Job ID = 9025508 sra ファイルのダウンロード中... Completed: 95818K bytes transferred in 3 seconds (197249K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:08 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:09 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:09 --:--:-- 0 100 21558 0 21558 0 0 1993 0 --:--:-- 0:00:10 --:--:-- 5077 100 46574 0 46574 0 0 3986 0 --:--:-- 0:00:11 --:--:-- 11326 100 46574 0 46574 0 0 3986 0 --:--:-- 0:00:11 --:--:-- 14970 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 4094047 spots for /home/okishinya/chipatlas/results/ce10/SRX1388757/SRR2832473.sra Written 4094047 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: 00:01:07 4094047 reads; of these: 4094047 (100.00%) were unpaired; of these: 209812 (5.12%) aligned 0 times 3387566 (82.74%) aligned exactly 1 time 496669 (12.13%) aligned >1 times 94.88% overall alignment rate Time searching: 00:01:07 Overall time: 00:01:07 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] 331346 / 3884235 = 0.0853 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 04:11:51: # Command line: callpeak -t SRX1388757.bam -f BAM -g ce -n SRX1388757.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1388757.10 # format = BAM # ChIP-seq file = ['SRX1388757.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 04:11:51: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:11:51: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:11:51: # Command line: callpeak -t SRX1388757.bam -f BAM -g ce -n SRX1388757.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1388757.20 # format = BAM # ChIP-seq file = ['SRX1388757.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 04:11:51: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:11:51: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:11:51: # Command line: callpeak -t SRX1388757.bam -f BAM -g ce -n SRX1388757.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1388757.05 # format = BAM # ChIP-seq file = ['SRX1388757.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 04:11:51: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:11:51: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:11:59: 1000000 INFO @ Sat, 03 Jun 2017 04:11:59: 1000000 INFO @ Sat, 03 Jun 2017 04:11:59: 1000000 INFO @ Sat, 03 Jun 2017 04:12:06: 2000000 INFO @ Sat, 03 Jun 2017 04:12:06: 2000000 INFO @ Sat, 03 Jun 2017 04:12:07: 2000000 INFO @ Sat, 03 Jun 2017 04:12:14: 3000000 INFO @ Sat, 03 Jun 2017 04:12:14: 3000000 INFO @ Sat, 03 Jun 2017 04:12:15: 3000000 INFO @ Sat, 03 Jun 2017 04:12:18: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:12:18: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:12:18: #1 total tags in treatment: 3552889 INFO @ Sat, 03 Jun 2017 04:12:18: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:12:18: #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 04:12:18: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:12:18: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:12:18: #1 total tags in treatment: 3552889 INFO @ Sat, 03 Jun 2017 04:12:18: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:12:18: #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 04:12:18: #1 tags after filtering in treatment: 3552357 INFO @ Sat, 03 Jun 2017 04:12:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:12:18: #1 finished! INFO @ Sat, 03 Jun 2017 04:12:18: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:12:18: #1 tags after filtering in treatment: 3552357 INFO @ Sat, 03 Jun 2017 04:12:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:12:18: #1 finished! INFO @ Sat, 03 Jun 2017 04:12:18: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:12:19: #2 number of paired peaks: 2937 INFO @ Sat, 03 Jun 2017 04:12:19: start model_add_line... INFO @ Sat, 03 Jun 2017 04:12:19: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:12:19: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:12:19: #1 total tags in treatment: 3552889 INFO @ Sat, 03 Jun 2017 04:12:19: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:12:19: #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 04:12:19: #2 number of paired peaks: 2937 INFO @ Sat, 03 Jun 2017 04:12:19: start model_add_line... INFO @ Sat, 03 Jun 2017 04:12:20: #1 tags after filtering in treatment: 3552357 INFO @ Sat, 03 Jun 2017 04:12:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:12:20: #1 finished! INFO @ Sat, 03 Jun 2017 04:12:20: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:12:21: #2 number of paired peaks: 2937 INFO @ Sat, 03 Jun 2017 04:12:21: start model_add_line... INFO @ Sat, 03 Jun 2017 04:12:30: start X-correlation... INFO @ Sat, 03 Jun 2017 04:12:30: end of X-cor INFO @ Sat, 03 Jun 2017 04:12:30: #2 finished! INFO @ Sat, 03 Jun 2017 04:12:30: #2 predicted fragment length is 176 bps INFO @ Sat, 03 Jun 2017 04:12:30: #2 alternative fragment length(s) may be 4,176 bps INFO @ Sat, 03 Jun 2017 04:12:30: #2.2 Generate R script for model : SRX1388757.10_model.r INFO @ Sat, 03 Jun 2017 04:12:30: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:12:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:12:31: start X-correlation... INFO @ Sat, 03 Jun 2017 04:12:31: end of X-cor INFO @ Sat, 03 Jun 2017 04:12:31: #2 finished! INFO @ Sat, 03 Jun 2017 04:12:31: #2 predicted fragment length is 176 bps INFO @ Sat, 03 Jun 2017 04:12:31: #2 alternative fragment length(s) may be 4,176 bps INFO @ Sat, 03 Jun 2017 04:12:31: #2.2 Generate R script for model : SRX1388757.20_model.r INFO @ Sat, 03 Jun 2017 04:12:31: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:12:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:12:32: start X-correlation... INFO @ Sat, 03 Jun 2017 04:12:32: end of X-cor INFO @ Sat, 03 Jun 2017 04:12:32: #2 finished! INFO @ Sat, 03 Jun 2017 04:12:32: #2 predicted fragment length is 176 bps INFO @ Sat, 03 Jun 2017 04:12:32: #2 alternative fragment length(s) may be 4,176 bps INFO @ Sat, 03 Jun 2017 04:12:32: #2.2 Generate R script for model : SRX1388757.05_model.r INFO @ Sat, 03 Jun 2017 04:12:32: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:12:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:12:53: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:12:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:12:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:13:08: #4 Write output xls file... SRX1388757.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:13:08: #4 Write peak in narrowPeak format file... SRX1388757.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:13:08: #4 Write summits bed file... SRX1388757.20_summits.bed INFO @ Sat, 03 Jun 2017 04:13:08: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (330 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:13:10: #4 Write output xls file... SRX1388757.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:13:10: #4 Write peak in narrowPeak format file... SRX1388757.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:13:10: #4 Write summits bed file... SRX1388757.10_summits.bed INFO @ Sat, 03 Jun 2017 04:13:10: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1046 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:13:12: #4 Write output xls file... SRX1388757.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:13:12: #4 Write peak in narrowPeak format file... SRX1388757.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:13:12: #4 Write summits bed file... SRX1388757.05_summits.bed INFO @ Sat, 03 Jun 2017 04:13:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2441 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。