Job ID = 2162394 sra ファイルのダウンロード中... Completed: 505178K bytes transferred in 8 seconds (471150K 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 37926 0 37926 0 0 45491 0 --:--:-- --:--:-- --:--:-- 58982 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 25163079 spots for /home/okishinya/chipatlas/results/dm3/SRX084384/SRR314830.sra Written 25163079 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: 00:06:40 25163079 reads; of these: 25163079 (100.00%) were unpaired; of these: 1567767 (6.23%) aligned 0 times 18953472 (75.32%) aligned exactly 1 time 4641840 (18.45%) aligned >1 times 93.77% overall alignment rate Time searching: 00:06:41 Overall time: 00:06:41 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] 10869343 / 23595312 = 0.4607 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 13:54:56: # Command line: callpeak -t SRX084384.bam -f BAM -g dm -n SRX084384.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX084384.10 # format = BAM # ChIP-seq file = ['SRX084384.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 13:54:56: # Command line: callpeak -t SRX084384.bam -f BAM -g dm -n SRX084384.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX084384.20 # format = BAM # ChIP-seq file = ['SRX084384.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 13:54:56: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:54:56: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:54:56: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:54:56: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:54:56: # Command line: callpeak -t SRX084384.bam -f BAM -g dm -n SRX084384.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX084384.05 # format = BAM # ChIP-seq file = ['SRX084384.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 13:54:56: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:54:56: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:55:01: 1000000 INFO @ Tue, 21 Apr 2015 13:55:01: 1000000 INFO @ Tue, 21 Apr 2015 13:55:01: 1000000 INFO @ Tue, 21 Apr 2015 13:55:06: 2000000 INFO @ Tue, 21 Apr 2015 13:55:07: 2000000 INFO @ Tue, 21 Apr 2015 13:55:07: 2000000 INFO @ Tue, 21 Apr 2015 13:55:12: 3000000 INFO @ Tue, 21 Apr 2015 13:55:12: 3000000 INFO @ Tue, 21 Apr 2015 13:55:13: 3000000 INFO @ Tue, 21 Apr 2015 13:55:17: 4000000 INFO @ Tue, 21 Apr 2015 13:55:18: 4000000 INFO @ Tue, 21 Apr 2015 13:55:19: 4000000 INFO @ Tue, 21 Apr 2015 13:55:22: 5000000 INFO @ Tue, 21 Apr 2015 13:55:24: 5000000 INFO @ Tue, 21 Apr 2015 13:55:24: 5000000 INFO @ Tue, 21 Apr 2015 13:55:28: 6000000 INFO @ Tue, 21 Apr 2015 13:55:29: 6000000 INFO @ Tue, 21 Apr 2015 13:55:30: 6000000 INFO @ Tue, 21 Apr 2015 13:55:33: 7000000 INFO @ Tue, 21 Apr 2015 13:55:35: 7000000 INFO @ Tue, 21 Apr 2015 13:55:37: 7000000 INFO @ Tue, 21 Apr 2015 13:55:39: 8000000 INFO @ Tue, 21 Apr 2015 13:55:41: 8000000 INFO @ Tue, 21 Apr 2015 13:55:43: 8000000 INFO @ Tue, 21 Apr 2015 13:55:45: 9000000 INFO @ Tue, 21 Apr 2015 13:55:47: 9000000 INFO @ Tue, 21 Apr 2015 13:55:50: 9000000 INFO @ Tue, 21 Apr 2015 13:55:51: 10000000 INFO @ Tue, 21 Apr 2015 13:55:53: 10000000 INFO @ Tue, 21 Apr 2015 13:55:56: 10000000 INFO @ Tue, 21 Apr 2015 13:55:56: 11000000 INFO @ Tue, 21 Apr 2015 13:56:00: 11000000 INFO @ Tue, 21 Apr 2015 13:56:02: 12000000 INFO @ Tue, 21 Apr 2015 13:56:03: 11000000 INFO @ Tue, 21 Apr 2015 13:56:06: 12000000 INFO @ Tue, 21 Apr 2015 13:56:07: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:56:07: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:56:07: #1 total tags in treatment: 12725969 INFO @ Tue, 21 Apr 2015 13:56:07: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:56:07: #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 13:56:09: #1 tags after filtering in treatment: 12719709 INFO @ Tue, 21 Apr 2015 13:56:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:56:09: #1 finished! INFO @ Tue, 21 Apr 2015 13:56:09: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:56:10: 12000000 INFO @ Tue, 21 Apr 2015 13:56:10: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:56:10: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:56:10: #1 total tags in treatment: 12725969 INFO @ Tue, 21 Apr 2015 13:56:10: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:56:10: #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 13:56:12: #2 number of paired peaks: 4664 INFO @ Tue, 21 Apr 2015 13:56:12: start model_add_line... INFO @ Tue, 21 Apr 2015 13:56:13: #1 tags after filtering in treatment: 12719709 INFO @ Tue, 21 Apr 2015 13:56:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:56:13: #1 finished! INFO @ Tue, 21 Apr 2015 13:56:13: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:56:14: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:56:14: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:56:14: #1 total tags in treatment: 12725969 INFO @ Tue, 21 Apr 2015 13:56:14: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:56:14: #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 13:56:16: #2 number of paired peaks: 4664 INFO @ Tue, 21 Apr 2015 13:56:16: start model_add_line... INFO @ Tue, 21 Apr 2015 13:56:16: #1 tags after filtering in treatment: 12719709 INFO @ Tue, 21 Apr 2015 13:56:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:56:16: #1 finished! INFO @ Tue, 21 Apr 2015 13:56:16: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:56:19: #2 number of paired peaks: 4664 INFO @ Tue, 21 Apr 2015 13:56:19: start model_add_line... INFO @ Tue, 21 Apr 2015 13:56:50: start X-correlation... INFO @ Tue, 21 Apr 2015 13:56:50: end of X-cor INFO @ Tue, 21 Apr 2015 13:56:50: #2 finished! INFO @ Tue, 21 Apr 2015 13:56:50: #2 predicted fragment length is 147 bps INFO @ Tue, 21 Apr 2015 13:56:50: #2 alternative fragment length(s) may be 147 bps INFO @ Tue, 21 Apr 2015 13:56:50: #2.2 Generate R script for model : SRX084384.20_model.r INFO @ Tue, 21 Apr 2015 13:56:50: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:56:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:56:52: start X-correlation... INFO @ Tue, 21 Apr 2015 13:56:52: end of X-cor INFO @ Tue, 21 Apr 2015 13:56:52: #2 finished! INFO @ Tue, 21 Apr 2015 13:56:52: #2 predicted fragment length is 147 bps INFO @ Tue, 21 Apr 2015 13:56:52: #2 alternative fragment length(s) may be 147 bps INFO @ Tue, 21 Apr 2015 13:56:52: #2.2 Generate R script for model : SRX084384.10_model.r INFO @ Tue, 21 Apr 2015 13:56:52: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:56:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:56:55: start X-correlation... INFO @ Tue, 21 Apr 2015 13:56:55: end of X-cor INFO @ Tue, 21 Apr 2015 13:56:55: #2 finished! INFO @ Tue, 21 Apr 2015 13:56:55: #2 predicted fragment length is 147 bps INFO @ Tue, 21 Apr 2015 13:56:55: #2 alternative fragment length(s) may be 147 bps INFO @ Tue, 21 Apr 2015 13:56:55: #2.2 Generate R script for model : SRX084384.05_model.r INFO @ Tue, 21 Apr 2015 13:56:55: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:56:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:58:05: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:58:05: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:58:08: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:59:04: #4 Write output xls file... SRX084384.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:59:04: #4 Write peak in narrowPeak format file... SRX084384.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:59:04: #4 Write summits bed file... SRX084384.20_summits.bed INFO @ Tue, 21 Apr 2015 13:59:04: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9764 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:59:09: #4 Write output xls file... SRX084384.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:59:09: #4 Write peak in narrowPeak format file... SRX084384.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:59:09: #4 Write summits bed file... SRX084384.10_summits.bed INFO @ Tue, 21 Apr 2015 13:59:09: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (13701 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 21 Apr 2015 13:59:19: #4 Write output xls file... SRX084384.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:59:19: #4 Write peak in narrowPeak format file... SRX084384.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:59:19: #4 Write summits bed file... SRX084384.05_summits.bed INFO @ Tue, 21 Apr 2015 13:59:19: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (17989 records, 4 fields): 22 millis CompletedMACS2peakCalling BigWig に変換しました。