Job ID = 9025509 sra ファイルのダウンロード中... Completed: 104493K bytes transferred in 4 seconds (207414K 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 14324 0 14324 0 0 1882 0 --:--:-- 0:00:07 --:--:-- 13513 100 38318 0 38318 0 0 4452 0 --:--:-- 0:00:08 --:--:-- 18646 100 46318 0 46318 0 0 5255 0 --:--:-- 0:00:08 --:--:-- 20467 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 4494469 spots for /home/okishinya/chipatlas/results/ce10/SRX1388758/SRR2832474.sra Written 4494469 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: 00:01:20 4494469 reads; of these: 4494469 (100.00%) were unpaired; of these: 180647 (4.02%) aligned 0 times 3793444 (84.40%) aligned exactly 1 time 520378 (11.58%) aligned >1 times 95.98% overall alignment rate Time searching: 00:01:20 Overall time: 00:01:20 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 398723 / 4313822 = 0.0924 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 04:12:56: # Command line: callpeak -t SRX1388758.bam -f BAM -g ce -n SRX1388758.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1388758.20 # format = BAM # ChIP-seq file = ['SRX1388758.bam'] # control file = None # effective genome size = 9.00e+07 # 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 04:12:56: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:12:56: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:12:56: # Command line: callpeak -t SRX1388758.bam -f BAM -g ce -n SRX1388758.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1388758.05 # format = BAM # ChIP-seq file = ['SRX1388758.bam'] # control file = None # effective genome size = 9.00e+07 # 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 04:12:56: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:12:56: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:12:56: # Command line: callpeak -t SRX1388758.bam -f BAM -g ce -n SRX1388758.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1388758.10 # format = BAM # ChIP-seq file = ['SRX1388758.bam'] # control file = None # effective genome size = 9.00e+07 # 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 04:12:56: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:12:56: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:13:02: 1000000 INFO @ Sat, 03 Jun 2017 04:13:02: 1000000 INFO @ Sat, 03 Jun 2017 04:13:02: 1000000 INFO @ Sat, 03 Jun 2017 04:13:07: 2000000 INFO @ Sat, 03 Jun 2017 04:13:08: 2000000 INFO @ Sat, 03 Jun 2017 04:13:08: 2000000 INFO @ Sat, 03 Jun 2017 04:13:13: 3000000 INFO @ Sat, 03 Jun 2017 04:13:14: 3000000 INFO @ Sat, 03 Jun 2017 04:13:14: 3000000 INFO @ Sat, 03 Jun 2017 04:13:18: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:13:18: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:13:18: #1 total tags in treatment: 3915099 INFO @ Sat, 03 Jun 2017 04:13:18: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:13:18: #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 04:13:19: #1 tags after filtering in treatment: 3914472 INFO @ Sat, 03 Jun 2017 04:13:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:13:19: #1 finished! INFO @ Sat, 03 Jun 2017 04:13:19: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:13:19: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:13:19: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:13:19: #1 total tags in treatment: 3915099 INFO @ Sat, 03 Jun 2017 04:13:19: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:13:19: #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 04:13:19: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:13:19: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:13:19: #1 total tags in treatment: 3915099 INFO @ Sat, 03 Jun 2017 04:13:19: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:13:19: #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 04:13:20: #1 tags after filtering in treatment: 3914472 INFO @ Sat, 03 Jun 2017 04:13:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:13:20: #1 finished! INFO @ Sat, 03 Jun 2017 04:13:20: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:13:20: #1 tags after filtering in treatment: 3914472 INFO @ Sat, 03 Jun 2017 04:13:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:13:20: #1 finished! INFO @ Sat, 03 Jun 2017 04:13:20: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:13:20: #2 number of paired peaks: 3272 INFO @ Sat, 03 Jun 2017 04:13:20: start model_add_line... INFO @ Sat, 03 Jun 2017 04:13:21: #2 number of paired peaks: 3272 INFO @ Sat, 03 Jun 2017 04:13:21: start model_add_line... INFO @ Sat, 03 Jun 2017 04:13:21: #2 number of paired peaks: 3272 INFO @ Sat, 03 Jun 2017 04:13:21: start model_add_line... INFO @ Sat, 03 Jun 2017 04:13:34: start X-correlation... INFO @ Sat, 03 Jun 2017 04:13:34: end of X-cor INFO @ Sat, 03 Jun 2017 04:13:34: #2 finished! INFO @ Sat, 03 Jun 2017 04:13:34: #2 predicted fragment length is 186 bps INFO @ Sat, 03 Jun 2017 04:13:34: #2 alternative fragment length(s) may be 186 bps INFO @ Sat, 03 Jun 2017 04:13:34: #2.2 Generate R script for model : SRX1388758.05_model.r INFO @ Sat, 03 Jun 2017 04:13:34: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:13:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:13:34: start X-correlation... INFO @ Sat, 03 Jun 2017 04:13:34: end of X-cor INFO @ Sat, 03 Jun 2017 04:13:34: #2 finished! INFO @ Sat, 03 Jun 2017 04:13:34: #2 predicted fragment length is 186 bps INFO @ Sat, 03 Jun 2017 04:13:34: #2 alternative fragment length(s) may be 186 bps INFO @ Sat, 03 Jun 2017 04:13:34: #2.2 Generate R script for model : SRX1388758.10_model.r INFO @ Sat, 03 Jun 2017 04:13:34: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:13:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:13:34: start X-correlation... INFO @ Sat, 03 Jun 2017 04:13:34: end of X-cor INFO @ Sat, 03 Jun 2017 04:13:34: #2 finished! INFO @ Sat, 03 Jun 2017 04:13:34: #2 predicted fragment length is 186 bps INFO @ Sat, 03 Jun 2017 04:13:34: #2 alternative fragment length(s) may be 186 bps INFO @ Sat, 03 Jun 2017 04:13:34: #2.2 Generate R script for model : SRX1388758.20_model.r INFO @ Sat, 03 Jun 2017 04:13:34: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:13:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:13:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:14:00: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:14:00: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:14:18: #4 Write output xls file... SRX1388758.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:14:18: #4 Write peak in narrowPeak format file... SRX1388758.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:14:18: #4 Write summits bed file... SRX1388758.10_summits.bed INFO @ Sat, 03 Jun 2017 04:14:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1664 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:14:19: #4 Write output xls file... SRX1388758.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:14:19: #4 Write peak in narrowPeak format file... SRX1388758.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:14:19: #4 Write summits bed file... SRX1388758.20_summits.bed INFO @ Sat, 03 Jun 2017 04:14:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (616 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 04:14:20: #4 Write output xls file... SRX1388758.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:14:20: #4 Write peak in narrowPeak format file... SRX1388758.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:14:20: #4 Write summits bed file... SRX1388758.05_summits.bed INFO @ Sat, 03 Jun 2017 04:14:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3456 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。