFO @ Sun, 18 Mar 2018 11:01:56: 16000000 INFO @ Sun, 18 Mar 2018 11:01:58: 13000000 INFO @ Sun, 18 Mar 2018 11:02:01: 13000000 INFO @ Sun, 18 Mar 2018 11:02:04: 17000000 INFO @ Sun, 18 Mar 2018 11:02:12: 18000000 INFO @ Sun, 18 Mar 2018 11:02:13: 14000000 INFO @ Sun, 18 Mar 2018 11:02:13: 14000000 INFO @ Sun, 18 Mar 2018 11:02:19: 19000000 INFO @ Sun, 18 Mar 2018 11:02:21: 15000000 INFO @ Sun, 18 Mar 2018 11:02:22: 15000000 INFO @ Sun, 18 Mar 2018 11:02:27: #1 tag size is determined as 75 bps INFO @ Sun, 18 Mar 2018 11:02:27: #1 tag size = 75 INFO @ Sun, 18 Mar 2018 11:02:27: #1 total tags in treatment: 19975891 INFO @ Sun, 18 Mar 2018 11:02:27: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 11:02:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 11:02:28: #1 tags after filtering in treatment: 19975675 INFO @ Sun, 18 Mar 2018 11:02:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 11:02:28: #1 finished! INFO @ Sun, 18 Mar 2018 11:02:28: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 11:02:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 11:02:30: 16000000 INFO @ Sun, 18 Mar 2018 11:02:30: 16000000 INFO @ Sun, 18 Mar 2018 11:02:33: #2 number of paired peaks: 90638 INFO @ Sun, 18 Mar 2018 11:02:33: start model_add_line... INFO @ Sun, 18 Mar 2018 11:02:34: start X-correlation... INFO @ Sun, 18 Mar 2018 11:02:34: end of X-cor INFO @ Sun, 18 Mar 2018 11:02:34: #2 finished! INFO @ Sun, 18 Mar 2018 11:02:34: #2 predicted fragment length is 222 bps INFO @ Sun, 18 Mar 2018 11:02:34: #2 alternative fragment length(s) may be 222 bps INFO @ Sun, 18 Mar 2018 11:02:34: #2.2 Generate R script for model : SRX3358571.20_model.r INFO @ Sun, 18 Mar 2018 11:02:34: #3 Call peaks... INFO @ Sun, 18 Mar 2018 11:02:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:02:39: 17000000 INFO @ Sun, 18 Mar 2018 11:02:39: 17000000 INFO @ Sun, 18 Mar 2018 11:02:47: 18000000 INFO @ Sun, 18 Mar 2018 11:02:48: 18000000 INFO @ Sun, 18 Mar 2018 11:02:56: 19000000 INFO @ Sun, 18 Mar 2018 11:02:56: 19000000 INFO @ Sun, 18 Mar 2018 11:03:04: #1 tag size is determined as 75 bps INFO @ Sun, 18 Mar 2018 11:03:04: #1 tag size = 75 INFO @ Sun, 18 Mar 2018 11:03:04: #1 total tags in treatment: 19975891 INFO @ Sun, 18 Mar 2018 11:03:04: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 11:03:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 11:03:05: #1 tag size is determined as 75 bps INFO @ Sun, 18 Mar 2018 11:03:05: #1 tag size = 75 INFO @ Sun, 18 Mar 2018 11:03:05: #1 total tags in treatment: 19975891 INFO @ Sun, 18 Mar 2018 11:03:05: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 11:03:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 11:03:05: #1 tags after filtering in treatment: 19975675 INFO @ Sun, 18 Mar 2018 11:03:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 11:03:05: #1 finished! INFO @ Sun, 18 Mar 2018 11:03:05: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 11:03:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 11:03:05: #1 tags after filtering in treatment: 19975675 INFO @ Sun, 18 Mar 2018 11:03:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 11:03:05: #1 finished! INFO @ Sun, 18 Mar 2018 11:03:05: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 11:03:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 11:03:10: #2 number of paired peaks: 90638 INFO @ Sun, 18 Mar 2018 11:03:10: start model_add_line... INFO @ Sun, 18 Mar 2018 11:03:11: #2 number of paired peaks: 90638 INFO @ Sun, 18 Mar 2018 11:03:11: start model_add_line... INFO @ Sun, 18 Mar 2018 11:03:11: start X-correlation... INFO @ Sun, 18 Mar 2018 11:03:11: end of X-cor INFO @ Sun, 18 Mar 2018 11:03:11: #2 finished! INFO @ Sun, 18 Mar 2018 11:03:11: #2 predicted fragment length is 222 bps INFO @ Sun, 18 Mar 2018 11:03:11: #2 alternative fragment length(s) may be 222 bps INFO @ Sun, 18 Mar 2018 11:03:11: #2.2 Generate R script for model : SRX3358571.10_model.r INFO @ Sun, 18 Mar 2018 11:03:11: #3 Call peaks... INFO @ Sun, 18 Mar 2018 11:03:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:03:11: start X-correlation... INFO @ Sun, 18 Mar 2018 11:03:11: end of X-cor INFO @ Sun, 18 Mar 2018 11:03:11: #2 finished! INFO @ Sun, 18 Mar 2018 11:03:11: #2 predicted fragment length is 222 bps INFO @ Sun, 18 Mar 2018 11:03:11: #2 alternative fragment length(s) may be 222 bps INFO @ Sun, 18 Mar 2018 11:03:11: #2.2 Generate R script for model : SRX3358571.05_model.r INFO @ Sun, 18 Mar 2018 11:03:11: #3 Call peaks... INFO @ Sun, 18 Mar 2018 11:03:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:03:35: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:04:14: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:04:19: #4 Write output xls file... SRX3358571.20_peaks.xls INFO @ Sun, 18 Mar 2018 11:04:19: #4 Write peak in narrowPeak format file... SRX3358571.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:04:19: #4 Write summits bed file... SRX3358571.20_summits.bed INFO @ Sun, 18 Mar 2018 11:04:19: Done! pass1 - making usageList (64 chroms): 8 millis pass2 - checking and writing primary data (18029 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 11:04:27: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:05:05: #4 Write output xls file... SRX3358571.10_peaks.xls INFO @ Sun, 18 Mar 2018 11:05:06: #4 Write peak in narrowPeak format file... SRX3358571.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:05:06: #4 Write summits bed file... SRX3358571.10_summits.bed INFO @ Sun, 18 Mar 2018 11:05:06: Done! pass1 - making usageList (94 chroms): 10 millis pass2 - checking and writing primary data (29097 records, 4 fields): 73 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 11:05:17: #4 Write output xls file... SRX3358571.05_peaks.xls INFO @ Sun, 18 Mar 2018 11:05:18: #4 Write peak in narrowPeak format file... SRX3358571.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:05:18: #4 Write summits bed file... SRX3358571.05_summits.bed INFO @ Sun, 18 Mar 2018 11:05:18: Done! pass1 - making usageList (116 chroms): 11 millis pass2 - checking and writing primary data (40782 records, 4 fields): 109 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。