Job ID = 9030248 sra ファイルのダウンロード中... Completed: 522219K bytes transferred in 7 seconds (542804K 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 --:--:-- 0 100 14323 0 14323 0 0 1914 0 --:--:-- 0:00:07 --:--:-- 12915 100 46317 0 46317 0 0 5573 0 --:--:-- 0:00:08 --:--:-- 23874 100 62522 0 62522 0 0 7374 0 --:--:-- 0:00:08 --:--:-- 29701 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 15514865 spots for /home/okishinya/chipatlas/results/dm3/SRX287912/SRR870101.sra Written 15514865 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: 00:05:15 15514865 reads; of these: 15514865 (100.00%) were unpaired; of these: 988966 (6.37%) aligned 0 times 12266080 (79.06%) aligned exactly 1 time 2259819 (14.57%) aligned >1 times 93.63% overall alignment rate Time searching: 00:05:15 Overall time: 00:05:15 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_sort_core] merging from 8 files... [bam_rmdupse_core] 4273204 / 14525899 = 0.2942 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 17:26:31: # Command line: callpeak -t SRX287912.bam -f BAM -g dm -n SRX287912.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX287912.05 # format = BAM # ChIP-seq file = ['SRX287912.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 17:26:31: #1 read tag files... INFO @ Sat, 03 Jun 2017 17:26:31: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 17:26:31: # Command line: callpeak -t SRX287912.bam -f BAM -g dm -n SRX287912.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX287912.10 # format = BAM # ChIP-seq file = ['SRX287912.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 17:26:31: #1 read tag files... INFO @ Sat, 03 Jun 2017 17:26:31: # Command line: callpeak -t SRX287912.bam -f BAM -g dm -n SRX287912.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX287912.20 # format = BAM # ChIP-seq file = ['SRX287912.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 17:26:31: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 17:26:31: #1 read tag files... INFO @ Sat, 03 Jun 2017 17:26:31: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 17:26:38: 1000000 INFO @ Sat, 03 Jun 2017 17:26:39: 1000000 INFO @ Sat, 03 Jun 2017 17:26:39: 1000000 INFO @ Sat, 03 Jun 2017 17:26:45: 2000000 INFO @ Sat, 03 Jun 2017 17:26:46: 2000000 INFO @ Sat, 03 Jun 2017 17:26:46: 2000000 INFO @ Sat, 03 Jun 2017 17:26:51: 3000000 INFO @ Sat, 03 Jun 2017 17:26:52: 3000000 INFO @ Sat, 03 Jun 2017 17:26:52: 3000000 INFO @ Sat, 03 Jun 2017 17:26:57: 4000000 INFO @ Sat, 03 Jun 2017 17:26:59: 4000000 INFO @ Sat, 03 Jun 2017 17:26:59: 4000000 INFO @ Sat, 03 Jun 2017 17:27:04: 5000000 INFO @ Sat, 03 Jun 2017 17:27:06: 5000000 INFO @ Sat, 03 Jun 2017 17:27:06: 5000000 INFO @ Sat, 03 Jun 2017 17:27:10: 6000000 INFO @ Sat, 03 Jun 2017 17:27:13: 6000000 INFO @ Sat, 03 Jun 2017 17:27:13: 6000000 INFO @ Sat, 03 Jun 2017 17:27:17: 7000000 INFO @ Sat, 03 Jun 2017 17:27:20: 7000000 INFO @ Sat, 03 Jun 2017 17:27:20: 7000000 INFO @ Sat, 03 Jun 2017 17:27:23: 8000000 INFO @ Sat, 03 Jun 2017 17:27:27: 8000000 INFO @ Sat, 03 Jun 2017 17:27:27: 8000000 INFO @ Sat, 03 Jun 2017 17:27:30: 9000000 INFO @ Sat, 03 Jun 2017 17:27:35: 9000000 INFO @ Sat, 03 Jun 2017 17:27:35: 9000000 INFO @ Sat, 03 Jun 2017 17:27:39: 10000000 INFO @ Sat, 03 Jun 2017 17:27:41: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 17:27:41: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 17:27:41: #1 total tags in treatment: 10252695 INFO @ Sat, 03 Jun 2017 17:27:41: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 17:27:41: #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 17:27:43: 10000000 INFO @ Sat, 03 Jun 2017 17:27:43: 10000000 INFO @ Sat, 03 Jun 2017 17:27:43: #1 tags after filtering in treatment: 10250179 INFO @ Sat, 03 Jun 2017 17:27:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 17:27:43: #1 finished! INFO @ Sat, 03 Jun 2017 17:27:43: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 17:27:45: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 17:27:45: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 17:27:45: #1 total tags in treatment: 10252695 INFO @ Sat, 03 Jun 2017 17:27:45: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 17:27:45: #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 17:27:45: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 17:27:45: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 17:27:45: #1 total tags in treatment: 10252695 INFO @ Sat, 03 Jun 2017 17:27:45: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 17:27:45: #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 17:27:46: #2 number of paired peaks: 4121 INFO @ Sat, 03 Jun 2017 17:27:46: start model_add_line... INFO @ Sat, 03 Jun 2017 17:27:47: #1 tags after filtering in treatment: 10250179 INFO @ Sat, 03 Jun 2017 17:27:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 17:27:47: #1 finished! INFO @ Sat, 03 Jun 2017 17:27:47: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 17:27:47: #1 tags after filtering in treatment: 10250179 INFO @ Sat, 03 Jun 2017 17:27:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 17:27:47: #1 finished! INFO @ Sat, 03 Jun 2017 17:27:47: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 17:27:49: #2 number of paired peaks: 4121 INFO @ Sat, 03 Jun 2017 17:27:49: start model_add_line... INFO @ Sat, 03 Jun 2017 17:27:49: #2 number of paired peaks: 4121 INFO @ Sat, 03 Jun 2017 17:27:49: start model_add_line... INFO @ Sat, 03 Jun 2017 17:28:11: start X-correlation... INFO @ Sat, 03 Jun 2017 17:28:11: end of X-cor INFO @ Sat, 03 Jun 2017 17:28:11: #2 finished! INFO @ Sat, 03 Jun 2017 17:28:11: #2 predicted fragment length is 297 bps INFO @ Sat, 03 Jun 2017 17:28:11: #2 alternative fragment length(s) may be 297 bps INFO @ Sat, 03 Jun 2017 17:28:11: #2.2 Generate R script for model : SRX287912.10_model.r INFO @ Sat, 03 Jun 2017 17:28:11: #3 Call peaks... INFO @ Sat, 03 Jun 2017 17:28:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 17:28:15: start X-correlation... INFO @ Sat, 03 Jun 2017 17:28:15: end of X-cor INFO @ Sat, 03 Jun 2017 17:28:15: #2 finished! INFO @ Sat, 03 Jun 2017 17:28:15: #2 predicted fragment length is 297 bps INFO @ Sat, 03 Jun 2017 17:28:15: #2 alternative fragment length(s) may be 297 bps INFO @ Sat, 03 Jun 2017 17:28:15: #2.2 Generate R script for model : SRX287912.05_model.r INFO @ Sat, 03 Jun 2017 17:28:15: #3 Call peaks... INFO @ Sat, 03 Jun 2017 17:28:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 17:28:15: start X-correlation... INFO @ Sat, 03 Jun 2017 17:28:15: end of X-cor INFO @ Sat, 03 Jun 2017 17:28:15: #2 finished! INFO @ Sat, 03 Jun 2017 17:28:15: #2 predicted fragment length is 297 bps INFO @ Sat, 03 Jun 2017 17:28:15: #2 alternative fragment length(s) may be 297 bps INFO @ Sat, 03 Jun 2017 17:28:15: #2.2 Generate R script for model : SRX287912.20_model.r INFO @ Sat, 03 Jun 2017 17:28:15: #3 Call peaks... INFO @ Sat, 03 Jun 2017 17:28:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 17:29:25: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 17:29:28: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 17:29:30: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 17:30:20: #4 Write output xls file... SRX287912.10_peaks.xls INFO @ Sat, 03 Jun 2017 17:30:20: #4 Write peak in narrowPeak format file... SRX287912.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 17:30:20: #4 Write summits bed file... SRX287912.10_summits.bed INFO @ Sat, 03 Jun 2017 17:30:20: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6241 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 17:30:24: #4 Write output xls file... SRX287912.20_peaks.xls INFO @ Sat, 03 Jun 2017 17:30:24: #4 Write peak in narrowPeak format file... SRX287912.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 17:30:24: #4 Write summits bed file... SRX287912.20_summits.bed INFO @ Sat, 03 Jun 2017 17:30:24: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4766 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 17:30:31: #4 Write output xls file... SRX287912.05_peaks.xls INFO @ Sat, 03 Jun 2017 17:30:31: #4 Write peak in narrowPeak format file... SRX287912.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 17:30:31: #4 Write summits bed file... SRX287912.05_summits.bed INFO @ Sat, 03 Jun 2017 17:30:31: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7535 records, 4 fields): 11 millis CompletedMACS2peakCalling BigWig に変換しました。