Job ID = 2236876 sra ファイルのダウンロード中... Completed: 465835K bytes transferred in 26 seconds (142262K 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 34650 0 34650 0 0 47441 0 --:--:-- --:--:-- --:--:-- 64285 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 15991314 spots for /home/okishinya/chipatlas/results/ce10/SRX059252/SRR190692.sra Written 15991314 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: 00:03:18 15991314 reads; of these: 15991314 (100.00%) were unpaired; of these: 1057385 (6.61%) aligned 0 times 12426850 (77.71%) aligned exactly 1 time 2507079 (15.68%) aligned >1 times 93.39% overall alignment rate Time searching: 00:03:19 Overall time: 00:03:19 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 3467793 / 14933929 = 0.2322 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 @ Thu, 30 Apr 2015 11:18:54: # Command line: callpeak -t SRX059252.bam -f BAM -g ce -n SRX059252.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX059252.10 # format = BAM # ChIP-seq file = ['SRX059252.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 30 Apr 2015 11:18:54: # Command line: callpeak -t SRX059252.bam -f BAM -g ce -n SRX059252.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX059252.05 # format = BAM # ChIP-seq file = ['SRX059252.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 30 Apr 2015 11:18:54: # Command line: callpeak -t SRX059252.bam -f BAM -g ce -n SRX059252.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX059252.20 # format = BAM # ChIP-seq file = ['SRX059252.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 30 Apr 2015 11:18:54: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:18:54: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:18:54: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:18:54: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:18:54: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:18:54: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:19:00: 1000000 INFO @ Thu, 30 Apr 2015 11:19:00: 1000000 INFO @ Thu, 30 Apr 2015 11:19:00: 1000000 INFO @ Thu, 30 Apr 2015 11:19:05: 2000000 INFO @ Thu, 30 Apr 2015 11:19:06: 2000000 INFO @ Thu, 30 Apr 2015 11:19:06: 2000000 INFO @ Thu, 30 Apr 2015 11:19:11: 3000000 INFO @ Thu, 30 Apr 2015 11:19:12: 3000000 INFO @ Thu, 30 Apr 2015 11:19:12: 3000000 INFO @ Thu, 30 Apr 2015 11:19:16: 4000000 INFO @ Thu, 30 Apr 2015 11:19:17: 4000000 INFO @ Thu, 30 Apr 2015 11:19:17: 4000000 INFO @ Thu, 30 Apr 2015 11:19:22: 5000000 INFO @ Thu, 30 Apr 2015 11:19:23: 5000000 INFO @ Thu, 30 Apr 2015 11:19:23: 5000000 INFO @ Thu, 30 Apr 2015 11:19:27: 6000000 INFO @ Thu, 30 Apr 2015 11:19:29: 6000000 INFO @ Thu, 30 Apr 2015 11:19:29: 6000000 INFO @ Thu, 30 Apr 2015 11:19:33: 7000000 INFO @ Thu, 30 Apr 2015 11:19:35: 7000000 INFO @ Thu, 30 Apr 2015 11:19:35: 7000000 INFO @ Thu, 30 Apr 2015 11:19:39: 8000000 INFO @ Thu, 30 Apr 2015 11:19:41: 8000000 INFO @ Thu, 30 Apr 2015 11:19:41: 8000000 INFO @ Thu, 30 Apr 2015 11:19:44: 9000000 INFO @ Thu, 30 Apr 2015 11:19:47: 9000000 INFO @ Thu, 30 Apr 2015 11:19:47: 9000000 INFO @ Thu, 30 Apr 2015 11:19:50: 10000000 INFO @ Thu, 30 Apr 2015 11:19:53: 10000000 INFO @ Thu, 30 Apr 2015 11:19:54: 10000000 INFO @ Thu, 30 Apr 2015 11:19:55: 11000000 INFO @ Thu, 30 Apr 2015 11:19:58: #1 tag size is determined as 42 bps INFO @ Thu, 30 Apr 2015 11:19:58: #1 tag size = 42 INFO @ Thu, 30 Apr 2015 11:19:58: #1 total tags in treatment: 11466136 INFO @ Thu, 30 Apr 2015 11:19:58: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:19:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:19:59: 11000000 INFO @ Thu, 30 Apr 2015 11:20:00: 11000000 INFO @ Thu, 30 Apr 2015 11:20:00: #1 tags after filtering in treatment: 11464657 INFO @ Thu, 30 Apr 2015 11:20:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:20:00: #1 finished! INFO @ Thu, 30 Apr 2015 11:20:00: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:20:02: #1 tag size is determined as 42 bps INFO @ Thu, 30 Apr 2015 11:20:02: #1 tag size = 42 INFO @ Thu, 30 Apr 2015 11:20:02: #1 total tags in treatment: 11466136 INFO @ Thu, 30 Apr 2015 11:20:02: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:20:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:20:02: #2 number of paired peaks: 573 WARNING @ Thu, 30 Apr 2015 11:20:02: Fewer paired peaks (573) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 573 pairs to build model! INFO @ Thu, 30 Apr 2015 11:20:02: start model_add_line... INFO @ Thu, 30 Apr 2015 11:20:03: #1 tag size is determined as 42 bps INFO @ Thu, 30 Apr 2015 11:20:03: #1 tag size = 42 INFO @ Thu, 30 Apr 2015 11:20:03: #1 total tags in treatment: 11466136 INFO @ Thu, 30 Apr 2015 11:20:03: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:20:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:20:04: #1 tags after filtering in treatment: 11464657 INFO @ Thu, 30 Apr 2015 11:20:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:20:04: #1 finished! INFO @ Thu, 30 Apr 2015 11:20:04: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:20:05: #1 tags after filtering in treatment: 11464657 INFO @ Thu, 30 Apr 2015 11:20:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:20:05: #1 finished! INFO @ Thu, 30 Apr 2015 11:20:05: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:20:06: #2 number of paired peaks: 573 WARNING @ Thu, 30 Apr 2015 11:20:06: Fewer paired peaks (573) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 573 pairs to build model! INFO @ Thu, 30 Apr 2015 11:20:06: start model_add_line... INFO @ Thu, 30 Apr 2015 11:20:06: #2 number of paired peaks: 573 WARNING @ Thu, 30 Apr 2015 11:20:06: Fewer paired peaks (573) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 573 pairs to build model! INFO @ Thu, 30 Apr 2015 11:20:06: start model_add_line... INFO @ Thu, 30 Apr 2015 11:20:08: start X-correlation... INFO @ Thu, 30 Apr 2015 11:20:08: end of X-cor INFO @ Thu, 30 Apr 2015 11:20:08: #2 finished! INFO @ Thu, 30 Apr 2015 11:20:08: #2 predicted fragment length is 130 bps INFO @ Thu, 30 Apr 2015 11:20:08: #2 alternative fragment length(s) may be 130 bps INFO @ Thu, 30 Apr 2015 11:20:08: #2.2 Generate R script for model : SRX059252.10_model.r INFO @ Thu, 30 Apr 2015 11:20:08: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:20:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:20:12: start X-correlation... INFO @ Thu, 30 Apr 2015 11:20:12: end of X-cor INFO @ Thu, 30 Apr 2015 11:20:12: #2 finished! INFO @ Thu, 30 Apr 2015 11:20:12: #2 predicted fragment length is 130 bps INFO @ Thu, 30 Apr 2015 11:20:12: #2 alternative fragment length(s) may be 130 bps INFO @ Thu, 30 Apr 2015 11:20:12: #2.2 Generate R script for model : SRX059252.20_model.r INFO @ Thu, 30 Apr 2015 11:20:12: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:20:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:20:12: start X-correlation... INFO @ Thu, 30 Apr 2015 11:20:12: end of X-cor INFO @ Thu, 30 Apr 2015 11:20:12: #2 finished! INFO @ Thu, 30 Apr 2015 11:20:12: #2 predicted fragment length is 130 bps INFO @ Thu, 30 Apr 2015 11:20:12: #2 alternative fragment length(s) may be 130 bps INFO @ Thu, 30 Apr 2015 11:20:12: #2.2 Generate R script for model : SRX059252.05_model.r INFO @ Thu, 30 Apr 2015 11:20:12: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:20:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:21:12: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:21:13: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:21:14: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:21:56: #4 Write output xls file... SRX059252.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:21:56: #4 Write peak in narrowPeak format file... SRX059252.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:21:56: #4 Write summits bed file... SRX059252.20_summits.bed INFO @ Thu, 30 Apr 2015 11:21:56: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1646 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:22:01: #4 Write output xls file... SRX059252.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:22:01: #4 Write peak in narrowPeak format file... SRX059252.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:22:01: #4 Write summits bed file... SRX059252.10_summits.bed INFO @ Thu, 30 Apr 2015 11:22:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2530 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:22:05: #4 Write output xls file... SRX059252.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:22:05: #4 Write peak in narrowPeak format file... SRX059252.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:22:05: #4 Write summits bed file... SRX059252.05_summits.bed INFO @ Thu, 30 Apr 2015 11:22:05: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4863 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。