Job ID = 9029467 sra ファイルのダウンロード中... Completed: 234073K bytes transferred in 5 seconds (370748K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 22318 0 22318 0 0 2957 0 --:--:-- 0:00:07 --:--:-- 19124 100 53240 0 53240 0 0 6484 0 --:--:-- 0:00:08 --:--:-- 29077 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 9205398 spots for /home/okishinya/chipatlas/results/dm3/SRX1794220/SRR3575253.sra Written 9205398 spots total 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:25 9205398 reads; of these: 9205398 (100.00%) were unpaired; of these: 293340 (3.19%) aligned 0 times 7269216 (78.97%) aligned exactly 1 time 1642842 (17.85%) aligned >1 times 96.81% overall alignment rate Time searching: 00:03:25 Overall time: 00:03:25 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 536373 / 8912058 = 0.0602 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 @ Sat, 03 Jun 2017 13:55:52: # Command line: callpeak -t SRX1794220.bam -f BAM -g dm -n SRX1794220.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1794220.10 # format = BAM # ChIP-seq file = ['SRX1794220.bam'] # control file = None # effective genome size = 1.20e+08 # 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 INFO @ Sat, 03 Jun 2017 13:55:52: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:55:52: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:55:52: # Command line: callpeak -t SRX1794220.bam -f BAM -g dm -n SRX1794220.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1794220.20 # format = BAM # ChIP-seq file = ['SRX1794220.bam'] # control file = None # effective genome size = 1.20e+08 # 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 INFO @ Sat, 03 Jun 2017 13:55:52: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:55:52: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:55:52: # Command line: callpeak -t SRX1794220.bam -f BAM -g dm -n SRX1794220.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1794220.05 # format = BAM # ChIP-seq file = ['SRX1794220.bam'] # control file = None # effective genome size = 1.20e+08 # 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 INFO @ Sat, 03 Jun 2017 13:55:52: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:55:52: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:55:59: 1000000 INFO @ Sat, 03 Jun 2017 13:55:59: 1000000 INFO @ Sat, 03 Jun 2017 13:55:59: 1000000 INFO @ Sat, 03 Jun 2017 13:56:05: 2000000 INFO @ Sat, 03 Jun 2017 13:56:05: 2000000 INFO @ Sat, 03 Jun 2017 13:56:05: 2000000 INFO @ Sat, 03 Jun 2017 13:56:11: 3000000 INFO @ Sat, 03 Jun 2017 13:56:11: 3000000 INFO @ Sat, 03 Jun 2017 13:56:11: 3000000 INFO @ Sat, 03 Jun 2017 13:56:17: 4000000 INFO @ Sat, 03 Jun 2017 13:56:17: 4000000 INFO @ Sat, 03 Jun 2017 13:56:17: 4000000 INFO @ Sat, 03 Jun 2017 13:56:23: 5000000 INFO @ Sat, 03 Jun 2017 13:56:23: 5000000 INFO @ Sat, 03 Jun 2017 13:56:23: 5000000 INFO @ Sat, 03 Jun 2017 13:56:29: 6000000 INFO @ Sat, 03 Jun 2017 13:56:30: 6000000 INFO @ Sat, 03 Jun 2017 13:56:30: 6000000 INFO @ Sat, 03 Jun 2017 13:56:36: 7000000 INFO @ Sat, 03 Jun 2017 13:56:36: 7000000 INFO @ Sat, 03 Jun 2017 13:56:36: 7000000 INFO @ Sat, 03 Jun 2017 13:56:42: 8000000 INFO @ Sat, 03 Jun 2017 13:56:42: 8000000 INFO @ Sat, 03 Jun 2017 13:56:42: 8000000 INFO @ Sat, 03 Jun 2017 13:56:45: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:56:45: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:56:45: #1 total tags in treatment: 8375685 INFO @ Sat, 03 Jun 2017 13:56:45: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:56:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:56:45: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:56:45: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:56:45: #1 total tags in treatment: 8375685 INFO @ Sat, 03 Jun 2017 13:56:45: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:56:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:56:45: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:56:45: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:56:45: #1 total tags in treatment: 8375685 INFO @ Sat, 03 Jun 2017 13:56:45: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:56:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:56:46: #1 tags after filtering in treatment: 8374193 INFO @ Sat, 03 Jun 2017 13:56:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:56:46: #1 finished! INFO @ Sat, 03 Jun 2017 13:56:46: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:56:46: #1 tags after filtering in treatment: 8374193 INFO @ Sat, 03 Jun 2017 13:56:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:56:46: #1 finished! INFO @ Sat, 03 Jun 2017 13:56:46: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:56:46: #1 tags after filtering in treatment: 8374193 INFO @ Sat, 03 Jun 2017 13:56:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:56:46: #1 finished! INFO @ Sat, 03 Jun 2017 13:56:46: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:56:48: #2 number of paired peaks: 2968 INFO @ Sat, 03 Jun 2017 13:56:48: start model_add_line... INFO @ Sat, 03 Jun 2017 13:56:48: #2 number of paired peaks: 2968 INFO @ Sat, 03 Jun 2017 13:56:48: start model_add_line... INFO @ Sat, 03 Jun 2017 13:56:48: #2 number of paired peaks: 2968 INFO @ Sat, 03 Jun 2017 13:56:48: start model_add_line... INFO @ Sat, 03 Jun 2017 13:57:04: start X-correlation... INFO @ Sat, 03 Jun 2017 13:57:04: end of X-cor INFO @ Sat, 03 Jun 2017 13:57:04: #2 finished! INFO @ Sat, 03 Jun 2017 13:57:04: #2 predicted fragment length is 140 bps INFO @ Sat, 03 Jun 2017 13:57:04: #2 alternative fragment length(s) may be 4,140 bps INFO @ Sat, 03 Jun 2017 13:57:04: #2.2 Generate R script for model : SRX1794220.10_model.r INFO @ Sat, 03 Jun 2017 13:57:04: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:57:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:57:05: start X-correlation... INFO @ Sat, 03 Jun 2017 13:57:05: end of X-cor INFO @ Sat, 03 Jun 2017 13:57:05: #2 finished! INFO @ Sat, 03 Jun 2017 13:57:05: #2 predicted fragment length is 140 bps INFO @ Sat, 03 Jun 2017 13:57:05: #2 alternative fragment length(s) may be 4,140 bps INFO @ Sat, 03 Jun 2017 13:57:05: #2.2 Generate R script for model : SRX1794220.05_model.r INFO @ Sat, 03 Jun 2017 13:57:05: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:57:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:57:05: start X-correlation... INFO @ Sat, 03 Jun 2017 13:57:05: end of X-cor INFO @ Sat, 03 Jun 2017 13:57:05: #2 finished! INFO @ Sat, 03 Jun 2017 13:57:05: #2 predicted fragment length is 140 bps INFO @ Sat, 03 Jun 2017 13:57:05: #2 alternative fragment length(s) may be 4,140 bps INFO @ Sat, 03 Jun 2017 13:57:05: #2.2 Generate R script for model : SRX1794220.20_model.r INFO @ Sat, 03 Jun 2017 13:57:05: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:57:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:57:51: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:57:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:57:57: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:58:27: #4 Write output xls file... SRX1794220.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:58:27: #4 Write peak in narrowPeak format file... SRX1794220.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:58:27: #4 Write summits bed file... SRX1794220.10_summits.bed INFO @ Sat, 03 Jun 2017 13:58:27: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2375 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:58:33: #4 Write output xls file... SRX1794220.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:58:34: #4 Write peak in narrowPeak format file... SRX1794220.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:58:34: #4 Write summits bed file... SRX1794220.20_summits.bed INFO @ Sat, 03 Jun 2017 13:58:34: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (580 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:58:36: #4 Write output xls file... SRX1794220.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:58:36: #4 Write peak in narrowPeak format file... SRX1794220.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:58:36: #4 Write summits bed file... SRX1794220.05_summits.bed INFO @ Sat, 03 Jun 2017 13:58:36: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6437 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。