Job ID = 2162396 sra ファイルのダウンロード中... Completed: 936561K bytes transferred in 10 seconds (702980K 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 4007 0 4007 0 0 7223 0 --:--:-- --:--:-- --:--:-- 11008 100 36333 0 36333 0 0 48816 0 --:--:-- --:--:-- --:--:-- 65583 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 42129254 spots for /home/okishinya/chipatlas/results/dm3/SRX084579/SRR315119.sra Written 42129254 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: 00:10:36 42129254 reads; of these: 42129254 (100.00%) were unpaired; of these: 12022013 (28.54%) aligned 0 times 21630106 (51.34%) aligned exactly 1 time 8477135 (20.12%) aligned >1 times 71.46% overall alignment rate Time searching: 00:10:37 Overall time: 00:10:37 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] 14596436 / 30107241 = 0.4848 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 14:01:48: # Command line: callpeak -t SRX084579.bam -f BAM -g dm -n SRX084579.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX084579.05 # format = BAM # ChIP-seq file = ['SRX084579.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 14:01:48: # Command line: callpeak -t SRX084579.bam -f BAM -g dm -n SRX084579.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX084579.20 # format = BAM # ChIP-seq file = ['SRX084579.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 14:01:48: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:01:48: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:01:48: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:01:48: # Command line: callpeak -t SRX084579.bam -f BAM -g dm -n SRX084579.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX084579.10 # format = BAM # ChIP-seq file = ['SRX084579.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 14:01:48: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:01:48: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:01:48: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:01:56: 1000000 INFO @ Tue, 21 Apr 2015 14:01:56: 1000000 INFO @ Tue, 21 Apr 2015 14:01:56: 1000000 INFO @ Tue, 21 Apr 2015 14:02:03: 2000000 INFO @ Tue, 21 Apr 2015 14:02:03: 2000000 INFO @ Tue, 21 Apr 2015 14:02:03: 2000000 INFO @ Tue, 21 Apr 2015 14:02:10: 3000000 INFO @ Tue, 21 Apr 2015 14:02:10: 3000000 INFO @ Tue, 21 Apr 2015 14:02:10: 3000000 INFO @ Tue, 21 Apr 2015 14:02:17: 4000000 INFO @ Tue, 21 Apr 2015 14:02:17: 4000000 INFO @ Tue, 21 Apr 2015 14:02:17: 4000000 INFO @ Tue, 21 Apr 2015 14:02:24: 5000000 INFO @ Tue, 21 Apr 2015 14:02:24: 5000000 INFO @ Tue, 21 Apr 2015 14:02:24: 5000000 INFO @ Tue, 21 Apr 2015 14:02:31: 6000000 INFO @ Tue, 21 Apr 2015 14:02:31: 6000000 INFO @ Tue, 21 Apr 2015 14:02:31: 6000000 INFO @ Tue, 21 Apr 2015 14:02:38: 7000000 INFO @ Tue, 21 Apr 2015 14:02:38: 7000000 INFO @ Tue, 21 Apr 2015 14:02:38: 7000000 INFO @ Tue, 21 Apr 2015 14:02:45: 8000000 INFO @ Tue, 21 Apr 2015 14:02:45: 8000000 INFO @ Tue, 21 Apr 2015 14:02:45: 8000000 INFO @ Tue, 21 Apr 2015 14:02:52: 9000000 INFO @ Tue, 21 Apr 2015 14:02:52: 9000000 INFO @ Tue, 21 Apr 2015 14:02:52: 9000000 INFO @ Tue, 21 Apr 2015 14:02:58: 10000000 INFO @ Tue, 21 Apr 2015 14:02:58: 10000000 INFO @ Tue, 21 Apr 2015 14:02:58: 10000000 INFO @ Tue, 21 Apr 2015 14:03:05: 11000000 INFO @ Tue, 21 Apr 2015 14:03:05: 11000000 INFO @ Tue, 21 Apr 2015 14:03:05: 11000000 INFO @ Tue, 21 Apr 2015 14:03:12: 12000000 INFO @ Tue, 21 Apr 2015 14:03:12: 12000000 INFO @ Tue, 21 Apr 2015 14:03:12: 12000000 INFO @ Tue, 21 Apr 2015 14:03:19: 13000000 INFO @ Tue, 21 Apr 2015 14:03:19: 13000000 INFO @ Tue, 21 Apr 2015 14:03:19: 13000000 INFO @ Tue, 21 Apr 2015 14:03:26: 14000000 INFO @ Tue, 21 Apr 2015 14:03:26: 14000000 INFO @ Tue, 21 Apr 2015 14:03:26: 14000000 INFO @ Tue, 21 Apr 2015 14:03:33: 15000000 INFO @ Tue, 21 Apr 2015 14:03:33: 15000000 INFO @ Tue, 21 Apr 2015 14:03:33: 15000000 INFO @ Tue, 21 Apr 2015 14:03:37: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:03:37: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:03:37: #1 total tags in treatment: 15510805 INFO @ Tue, 21 Apr 2015 14:03:37: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:03:37: #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 14:03:37: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:03:37: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:03:37: #1 total tags in treatment: 15510805 INFO @ Tue, 21 Apr 2015 14:03:37: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:03:37: #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 14:03:37: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:03:37: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:03:37: #1 total tags in treatment: 15510805 INFO @ Tue, 21 Apr 2015 14:03:37: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:03:37: #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 14:03:40: #1 tags after filtering in treatment: 15507658 INFO @ Tue, 21 Apr 2015 14:03:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:03:40: #1 finished! INFO @ Tue, 21 Apr 2015 14:03:40: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:03:40: #1 tags after filtering in treatment: 15507658 INFO @ Tue, 21 Apr 2015 14:03:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:03:40: #1 finished! INFO @ Tue, 21 Apr 2015 14:03:40: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:03:40: #1 tags after filtering in treatment: 15507658 INFO @ Tue, 21 Apr 2015 14:03:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:03:40: #1 finished! INFO @ Tue, 21 Apr 2015 14:03:40: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:03:43: #2 number of paired peaks: 2508 INFO @ Tue, 21 Apr 2015 14:03:43: start model_add_line... INFO @ Tue, 21 Apr 2015 14:03:43: #2 number of paired peaks: 2508 INFO @ Tue, 21 Apr 2015 14:03:43: start model_add_line... INFO @ Tue, 21 Apr 2015 14:03:43: #2 number of paired peaks: 2508 INFO @ Tue, 21 Apr 2015 14:03:43: start model_add_line... INFO @ Tue, 21 Apr 2015 14:04:07: start X-correlation... INFO @ Tue, 21 Apr 2015 14:04:08: end of X-cor INFO @ Tue, 21 Apr 2015 14:04:08: #2 finished! INFO @ Tue, 21 Apr 2015 14:04:08: #2 predicted fragment length is 80 bps INFO @ Tue, 21 Apr 2015 14:04:08: #2 alternative fragment length(s) may be 80 bps INFO @ Tue, 21 Apr 2015 14:04:08: #2.2 Generate R script for model : SRX084579.10_model.r INFO @ Tue, 21 Apr 2015 14:04:08: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:04:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:04:08: start X-correlation... INFO @ Tue, 21 Apr 2015 14:04:08: end of X-cor INFO @ Tue, 21 Apr 2015 14:04:08: #2 finished! INFO @ Tue, 21 Apr 2015 14:04:08: #2 predicted fragment length is 80 bps INFO @ Tue, 21 Apr 2015 14:04:08: #2 alternative fragment length(s) may be 80 bps INFO @ Tue, 21 Apr 2015 14:04:08: #2.2 Generate R script for model : SRX084579.05_model.r INFO @ Tue, 21 Apr 2015 14:04:08: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:04:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:04:08: start X-correlation... INFO @ Tue, 21 Apr 2015 14:04:08: end of X-cor INFO @ Tue, 21 Apr 2015 14:04:08: #2 finished! INFO @ Tue, 21 Apr 2015 14:04:08: #2 predicted fragment length is 80 bps INFO @ Tue, 21 Apr 2015 14:04:08: #2 alternative fragment length(s) may be 80 bps INFO @ Tue, 21 Apr 2015 14:04:08: #2.2 Generate R script for model : SRX084579.20_model.r INFO @ Tue, 21 Apr 2015 14:04:08: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:04:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:05:29: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:05:30: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:05:35: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:06:36: #4 Write output xls file... SRX084579.10_peaks.xls INFO @ Tue, 21 Apr 2015 14:06:36: #4 Write peak in narrowPeak format file... SRX084579.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:06:36: #4 Write summits bed file... SRX084579.10_summits.bed INFO @ Tue, 21 Apr 2015 14:06:36: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11364 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:06:39: #4 Write output xls file... SRX084579.20_peaks.xls INFO @ Tue, 21 Apr 2015 14:06:39: #4 Write peak in narrowPeak format file... SRX084579.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:06:39: #4 Write summits bed file... SRX084579.20_summits.bed INFO @ Tue, 21 Apr 2015 14:06:39: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8184 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:06:40: #4 Write output xls file... SRX084579.05_peaks.xls INFO @ Tue, 21 Apr 2015 14:06:40: #4 Write peak in narrowPeak format file... SRX084579.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:06:40: #4 Write summits bed file... SRX084579.05_summits.bed INFO @ Tue, 21 Apr 2015 14:06:40: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (15549 records, 4 fields): 20 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。