Job ID = 9032357 sra ファイルのダウンロード中... Completed: 81885K bytes transferred in 3 seconds (173301K 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 14324 0 14324 0 0 1884 0 --:--:-- 0:00:07 --:--:-- 13920 100 31842 0 31842 0 0 3776 0 --:--:-- 0:00:08 --:--:-- 17137 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 6874820 spots for /home/okishinya/chipatlas/results/dm3/SRX858993/SRR1779549.sra Written 6874820 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: 00:01:01 6874820 reads; of these: 6874820 (100.00%) were unpaired; of these: 165528 (2.41%) aligned 0 times 6533118 (95.03%) aligned exactly 1 time 176174 (2.56%) aligned >1 times 97.59% overall alignment rate Time searching: 00:01:02 Overall time: 00:01:02 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] 248 / 6709292 = 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 23:44:15: # Command line: callpeak -t SRX858993.bam -f BAM -g dm -n SRX858993.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX858993.05 # format = BAM # ChIP-seq file = ['SRX858993.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 23:44:15: #1 read tag files... INFO @ Sat, 03 Jun 2017 23:44:15: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 23:44:15: # Command line: callpeak -t SRX858993.bam -f BAM -g dm -n SRX858993.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX858993.10 # format = BAM # ChIP-seq file = ['SRX858993.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 23:44:15: #1 read tag files... INFO @ Sat, 03 Jun 2017 23:44:15: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 23:44:15: # Command line: callpeak -t SRX858993.bam -f BAM -g dm -n SRX858993.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX858993.20 # format = BAM # ChIP-seq file = ['SRX858993.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 23:44:15: #1 read tag files... INFO @ Sat, 03 Jun 2017 23:44:15: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 23:44:21: 1000000 INFO @ Sat, 03 Jun 2017 23:44:22: 1000000 INFO @ Sat, 03 Jun 2017 23:44:22: 1000000 INFO @ Sat, 03 Jun 2017 23:44:28: 2000000 INFO @ Sat, 03 Jun 2017 23:44:28: 2000000 INFO @ Sat, 03 Jun 2017 23:44:28: 2000000 INFO @ Sat, 03 Jun 2017 23:44:34: 3000000 INFO @ Sat, 03 Jun 2017 23:44:35: 3000000 INFO @ Sat, 03 Jun 2017 23:44:35: 3000000 INFO @ Sat, 03 Jun 2017 23:44:41: 4000000 INFO @ Sat, 03 Jun 2017 23:44:41: 4000000 INFO @ Sat, 03 Jun 2017 23:44:41: 4000000 INFO @ Sat, 03 Jun 2017 23:44:47: 5000000 INFO @ Sat, 03 Jun 2017 23:44:48: 5000000 INFO @ Sat, 03 Jun 2017 23:44:48: 5000000 INFO @ Sat, 03 Jun 2017 23:44:53: 6000000 INFO @ Sat, 03 Jun 2017 23:44:54: 6000000 INFO @ Sat, 03 Jun 2017 23:44:54: 6000000 INFO @ Sat, 03 Jun 2017 23:44:58: #1 tag size is determined as 34 bps INFO @ Sat, 03 Jun 2017 23:44:58: #1 tag size = 34 INFO @ Sat, 03 Jun 2017 23:44:58: #1 total tags in treatment: 6709044 INFO @ Sat, 03 Jun 2017 23:44:58: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 23:44:58: #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 23:44:59: #1 tag size is determined as 34 bps INFO @ Sat, 03 Jun 2017 23:44:59: #1 tag size = 34 INFO @ Sat, 03 Jun 2017 23:44:59: #1 total tags in treatment: 6709044 INFO @ Sat, 03 Jun 2017 23:44:59: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 23:44:59: #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 23:44:59: #1 tag size is determined as 34 bps INFO @ Sat, 03 Jun 2017 23:44:59: #1 tag size = 34 INFO @ Sat, 03 Jun 2017 23:44:59: #1 total tags in treatment: 6709044 INFO @ Sat, 03 Jun 2017 23:44:59: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 23:44:59: #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 23:44:59: #1 tags after filtering in treatment: 6709009 INFO @ Sat, 03 Jun 2017 23:44:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 23:44:59: #1 finished! INFO @ Sat, 03 Jun 2017 23:44:59: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 23:45:00: #1 tags after filtering in treatment: 6709009 INFO @ Sat, 03 Jun 2017 23:45:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 23:45:00: #1 finished! INFO @ Sat, 03 Jun 2017 23:45:00: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 23:45:00: #1 tags after filtering in treatment: 6709009 INFO @ Sat, 03 Jun 2017 23:45:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 23:45:00: #1 finished! INFO @ Sat, 03 Jun 2017 23:45:00: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 23:45:01: #2 number of paired peaks: 2691 INFO @ Sat, 03 Jun 2017 23:45:01: start model_add_line... INFO @ Sat, 03 Jun 2017 23:45:01: #2 number of paired peaks: 2691 INFO @ Sat, 03 Jun 2017 23:45:01: start model_add_line... INFO @ Sat, 03 Jun 2017 23:45:02: #2 number of paired peaks: 2691 INFO @ Sat, 03 Jun 2017 23:45:02: start model_add_line... INFO @ Sat, 03 Jun 2017 23:45:15: start X-correlation... INFO @ Sat, 03 Jun 2017 23:45:15: end of X-cor INFO @ Sat, 03 Jun 2017 23:45:15: #2 finished! INFO @ Sat, 03 Jun 2017 23:45:15: #2 predicted fragment length is 98 bps INFO @ Sat, 03 Jun 2017 23:45:15: #2 alternative fragment length(s) may be 98 bps INFO @ Sat, 03 Jun 2017 23:45:15: #2.2 Generate R script for model : SRX858993.05_model.r INFO @ Sat, 03 Jun 2017 23:45:15: #3 Call peaks... INFO @ Sat, 03 Jun 2017 23:45:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 23:45:16: start X-correlation... INFO @ Sat, 03 Jun 2017 23:45:16: end of X-cor INFO @ Sat, 03 Jun 2017 23:45:16: #2 finished! INFO @ Sat, 03 Jun 2017 23:45:16: #2 predicted fragment length is 98 bps INFO @ Sat, 03 Jun 2017 23:45:16: #2 alternative fragment length(s) may be 98 bps INFO @ Sat, 03 Jun 2017 23:45:16: #2.2 Generate R script for model : SRX858993.10_model.r INFO @ Sat, 03 Jun 2017 23:45:16: #3 Call peaks... INFO @ Sat, 03 Jun 2017 23:45:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 23:45:16: start X-correlation... INFO @ Sat, 03 Jun 2017 23:45:16: end of X-cor INFO @ Sat, 03 Jun 2017 23:45:16: #2 finished! INFO @ Sat, 03 Jun 2017 23:45:16: #2 predicted fragment length is 98 bps INFO @ Sat, 03 Jun 2017 23:45:16: #2 alternative fragment length(s) may be 98 bps INFO @ Sat, 03 Jun 2017 23:45:16: #2.2 Generate R script for model : SRX858993.20_model.r INFO @ Sat, 03 Jun 2017 23:45:16: #3 Call peaks... INFO @ Sat, 03 Jun 2017 23:45:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 23:45:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 23:45:55: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 23:45:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 23:46:24: #4 Write output xls file... SRX858993.10_peaks.xls INFO @ Sat, 03 Jun 2017 23:46:24: #4 Write peak in narrowPeak format file... SRX858993.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 23:46:24: #4 Write summits bed file... SRX858993.10_summits.bed INFO @ Sat, 03 Jun 2017 23:46:25: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5049 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 23:46:29: #4 Write output xls file... SRX858993.20_peaks.xls INFO @ Sat, 03 Jun 2017 23:46:29: #4 Write peak in narrowPeak format file... SRX858993.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 23:46:29: #4 Write summits bed file... SRX858993.20_summits.bed INFO @ Sat, 03 Jun 2017 23:46:29: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2449 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 23:46:33: #4 Write output xls file... SRX858993.05_peaks.xls INFO @ Sat, 03 Jun 2017 23:46:33: #4 Write peak in narrowPeak format file... SRX858993.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 23:46:33: #4 Write summits bed file... SRX858993.05_summits.bed INFO @ Sat, 03 Jun 2017 23:46:33: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8623 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。