Job ID = 2161091 sra ファイルのダウンロード中... Completed: 152563K bytes transferred in 5 seconds (245324K 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 --:--:-- --:--:-- --:--:-- 0 100 34569 0 34569 0 0 46574 0 --:--:-- --:--:-- --:--:-- 62852 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 6402844 spots for /home/okishinya/chipatlas/results/dm3/SRX013019/SRR030285.sra Written 6402844 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: 00:01:23 6402844 reads; of these: 6402844 (100.00%) were unpaired; of these: 681602 (10.65%) aligned 0 times 5035041 (78.64%) aligned exactly 1 time 686201 (10.72%) aligned >1 times 89.35% overall alignment rate Time searching: 00:01:24 Overall time: 00:01:24 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] 448047 / 5721242 = 0.0783 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 @ Tue, 21 Apr 2015 11:58:39: # Command line: callpeak -t SRX013019.bam -f BAM -g dm -n SRX013019.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013019.10 # format = BAM # ChIP-seq file = ['SRX013019.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 @ Tue, 21 Apr 2015 11:58:39: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:58:39: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 11:58:39: # Command line: callpeak -t SRX013019.bam -f BAM -g dm -n SRX013019.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013019.05 # format = BAM # ChIP-seq file = ['SRX013019.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 @ Tue, 21 Apr 2015 11:58:39: # Command line: callpeak -t SRX013019.bam -f BAM -g dm -n SRX013019.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013019.20 # format = BAM # ChIP-seq file = ['SRX013019.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 @ Tue, 21 Apr 2015 11:58:39: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:58:39: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:58:39: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 11:58:39: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 11:58:44: 1000000 INFO @ Tue, 21 Apr 2015 11:58:45: 1000000 INFO @ Tue, 21 Apr 2015 11:58:45: 1000000 INFO @ Tue, 21 Apr 2015 11:58:50: 2000000 INFO @ Tue, 21 Apr 2015 11:58:50: 2000000 INFO @ Tue, 21 Apr 2015 11:58:50: 2000000 INFO @ Tue, 21 Apr 2015 11:58:55: 3000000 INFO @ Tue, 21 Apr 2015 11:58:55: 3000000 INFO @ Tue, 21 Apr 2015 11:58:55: 3000000 INFO @ Tue, 21 Apr 2015 11:59:00: 4000000 INFO @ Tue, 21 Apr 2015 11:59:01: 4000000 INFO @ Tue, 21 Apr 2015 11:59:01: 4000000 INFO @ Tue, 21 Apr 2015 11:59:05: 5000000 INFO @ Tue, 21 Apr 2015 11:59:06: 5000000 INFO @ Tue, 21 Apr 2015 11:59:07: 5000000 INFO @ Tue, 21 Apr 2015 11:59:07: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 11:59:07: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 11:59:07: #1 total tags in treatment: 5273195 INFO @ Tue, 21 Apr 2015 11:59:07: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 11:59:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 11:59:08: #1 tags after filtering in treatment: 5272751 INFO @ Tue, 21 Apr 2015 11:59:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 11:59:08: #1 finished! INFO @ Tue, 21 Apr 2015 11:59:08: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 11:59:08: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 11:59:08: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 11:59:08: #1 total tags in treatment: 5273195 INFO @ Tue, 21 Apr 2015 11:59:08: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 11:59:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 11:59:08: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 11:59:08: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 11:59:08: #1 total tags in treatment: 5273195 INFO @ Tue, 21 Apr 2015 11:59:08: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 11:59:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 11:59:09: #1 tags after filtering in treatment: 5272751 INFO @ Tue, 21 Apr 2015 11:59:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 11:59:09: #1 finished! INFO @ Tue, 21 Apr 2015 11:59:09: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 11:59:09: #1 tags after filtering in treatment: 5272751 INFO @ Tue, 21 Apr 2015 11:59:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 11:59:09: #1 finished! INFO @ Tue, 21 Apr 2015 11:59:09: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 11:59:09: #2 number of paired peaks: 5223 INFO @ Tue, 21 Apr 2015 11:59:09: start model_add_line... INFO @ Tue, 21 Apr 2015 11:59:10: #2 number of paired peaks: 5223 INFO @ Tue, 21 Apr 2015 11:59:10: start model_add_line... INFO @ Tue, 21 Apr 2015 11:59:11: #2 number of paired peaks: 5223 INFO @ Tue, 21 Apr 2015 11:59:11: start model_add_line... INFO @ Tue, 21 Apr 2015 11:59:28: start X-correlation... INFO @ Tue, 21 Apr 2015 11:59:28: end of X-cor INFO @ Tue, 21 Apr 2015 11:59:28: #2 finished! INFO @ Tue, 21 Apr 2015 11:59:28: #2 predicted fragment length is 137 bps INFO @ Tue, 21 Apr 2015 11:59:28: #2 alternative fragment length(s) may be 137 bps INFO @ Tue, 21 Apr 2015 11:59:28: #2.2 Generate R script for model : SRX013019.05_model.r INFO @ Tue, 21 Apr 2015 11:59:28: #3 Call peaks... INFO @ Tue, 21 Apr 2015 11:59:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 11:59:28: start X-correlation... INFO @ Tue, 21 Apr 2015 11:59:28: start X-correlation... INFO @ Tue, 21 Apr 2015 11:59:28: end of X-cor INFO @ Tue, 21 Apr 2015 11:59:28: #2 finished! INFO @ Tue, 21 Apr 2015 11:59:28: #2 predicted fragment length is 137 bps INFO @ Tue, 21 Apr 2015 11:59:28: #2 alternative fragment length(s) may be 137 bps INFO @ Tue, 21 Apr 2015 11:59:28: #2.2 Generate R script for model : SRX013019.10_model.r INFO @ Tue, 21 Apr 2015 11:59:28: end of X-cor INFO @ Tue, 21 Apr 2015 11:59:28: #2 finished! INFO @ Tue, 21 Apr 2015 11:59:28: #2 predicted fragment length is 137 bps INFO @ Tue, 21 Apr 2015 11:59:28: #2 alternative fragment length(s) may be 137 bps INFO @ Tue, 21 Apr 2015 11:59:28: #2.2 Generate R script for model : SRX013019.20_model.r INFO @ Tue, 21 Apr 2015 11:59:28: #3 Call peaks... INFO @ Tue, 21 Apr 2015 11:59:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 11:59:28: #3 Call peaks... INFO @ Tue, 21 Apr 2015 11:59:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 11:59:56: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 11:59:57: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 11:59:58: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:00:23: #4 Write output xls file... SRX013019.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:00:23: #4 Write peak in narrowPeak format file... SRX013019.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:00:23: #4 Write summits bed file... SRX013019.20_summits.bed INFO @ Tue, 21 Apr 2015 12:00:23: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3358 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:00:25: #4 Write output xls file... SRX013019.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:00:25: #4 Write peak in narrowPeak format file... SRX013019.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:00:25: #4 Write summits bed file... SRX013019.10_summits.bed INFO @ Tue, 21 Apr 2015 12:00:25: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5504 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:00:26: #4 Write output xls file... SRX013019.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:00:26: #4 Write peak in narrowPeak format file... SRX013019.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:00:26: #4 Write summits bed file... SRX013019.05_summits.bed INFO @ Tue, 21 Apr 2015 12:00:26: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7834 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。