Job ID = 9029496 sra ファイルのダウンロード中... Completed: 313240K bytes transferred in 6 seconds (413893K 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 --:--:-- 0:00:07 --:--:-- 0 100 14324 0 14324 0 0 1849 0 --:--:-- 0:00:07 --:--:-- 12128 100 52659 0 52659 0 0 6142 0 --:--:-- 0:00:08 --:--:-- 26198 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 9053000 spots for /home/okishinya/chipatlas/results/dm3/SRX1794250/SRR3575294.sra Written 9053000 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: 00:02:45 9053000 reads; of these: 9053000 (100.00%) were unpaired; of these: 685763 (7.57%) aligned 0 times 6898318 (76.20%) aligned exactly 1 time 1468919 (16.23%) aligned >1 times 92.43% overall alignment rate Time searching: 00:02:45 Overall time: 00:02:45 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] 504931 / 8367237 = 0.0603 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 14:00:42: # Command line: callpeak -t SRX1794250.bam -f BAM -g dm -n SRX1794250.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1794250.10 # format = BAM # ChIP-seq file = ['SRX1794250.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 14:00:42: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:00:42: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:00:42: # Command line: callpeak -t SRX1794250.bam -f BAM -g dm -n SRX1794250.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1794250.20 # format = BAM # ChIP-seq file = ['SRX1794250.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 14:00:42: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:00:42: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:00:42: # Command line: callpeak -t SRX1794250.bam -f BAM -g dm -n SRX1794250.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1794250.05 # format = BAM # ChIP-seq file = ['SRX1794250.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 14:00:42: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:00:42: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:00:47: 1000000 INFO @ Sat, 03 Jun 2017 14:00:47: 1000000 INFO @ Sat, 03 Jun 2017 14:00:47: 1000000 INFO @ Sat, 03 Jun 2017 14:00:53: 2000000 INFO @ Sat, 03 Jun 2017 14:00:53: 2000000 INFO @ Sat, 03 Jun 2017 14:00:53: 2000000 INFO @ Sat, 03 Jun 2017 14:00:59: 3000000 INFO @ Sat, 03 Jun 2017 14:00:59: 3000000 INFO @ Sat, 03 Jun 2017 14:00:59: 3000000 INFO @ Sat, 03 Jun 2017 14:01:04: 4000000 INFO @ Sat, 03 Jun 2017 14:01:04: 4000000 INFO @ Sat, 03 Jun 2017 14:01:05: 4000000 INFO @ Sat, 03 Jun 2017 14:01:10: 5000000 INFO @ Sat, 03 Jun 2017 14:01:10: 5000000 INFO @ Sat, 03 Jun 2017 14:01:10: 5000000 INFO @ Sat, 03 Jun 2017 14:01:16: 6000000 INFO @ Sat, 03 Jun 2017 14:01:16: 6000000 INFO @ Sat, 03 Jun 2017 14:01:17: 6000000 INFO @ Sat, 03 Jun 2017 14:01:22: 7000000 INFO @ Sat, 03 Jun 2017 14:01:22: 7000000 INFO @ Sat, 03 Jun 2017 14:01:23: 7000000 INFO @ Sat, 03 Jun 2017 14:01:27: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:01:27: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:01:27: #1 total tags in treatment: 7862306 INFO @ Sat, 03 Jun 2017 14:01:27: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:01:27: #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 14:01:28: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:01:28: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:01:28: #1 total tags in treatment: 7862306 INFO @ Sat, 03 Jun 2017 14:01:28: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:01:28: #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 14:01:28: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:01:28: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:01:28: #1 total tags in treatment: 7862306 INFO @ Sat, 03 Jun 2017 14:01:28: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:01:28: #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 14:01:29: #1 tags after filtering in treatment: 7860803 INFO @ Sat, 03 Jun 2017 14:01:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:01:29: #1 finished! INFO @ Sat, 03 Jun 2017 14:01:29: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:01:30: #1 tags after filtering in treatment: 7860803 INFO @ Sat, 03 Jun 2017 14:01:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:01:30: #1 finished! INFO @ Sat, 03 Jun 2017 14:01:30: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:01:30: #1 tags after filtering in treatment: 7860803 INFO @ Sat, 03 Jun 2017 14:01:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:01:30: #1 finished! INFO @ Sat, 03 Jun 2017 14:01:30: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:01:30: #2 number of paired peaks: 3104 INFO @ Sat, 03 Jun 2017 14:01:30: start model_add_line... INFO @ Sat, 03 Jun 2017 14:01:31: #2 number of paired peaks: 3104 INFO @ Sat, 03 Jun 2017 14:01:31: start model_add_line... INFO @ Sat, 03 Jun 2017 14:01:32: #2 number of paired peaks: 3104 INFO @ Sat, 03 Jun 2017 14:01:32: start model_add_line... INFO @ Sat, 03 Jun 2017 14:01:46: start X-correlation... INFO @ Sat, 03 Jun 2017 14:01:46: end of X-cor INFO @ Sat, 03 Jun 2017 14:01:46: #2 finished! INFO @ Sat, 03 Jun 2017 14:01:46: #2 predicted fragment length is 164 bps INFO @ Sat, 03 Jun 2017 14:01:46: #2 alternative fragment length(s) may be 4,164 bps INFO @ Sat, 03 Jun 2017 14:01:46: #2.2 Generate R script for model : SRX1794250.05_model.r INFO @ Sat, 03 Jun 2017 14:01:46: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:01:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:01:48: start X-correlation... INFO @ Sat, 03 Jun 2017 14:01:48: end of X-cor INFO @ Sat, 03 Jun 2017 14:01:48: #2 finished! INFO @ Sat, 03 Jun 2017 14:01:48: #2 predicted fragment length is 164 bps INFO @ Sat, 03 Jun 2017 14:01:48: #2 alternative fragment length(s) may be 4,164 bps INFO @ Sat, 03 Jun 2017 14:01:48: #2.2 Generate R script for model : SRX1794250.10_model.r INFO @ Sat, 03 Jun 2017 14:01:48: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:01:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:01:48: start X-correlation... INFO @ Sat, 03 Jun 2017 14:01:48: end of X-cor INFO @ Sat, 03 Jun 2017 14:01:48: #2 finished! INFO @ Sat, 03 Jun 2017 14:01:48: #2 predicted fragment length is 164 bps INFO @ Sat, 03 Jun 2017 14:01:48: #2 alternative fragment length(s) may be 4,164 bps INFO @ Sat, 03 Jun 2017 14:01:48: #2.2 Generate R script for model : SRX1794250.20_model.r INFO @ Sat, 03 Jun 2017 14:01:48: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:01:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:02:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:02:34: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:02:36: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:03:09: #4 Write output xls file... SRX1794250.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:03:09: #4 Write peak in narrowPeak format file... SRX1794250.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:03:09: #4 Write summits bed file... SRX1794250.20_summits.bed INFO @ Sat, 03 Jun 2017 14:03:09: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (602 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:03:09: #4 Write output xls file... SRX1794250.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:03:09: #4 Write peak in narrowPeak format file... SRX1794250.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:03:09: #4 Write summits bed file... SRX1794250.10_summits.bed INFO @ Sat, 03 Jun 2017 14:03:10: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1993 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:03:10: #4 Write output xls file... SRX1794250.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:03:10: #4 Write peak in narrowPeak format file... SRX1794250.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:03:10: #4 Write summits bed file... SRX1794250.05_summits.bed INFO @ Sat, 03 Jun 2017 14:03:10: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5641 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。