Job ID = 2162417 sra ファイルのダウンロード中... Completed: 783089K bytes transferred in 10 seconds (587478K 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 29821 0 29821 0 0 36161 0 --:--:-- --:--:-- --:--:-- 47036 100 36338 0 36338 0 0 44022 0 --:--:-- --:--:-- --:--:-- 57225 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 33442200 spots for /home/okishinya/chipatlas/results/dm3/SRX089333/SRR327604.sra Written 33442200 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: 00:07:06 33442200 reads; of these: 33442200 (100.00%) were unpaired; of these: 10992197 (32.87%) aligned 0 times 17698904 (52.92%) aligned exactly 1 time 4751099 (14.21%) aligned >1 times 67.13% overall alignment rate Time searching: 00:07:06 Overall time: 00:07:06 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] 6004008 / 22450003 = 0.2674 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 14:06:34: # Command line: callpeak -t SRX089333.bam -f BAM -g dm -n SRX089333.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX089333.10 # format = BAM # ChIP-seq file = ['SRX089333.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 14:06:34: # Command line: callpeak -t SRX089333.bam -f BAM -g dm -n SRX089333.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX089333.05 # format = BAM # ChIP-seq file = ['SRX089333.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 14:06:34: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:06:34: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:06:34: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:06:34: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:06:34: # Command line: callpeak -t SRX089333.bam -f BAM -g dm -n SRX089333.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX089333.20 # format = BAM # ChIP-seq file = ['SRX089333.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 14:06:34: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:06:34: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:06:40: 1000000 INFO @ Tue, 21 Apr 2015 14:06:40: 1000000 INFO @ Tue, 21 Apr 2015 14:06:41: 1000000 INFO @ Tue, 21 Apr 2015 14:06:46: 2000000 INFO @ Tue, 21 Apr 2015 14:06:46: 2000000 INFO @ Tue, 21 Apr 2015 14:06:47: 2000000 INFO @ Tue, 21 Apr 2015 14:06:52: 3000000 INFO @ Tue, 21 Apr 2015 14:06:52: 3000000 INFO @ Tue, 21 Apr 2015 14:06:54: 3000000 INFO @ Tue, 21 Apr 2015 14:06:57: 4000000 INFO @ Tue, 21 Apr 2015 14:06:57: 4000000 INFO @ Tue, 21 Apr 2015 14:07:01: 4000000 INFO @ Tue, 21 Apr 2015 14:07:03: 5000000 INFO @ Tue, 21 Apr 2015 14:07:03: 5000000 INFO @ Tue, 21 Apr 2015 14:07:07: 5000000 INFO @ Tue, 21 Apr 2015 14:07:09: 6000000 INFO @ Tue, 21 Apr 2015 14:07:09: 6000000 INFO @ Tue, 21 Apr 2015 14:07:14: 6000000 INFO @ Tue, 21 Apr 2015 14:07:15: 7000000 INFO @ Tue, 21 Apr 2015 14:07:15: 7000000 INFO @ Tue, 21 Apr 2015 14:07:21: 7000000 INFO @ Tue, 21 Apr 2015 14:07:21: 8000000 INFO @ Tue, 21 Apr 2015 14:07:21: 8000000 INFO @ Tue, 21 Apr 2015 14:07:26: 9000000 INFO @ Tue, 21 Apr 2015 14:07:26: 9000000 INFO @ Tue, 21 Apr 2015 14:07:27: 8000000 INFO @ Tue, 21 Apr 2015 14:07:31: 10000000 INFO @ Tue, 21 Apr 2015 14:07:31: 10000000 INFO @ Tue, 21 Apr 2015 14:07:33: 9000000 INFO @ Tue, 21 Apr 2015 14:07:36: 11000000 INFO @ Tue, 21 Apr 2015 14:07:36: 11000000 INFO @ Tue, 21 Apr 2015 14:07:38: 10000000 INFO @ Tue, 21 Apr 2015 14:07:41: 12000000 INFO @ Tue, 21 Apr 2015 14:07:41: 12000000 INFO @ Tue, 21 Apr 2015 14:07:43: 11000000 INFO @ Tue, 21 Apr 2015 14:07:46: 13000000 INFO @ Tue, 21 Apr 2015 14:07:46: 13000000 INFO @ Tue, 21 Apr 2015 14:07:48: 12000000 INFO @ Tue, 21 Apr 2015 14:07:51: 14000000 INFO @ Tue, 21 Apr 2015 14:07:52: 14000000 INFO @ Tue, 21 Apr 2015 14:07:53: 13000000 INFO @ Tue, 21 Apr 2015 14:07:56: 15000000 INFO @ Tue, 21 Apr 2015 14:07:57: 15000000 INFO @ Tue, 21 Apr 2015 14:07:58: 14000000 INFO @ Tue, 21 Apr 2015 14:08:02: 16000000 INFO @ Tue, 21 Apr 2015 14:08:02: 16000000 INFO @ Tue, 21 Apr 2015 14:08:04: 15000000 INFO @ Tue, 21 Apr 2015 14:08:04: #1 tag size is determined as 38 bps INFO @ Tue, 21 Apr 2015 14:08:04: #1 tag size = 38 INFO @ Tue, 21 Apr 2015 14:08:04: #1 total tags in treatment: 16445995 INFO @ Tue, 21 Apr 2015 14:08:04: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:08:04: #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 14:08:04: #1 tag size is determined as 38 bps INFO @ Tue, 21 Apr 2015 14:08:04: #1 tag size = 38 INFO @ Tue, 21 Apr 2015 14:08:04: #1 total tags in treatment: 16445995 INFO @ Tue, 21 Apr 2015 14:08:04: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:08:04: #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 14:08:07: #1 tags after filtering in treatment: 16442780 INFO @ Tue, 21 Apr 2015 14:08:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:08:07: #1 finished! INFO @ Tue, 21 Apr 2015 14:08:07: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:08:07: #1 tags after filtering in treatment: 16442780 INFO @ Tue, 21 Apr 2015 14:08:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:08:07: #1 finished! INFO @ Tue, 21 Apr 2015 14:08:07: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:08:09: 16000000 INFO @ Tue, 21 Apr 2015 14:08:10: #2 number of paired peaks: 1606 INFO @ Tue, 21 Apr 2015 14:08:10: start model_add_line... INFO @ Tue, 21 Apr 2015 14:08:11: #2 number of paired peaks: 1606 INFO @ Tue, 21 Apr 2015 14:08:11: start model_add_line... INFO @ Tue, 21 Apr 2015 14:08:11: #1 tag size is determined as 38 bps INFO @ Tue, 21 Apr 2015 14:08:11: #1 tag size = 38 INFO @ Tue, 21 Apr 2015 14:08:11: #1 total tags in treatment: 16445995 INFO @ Tue, 21 Apr 2015 14:08:11: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:08:11: #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 14:08:14: #1 tags after filtering in treatment: 16442780 INFO @ Tue, 21 Apr 2015 14:08:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:08:14: #1 finished! INFO @ Tue, 21 Apr 2015 14:08:14: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:08:17: #2 number of paired peaks: 1606 INFO @ Tue, 21 Apr 2015 14:08:17: start model_add_line... INFO @ Tue, 21 Apr 2015 14:08:26: start X-correlation... INFO @ Tue, 21 Apr 2015 14:08:26: end of X-cor INFO @ Tue, 21 Apr 2015 14:08:26: #2 finished! INFO @ Tue, 21 Apr 2015 14:08:26: #2 predicted fragment length is 81 bps INFO @ Tue, 21 Apr 2015 14:08:26: #2 alternative fragment length(s) may be 81 bps INFO @ Tue, 21 Apr 2015 14:08:26: #2.2 Generate R script for model : SRX089333.05_model.r INFO @ Tue, 21 Apr 2015 14:08:26: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:08:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:08:27: start X-correlation... INFO @ Tue, 21 Apr 2015 14:08:27: end of X-cor INFO @ Tue, 21 Apr 2015 14:08:27: #2 finished! INFO @ Tue, 21 Apr 2015 14:08:27: #2 predicted fragment length is 81 bps INFO @ Tue, 21 Apr 2015 14:08:27: #2 alternative fragment length(s) may be 81 bps INFO @ Tue, 21 Apr 2015 14:08:27: #2.2 Generate R script for model : SRX089333.10_model.r INFO @ Tue, 21 Apr 2015 14:08:27: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:08:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:08:34: start X-correlation... INFO @ Tue, 21 Apr 2015 14:08:34: end of X-cor INFO @ Tue, 21 Apr 2015 14:08:34: #2 finished! INFO @ Tue, 21 Apr 2015 14:08:34: #2 predicted fragment length is 81 bps INFO @ Tue, 21 Apr 2015 14:08:34: #2 alternative fragment length(s) may be 81 bps INFO @ Tue, 21 Apr 2015 14:08:34: #2.2 Generate R script for model : SRX089333.20_model.r INFO @ Tue, 21 Apr 2015 14:08:34: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:08:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:09:49: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:10:00: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:10:02: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:10:55: #4 Write output xls file... SRX089333.10_peaks.xls INFO @ Tue, 21 Apr 2015 14:10:55: #4 Write peak in narrowPeak format file... SRX089333.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:10:55: #4 Write summits bed file... SRX089333.10_summits.bed INFO @ Tue, 21 Apr 2015 14:10:55: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9457 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:11:07: #4 Write output xls file... SRX089333.20_peaks.xls INFO @ Tue, 21 Apr 2015 14:11:07: #4 Write peak in narrowPeak format file... SRX089333.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:11:07: #4 Write summits bed file... SRX089333.20_summits.bed INFO @ Tue, 21 Apr 2015 14:11:07: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4810 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:11:09: #4 Write output xls file... SRX089333.05_peaks.xls INFO @ Tue, 21 Apr 2015 14:11:09: #4 Write peak in narrowPeak format file... SRX089333.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:11:10: #4 Write summits bed file... SRX089333.05_summits.bed INFO @ Tue, 21 Apr 2015 14:11:10: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (14269 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。