Job ID = 2162398 sra ファイルのダウンロード中... Completed: 884670K bytes transferred in 10 seconds (716070K 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 36331 0 36331 0 0 46548 0 --:--:-- --:--:-- --:--:-- 61787 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 40556877 spots for /home/okishinya/chipatlas/results/dm3/SRX084580/SRR315120.sra Written 40556877 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: 00:10:16 40556877 reads; of these: 40556877 (100.00%) were unpaired; of these: 12942806 (31.91%) aligned 0 times 19543328 (48.19%) aligned exactly 1 time 8070743 (19.90%) aligned >1 times 68.09% overall alignment rate Time searching: 00:10:17 Overall time: 00:10:17 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] 12954100 / 27614071 = 0.4691 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 14:01:49: # Command line: callpeak -t SRX084580.bam -f BAM -g dm -n SRX084580.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX084580.05 # format = BAM # ChIP-seq file = ['SRX084580.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 14:01:49: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:01:49: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:01:49: # Command line: callpeak -t SRX084580.bam -f BAM -g dm -n SRX084580.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX084580.10 # format = BAM # ChIP-seq file = ['SRX084580.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 14:01:49: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:01:49: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:01:49: # Command line: callpeak -t SRX084580.bam -f BAM -g dm -n SRX084580.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX084580.20 # format = BAM # ChIP-seq file = ['SRX084580.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 14:01:49: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:01:49: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:01:54: 1000000 INFO @ Tue, 21 Apr 2015 14:01:54: 1000000 INFO @ Tue, 21 Apr 2015 14:01:54: 1000000 INFO @ Tue, 21 Apr 2015 14:02:00: 2000000 INFO @ Tue, 21 Apr 2015 14:02:00: 2000000 INFO @ Tue, 21 Apr 2015 14:02:00: 2000000 INFO @ Tue, 21 Apr 2015 14:02:05: 3000000 INFO @ Tue, 21 Apr 2015 14:02:05: 3000000 INFO @ Tue, 21 Apr 2015 14:02:06: 3000000 INFO @ Tue, 21 Apr 2015 14:02:10: 4000000 INFO @ Tue, 21 Apr 2015 14:02:11: 4000000 INFO @ Tue, 21 Apr 2015 14:02:11: 4000000 INFO @ Tue, 21 Apr 2015 14:02:16: 5000000 INFO @ Tue, 21 Apr 2015 14:02:17: 5000000 INFO @ Tue, 21 Apr 2015 14:02:17: 5000000 INFO @ Tue, 21 Apr 2015 14:02:21: 6000000 INFO @ Tue, 21 Apr 2015 14:02:22: 6000000 INFO @ Tue, 21 Apr 2015 14:02:23: 6000000 INFO @ Tue, 21 Apr 2015 14:02:26: 7000000 INFO @ Tue, 21 Apr 2015 14:02:28: 7000000 INFO @ Tue, 21 Apr 2015 14:02:29: 7000000 INFO @ Tue, 21 Apr 2015 14:02:32: 8000000 INFO @ Tue, 21 Apr 2015 14:02:34: 8000000 INFO @ Tue, 21 Apr 2015 14:02:35: 8000000 INFO @ Tue, 21 Apr 2015 14:02:37: 9000000 INFO @ Tue, 21 Apr 2015 14:02:40: 9000000 INFO @ Tue, 21 Apr 2015 14:02:41: 9000000 INFO @ Tue, 21 Apr 2015 14:02:42: 10000000 INFO @ Tue, 21 Apr 2015 14:02:46: 10000000 INFO @ Tue, 21 Apr 2015 14:02:47: 10000000 INFO @ Tue, 21 Apr 2015 14:02:48: 11000000 INFO @ Tue, 21 Apr 2015 14:02:52: 11000000 INFO @ Tue, 21 Apr 2015 14:02:53: 12000000 INFO @ Tue, 21 Apr 2015 14:02:53: 11000000 INFO @ Tue, 21 Apr 2015 14:02:57: 12000000 INFO @ Tue, 21 Apr 2015 14:02:58: 13000000 INFO @ Tue, 21 Apr 2015 14:02:59: 12000000 INFO @ Tue, 21 Apr 2015 14:03:03: 13000000 INFO @ Tue, 21 Apr 2015 14:03:04: 14000000 INFO @ Tue, 21 Apr 2015 14:03:05: 13000000 INFO @ Tue, 21 Apr 2015 14:03:07: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:03:07: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:03:07: #1 total tags in treatment: 14659971 INFO @ Tue, 21 Apr 2015 14:03:07: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:03:07: #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 14:03:09: 14000000 INFO @ Tue, 21 Apr 2015 14:03:10: #1 tags after filtering in treatment: 14656587 INFO @ Tue, 21 Apr 2015 14:03:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:03:10: #1 finished! INFO @ Tue, 21 Apr 2015 14:03:10: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:03:11: 14000000 INFO @ Tue, 21 Apr 2015 14:03:13: #2 number of paired peaks: 2635 INFO @ Tue, 21 Apr 2015 14:03:13: start model_add_line... INFO @ Tue, 21 Apr 2015 14:03:13: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:03:13: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:03:13: #1 total tags in treatment: 14659971 INFO @ Tue, 21 Apr 2015 14:03:13: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:03:13: #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 14:03:15: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:03:15: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:03:15: #1 total tags in treatment: 14659971 INFO @ Tue, 21 Apr 2015 14:03:15: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:03:15: #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 14:03:16: #1 tags after filtering in treatment: 14656587 INFO @ Tue, 21 Apr 2015 14:03:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:03:16: #1 finished! INFO @ Tue, 21 Apr 2015 14:03:16: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:03:18: #1 tags after filtering in treatment: 14656587 INFO @ Tue, 21 Apr 2015 14:03:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:03:18: #1 finished! INFO @ Tue, 21 Apr 2015 14:03:18: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:03:18: #2 number of paired peaks: 2635 INFO @ Tue, 21 Apr 2015 14:03:18: start model_add_line... INFO @ Tue, 21 Apr 2015 14:03:21: #2 number of paired peaks: 2635 INFO @ Tue, 21 Apr 2015 14:03:21: start model_add_line... INFO @ Tue, 21 Apr 2015 14:03:37: start X-correlation... INFO @ Tue, 21 Apr 2015 14:03:37: end of X-cor INFO @ Tue, 21 Apr 2015 14:03:37: #2 finished! INFO @ Tue, 21 Apr 2015 14:03:37: #2 predicted fragment length is 80 bps INFO @ Tue, 21 Apr 2015 14:03:37: #2 alternative fragment length(s) may be 80 bps INFO @ Tue, 21 Apr 2015 14:03:37: #2.2 Generate R script for model : SRX084580.20_model.r INFO @ Tue, 21 Apr 2015 14:03:37: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:03:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:03:43: start X-correlation... INFO @ Tue, 21 Apr 2015 14:03:43: end of X-cor INFO @ Tue, 21 Apr 2015 14:03:43: #2 finished! INFO @ Tue, 21 Apr 2015 14:03:43: #2 predicted fragment length is 80 bps INFO @ Tue, 21 Apr 2015 14:03:43: #2 alternative fragment length(s) may be 80 bps INFO @ Tue, 21 Apr 2015 14:03:43: #2.2 Generate R script for model : SRX084580.10_model.r INFO @ Tue, 21 Apr 2015 14:03:43: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:03:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:03:46: start X-correlation... INFO @ Tue, 21 Apr 2015 14:03:46: end of X-cor INFO @ Tue, 21 Apr 2015 14:03:46: #2 finished! INFO @ Tue, 21 Apr 2015 14:03:46: #2 predicted fragment length is 80 bps INFO @ Tue, 21 Apr 2015 14:03:46: #2 alternative fragment length(s) may be 80 bps INFO @ Tue, 21 Apr 2015 14:03:46: #2.2 Generate R script for model : SRX084580.05_model.r INFO @ Tue, 21 Apr 2015 14:03:46: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:03:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:04:58: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:05:03: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:05:04: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:05:57: #4 Write output xls file... SRX084580.20_peaks.xls INFO @ Tue, 21 Apr 2015 14:05:57: #4 Write peak in narrowPeak format file... SRX084580.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:05:57: #4 Write summits bed file... SRX084580.20_summits.bed INFO @ Tue, 21 Apr 2015 14:05:57: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4240 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:06:04: #4 Write output xls file... SRX084580.10_peaks.xls INFO @ Tue, 21 Apr 2015 14:06:04: #4 Write peak in narrowPeak format file... SRX084580.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:06:04: #4 Write summits bed file... SRX084580.10_summits.bed INFO @ Tue, 21 Apr 2015 14:06:04: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8577 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:06:09: #4 Write output xls file... SRX084580.05_peaks.xls INFO @ Tue, 21 Apr 2015 14:06:09: #4 Write peak in narrowPeak format file... SRX084580.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:06:09: #4 Write summits bed file... SRX084580.05_summits.bed INFO @ Tue, 21 Apr 2015 14:06:10: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (15002 records, 4 fields): 19 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。