Job ID = 2161197 sra ファイルのダウンロード中... Completed: 177391K bytes transferred in 4 seconds (299605K 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 34575 0 34575 0 0 48898 0 --:--:-- --:--:-- --:--:-- 67135 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 6504449 spots for /home/okishinya/chipatlas/results/dm3/SRX013045/SRR030311.sra Written 6504449 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: 00:01:19 6504449 reads; of these: 6504449 (100.00%) were unpaired; of these: 1121356 (17.24%) aligned 0 times 4777952 (73.46%) aligned exactly 1 time 605141 (9.30%) aligned >1 times 82.76% overall alignment rate Time searching: 00:01:19 Overall time: 00:01:19 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 202374 / 5383093 = 0.0376 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 12:03:32: # Command line: callpeak -t SRX013045.bam -f BAM -g dm -n SRX013045.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013045.10 # format = BAM # ChIP-seq file = ['SRX013045.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 12:03:32: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:03:32: # Command line: callpeak -t SRX013045.bam -f BAM -g dm -n SRX013045.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013045.20 # format = BAM # ChIP-seq file = ['SRX013045.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 12:03:32: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:03:32: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:03:32: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:03:32: # Command line: callpeak -t SRX013045.bam -f BAM -g dm -n SRX013045.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013045.05 # format = BAM # ChIP-seq file = ['SRX013045.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 12:03:32: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:03:32: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:03:37: 1000000 INFO @ Tue, 21 Apr 2015 12:03:37: 1000000 INFO @ Tue, 21 Apr 2015 12:03:37: 1000000 INFO @ Tue, 21 Apr 2015 12:03:42: 2000000 INFO @ Tue, 21 Apr 2015 12:03:42: 2000000 INFO @ Tue, 21 Apr 2015 12:03:43: 2000000 INFO @ Tue, 21 Apr 2015 12:03:47: 3000000 INFO @ Tue, 21 Apr 2015 12:03:48: 3000000 INFO @ Tue, 21 Apr 2015 12:03:48: 3000000 INFO @ Tue, 21 Apr 2015 12:03:52: 4000000 INFO @ Tue, 21 Apr 2015 12:03:53: 4000000 INFO @ Tue, 21 Apr 2015 12:03:54: 4000000 INFO @ Tue, 21 Apr 2015 12:03:57: 5000000 INFO @ Tue, 21 Apr 2015 12:03:58: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:03:58: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:03:58: #1 total tags in treatment: 5180719 INFO @ Tue, 21 Apr 2015 12:03:58: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:03:58: #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 12:03:59: 5000000 INFO @ Tue, 21 Apr 2015 12:03:59: #1 tags after filtering in treatment: 5180477 INFO @ Tue, 21 Apr 2015 12:03:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:03:59: #1 finished! INFO @ Tue, 21 Apr 2015 12:03:59: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:04:00: 5000000 INFO @ Tue, 21 Apr 2015 12:04:00: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:04:00: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:04:00: #1 total tags in treatment: 5180719 INFO @ Tue, 21 Apr 2015 12:04:00: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:04:00: #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 12:04:00: #2 number of paired peaks: 765 WARNING @ Tue, 21 Apr 2015 12:04:00: Fewer paired peaks (765) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 765 pairs to build model! INFO @ Tue, 21 Apr 2015 12:04:00: start model_add_line... INFO @ Tue, 21 Apr 2015 12:04:01: #1 tags after filtering in treatment: 5180477 INFO @ Tue, 21 Apr 2015 12:04:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:04:01: #1 finished! INFO @ Tue, 21 Apr 2015 12:04:01: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:04:01: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:04:01: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:04:01: #1 total tags in treatment: 5180719 INFO @ Tue, 21 Apr 2015 12:04:01: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:04:01: #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 12:04:02: #2 number of paired peaks: 765 WARNING @ Tue, 21 Apr 2015 12:04:02: Fewer paired peaks (765) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 765 pairs to build model! INFO @ Tue, 21 Apr 2015 12:04:02: start model_add_line... INFO @ Tue, 21 Apr 2015 12:04:02: #1 tags after filtering in treatment: 5180477 INFO @ Tue, 21 Apr 2015 12:04:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:04:02: #1 finished! INFO @ Tue, 21 Apr 2015 12:04:02: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:04:03: #2 number of paired peaks: 765 WARNING @ Tue, 21 Apr 2015 12:04:03: Fewer paired peaks (765) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 765 pairs to build model! INFO @ Tue, 21 Apr 2015 12:04:03: start model_add_line... INFO @ Tue, 21 Apr 2015 12:04:03: start X-correlation... INFO @ Tue, 21 Apr 2015 12:04:03: end of X-cor INFO @ Tue, 21 Apr 2015 12:04:03: #2 finished! INFO @ Tue, 21 Apr 2015 12:04:03: #2 predicted fragment length is 171 bps INFO @ Tue, 21 Apr 2015 12:04:03: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 21 Apr 2015 12:04:03: #2.2 Generate R script for model : SRX013045.05_model.r INFO @ Tue, 21 Apr 2015 12:04:03: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:04:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:04:04: start X-correlation... INFO @ Tue, 21 Apr 2015 12:04:04: end of X-cor INFO @ Tue, 21 Apr 2015 12:04:04: #2 finished! INFO @ Tue, 21 Apr 2015 12:04:04: #2 predicted fragment length is 171 bps INFO @ Tue, 21 Apr 2015 12:04:04: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 21 Apr 2015 12:04:04: #2.2 Generate R script for model : SRX013045.10_model.r INFO @ Tue, 21 Apr 2015 12:04:04: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:04:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:04:05: start X-correlation... INFO @ Tue, 21 Apr 2015 12:04:05: end of X-cor INFO @ Tue, 21 Apr 2015 12:04:05: #2 finished! INFO @ Tue, 21 Apr 2015 12:04:05: #2 predicted fragment length is 171 bps INFO @ Tue, 21 Apr 2015 12:04:05: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 21 Apr 2015 12:04:05: #2.2 Generate R script for model : SRX013045.20_model.r INFO @ Tue, 21 Apr 2015 12:04:05: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:04:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:04:33: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:04:36: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:04:37: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:04:59: #4 Write output xls file... SRX013045.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:04:59: #4 Write peak in narrowPeak format file... SRX013045.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:04:59: #4 Write summits bed file... SRX013045.05_summits.bed INFO @ Tue, 21 Apr 2015 12:04:59: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3651 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:04:59: #4 Write output xls file... SRX013045.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:04:59: #4 Write peak in narrowPeak format file... SRX013045.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:04:59: #4 Write summits bed file... SRX013045.20_summits.bed INFO @ Tue, 21 Apr 2015 12:04:59: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (334 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:05:00: #4 Write output xls file... SRX013045.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:05:00: #4 Write peak in narrowPeak format file... SRX013045.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:05:00: #4 Write summits bed file... SRX013045.10_summits.bed INFO @ Tue, 21 Apr 2015 12:05:00: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1503 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。