Job ID = 9032346 sra ファイルのダウンロード中... Completed: 71994K bytes transferred in 3 seconds (152937K 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 1820 0 --:--:-- 0:00:07 --:--:-- 10818 100 31841 0 31841 0 0 3660 0 --:--:-- 0:00:08 --:--:-- 14789 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 5589244 spots for /home/okishinya/chipatlas/results/dm3/SRX858991/SRR1779547.sra Written 5589244 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:08 5589244 reads; of these: 5589244 (100.00%) were unpaired; of these: 85009 (1.52%) aligned 0 times 5354721 (95.80%) aligned exactly 1 time 149514 (2.68%) aligned >1 times 98.48% overall alignment rate Time searching: 00:01:09 Overall time: 00:01:09 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] 187 / 5504235 = 0.0000 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 23:43:33: # Command line: callpeak -t SRX858991.bam -f BAM -g dm -n SRX858991.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX858991.05 # format = BAM # ChIP-seq file = ['SRX858991.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 23:43:33: # Command line: callpeak -t SRX858991.bam -f BAM -g dm -n SRX858991.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX858991.10 # format = BAM # ChIP-seq file = ['SRX858991.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 23:43:33: #1 read tag files... INFO @ Sat, 03 Jun 2017 23:43:33: # Command line: callpeak -t SRX858991.bam -f BAM -g dm -n SRX858991.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX858991.20 # format = BAM # ChIP-seq file = ['SRX858991.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 23:43:33: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 23:43:33: #1 read tag files... INFO @ Sat, 03 Jun 2017 23:43:33: #1 read tag files... INFO @ Sat, 03 Jun 2017 23:43:33: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 23:43:33: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 23:43:38: 1000000 INFO @ Sat, 03 Jun 2017 23:43:39: 1000000 INFO @ Sat, 03 Jun 2017 23:43:39: 1000000 INFO @ Sat, 03 Jun 2017 23:43:44: 2000000 INFO @ Sat, 03 Jun 2017 23:43:44: 2000000 INFO @ Sat, 03 Jun 2017 23:43:44: 2000000 INFO @ Sat, 03 Jun 2017 23:43:49: 3000000 INFO @ Sat, 03 Jun 2017 23:43:49: 3000000 INFO @ Sat, 03 Jun 2017 23:43:49: 3000000 INFO @ Sat, 03 Jun 2017 23:43:54: 4000000 INFO @ Sat, 03 Jun 2017 23:43:55: 4000000 INFO @ Sat, 03 Jun 2017 23:43:55: 4000000 INFO @ Sat, 03 Jun 2017 23:43:59: 5000000 INFO @ Sat, 03 Jun 2017 23:44:00: 5000000 INFO @ Sat, 03 Jun 2017 23:44:00: 5000000 INFO @ Sat, 03 Jun 2017 23:44:01: #1 tag size is determined as 34 bps INFO @ Sat, 03 Jun 2017 23:44:01: #1 tag size = 34 INFO @ Sat, 03 Jun 2017 23:44:01: #1 total tags in treatment: 5504048 INFO @ Sat, 03 Jun 2017 23:44:01: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 23:44:01: #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 23:44:03: #1 tags after filtering in treatment: 5504014 INFO @ Sat, 03 Jun 2017 23:44:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 23:44:03: #1 finished! INFO @ Sat, 03 Jun 2017 23:44:03: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 23:44:03: #1 tag size is determined as 34 bps INFO @ Sat, 03 Jun 2017 23:44:03: #1 tag size is determined as 34 bps INFO @ Sat, 03 Jun 2017 23:44:03: #1 tag size = 34 INFO @ Sat, 03 Jun 2017 23:44:03: #1 tag size = 34 INFO @ Sat, 03 Jun 2017 23:44:03: #1 total tags in treatment: 5504048 INFO @ Sat, 03 Jun 2017 23:44:03: #1 total tags in treatment: 5504048 INFO @ Sat, 03 Jun 2017 23:44:03: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 23:44:03: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 23:44:03: #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 23:44:03: #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 23:44:04: #1 tags after filtering in treatment: 5504014 INFO @ Sat, 03 Jun 2017 23:44:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 23:44:04: #1 finished! INFO @ Sat, 03 Jun 2017 23:44:04: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 23:44:04: #1 tags after filtering in treatment: 5504014 INFO @ Sat, 03 Jun 2017 23:44:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 23:44:04: #1 finished! INFO @ Sat, 03 Jun 2017 23:44:04: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 23:44:04: #2 number of paired peaks: 3550 INFO @ Sat, 03 Jun 2017 23:44:04: start model_add_line... INFO @ Sat, 03 Jun 2017 23:44:05: #2 number of paired peaks: 3550 INFO @ Sat, 03 Jun 2017 23:44:05: start model_add_line... INFO @ Sat, 03 Jun 2017 23:44:06: #2 number of paired peaks: 3550 INFO @ Sat, 03 Jun 2017 23:44:06: start model_add_line... INFO @ Sat, 03 Jun 2017 23:44:21: start X-correlation... INFO @ Sat, 03 Jun 2017 23:44:21: end of X-cor INFO @ Sat, 03 Jun 2017 23:44:21: #2 finished! INFO @ Sat, 03 Jun 2017 23:44:21: #2 predicted fragment length is 105 bps INFO @ Sat, 03 Jun 2017 23:44:21: #2 alternative fragment length(s) may be 105 bps INFO @ Sat, 03 Jun 2017 23:44:21: #2.2 Generate R script for model : SRX858991.10_model.r INFO @ Sat, 03 Jun 2017 23:44:21: #3 Call peaks... INFO @ Sat, 03 Jun 2017 23:44:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 23:44:22: start X-correlation... INFO @ Sat, 03 Jun 2017 23:44:22: end of X-cor INFO @ Sat, 03 Jun 2017 23:44:22: #2 finished! INFO @ Sat, 03 Jun 2017 23:44:22: #2 predicted fragment length is 105 bps INFO @ Sat, 03 Jun 2017 23:44:22: #2 alternative fragment length(s) may be 105 bps INFO @ Sat, 03 Jun 2017 23:44:22: #2.2 Generate R script for model : SRX858991.05_model.r INFO @ Sat, 03 Jun 2017 23:44:22: #3 Call peaks... INFO @ Sat, 03 Jun 2017 23:44:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 23:44:23: start X-correlation... INFO @ Sat, 03 Jun 2017 23:44:23: end of X-cor INFO @ Sat, 03 Jun 2017 23:44:23: #2 finished! INFO @ Sat, 03 Jun 2017 23:44:23: #2 predicted fragment length is 105 bps INFO @ Sat, 03 Jun 2017 23:44:23: #2 alternative fragment length(s) may be 105 bps INFO @ Sat, 03 Jun 2017 23:44:23: #2.2 Generate R script for model : SRX858991.20_model.r INFO @ Sat, 03 Jun 2017 23:44:23: #3 Call peaks... INFO @ Sat, 03 Jun 2017 23:44:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 23:44:52: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 23:44:57: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 23:44:58: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 23:45:19: #4 Write output xls file... SRX858991.10_peaks.xls INFO @ Sat, 03 Jun 2017 23:45:19: #4 Write peak in narrowPeak format file... SRX858991.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 23:45:19: #4 Write summits bed file... SRX858991.10_summits.bed INFO @ Sat, 03 Jun 2017 23:45:19: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5952 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 23:45:22: #4 Write output xls file... SRX858991.20_peaks.xls INFO @ Sat, 03 Jun 2017 23:45:22: #4 Write peak in narrowPeak format file... SRX858991.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 23:45:22: #4 Write summits bed file... SRX858991.20_summits.bed INFO @ Sat, 03 Jun 2017 23:45:22: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3046 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 23:45:26: #4 Write output xls file... SRX858991.05_peaks.xls INFO @ Sat, 03 Jun 2017 23:45:26: #4 Write peak in narrowPeak format file... SRX858991.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 23:45:26: #4 Write summits bed file... SRX858991.05_summits.bed INFO @ Sat, 03 Jun 2017 23:45:27: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9446 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。