Job ID = 2237073 sra ファイルのダウンロード中... Completed: 329878K bytes transferred in 7 seconds (346413K 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 36848 0 36848 0 0 49272 0 --:--:-- --:--:-- --:--:-- 66273 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 15876751 spots for /home/okishinya/chipatlas/results/ce10/SRX113611/SRR393711.sra Written 15876751 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: 00:04:31 15876751 reads; of these: 15876751 (100.00%) were unpaired; of these: 903524 (5.69%) aligned 0 times 9943676 (62.63%) aligned exactly 1 time 5029551 (31.68%) aligned >1 times 94.31% overall alignment rate Time searching: 00:04:31 Overall time: 00:04:31 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] 7770889 / 14973227 = 0.5190 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 11:34:21: # Command line: callpeak -t SRX113611.bam -f BAM -g ce -n SRX113611.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX113611.10 # format = BAM # ChIP-seq file = ['SRX113611.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 11:34:21: # Command line: callpeak -t SRX113611.bam -f BAM -g ce -n SRX113611.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX113611.20 # format = BAM # ChIP-seq file = ['SRX113611.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 11:34:21: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:34:21: # Command line: callpeak -t SRX113611.bam -f BAM -g ce -n SRX113611.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX113611.05 # format = BAM # ChIP-seq file = ['SRX113611.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 11:34:21: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:34:21: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:34:21: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:34:21: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:34:21: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:34:27: 1000000 INFO @ Thu, 30 Apr 2015 11:34:27: 1000000 INFO @ Thu, 30 Apr 2015 11:34:27: 1000000 INFO @ Thu, 30 Apr 2015 11:34:32: 2000000 INFO @ Thu, 30 Apr 2015 11:34:32: 2000000 INFO @ Thu, 30 Apr 2015 11:34:32: 2000000 INFO @ Thu, 30 Apr 2015 11:34:37: 3000000 INFO @ Thu, 30 Apr 2015 11:34:37: 3000000 INFO @ Thu, 30 Apr 2015 11:34:38: 3000000 INFO @ Thu, 30 Apr 2015 11:34:42: 4000000 INFO @ Thu, 30 Apr 2015 11:34:43: 4000000 INFO @ Thu, 30 Apr 2015 11:34:43: 4000000 INFO @ Thu, 30 Apr 2015 11:34:48: 5000000 INFO @ Thu, 30 Apr 2015 11:34:48: 5000000 INFO @ Thu, 30 Apr 2015 11:34:49: 5000000 INFO @ Thu, 30 Apr 2015 11:34:53: 6000000 INFO @ Thu, 30 Apr 2015 11:34:53: 6000000 INFO @ Thu, 30 Apr 2015 11:34:55: 6000000 INFO @ Thu, 30 Apr 2015 11:34:59: 7000000 INFO @ Thu, 30 Apr 2015 11:34:59: 7000000 INFO @ Thu, 30 Apr 2015 11:35:00: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:35:00: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:35:00: #1 total tags in treatment: 7202338 INFO @ Thu, 30 Apr 2015 11:35:00: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:35:00: #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 11:35:00: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:35:00: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:35:00: #1 total tags in treatment: 7202338 INFO @ Thu, 30 Apr 2015 11:35:00: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:35:00: #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 11:35:01: 7000000 INFO @ Thu, 30 Apr 2015 11:35:01: #1 tags after filtering in treatment: 7168673 INFO @ Thu, 30 Apr 2015 11:35:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:35:01: #1 finished! INFO @ Thu, 30 Apr 2015 11:35:01: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:35:01: #1 tags after filtering in treatment: 7168673 INFO @ Thu, 30 Apr 2015 11:35:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:35:01: #1 finished! INFO @ Thu, 30 Apr 2015 11:35:01: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:35:02: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:35:02: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:35:02: #1 total tags in treatment: 7202338 INFO @ Thu, 30 Apr 2015 11:35:02: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:35:02: #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 11:35:03: #1 tags after filtering in treatment: 7168673 INFO @ Thu, 30 Apr 2015 11:35:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:35:03: #1 finished! INFO @ Thu, 30 Apr 2015 11:35:03: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:35:03: #2 number of paired peaks: 5699 INFO @ Thu, 30 Apr 2015 11:35:03: start model_add_line... INFO @ Thu, 30 Apr 2015 11:35:03: #2 number of paired peaks: 5699 INFO @ Thu, 30 Apr 2015 11:35:03: start model_add_line... INFO @ Thu, 30 Apr 2015 11:35:05: #2 number of paired peaks: 5699 INFO @ Thu, 30 Apr 2015 11:35:05: start model_add_line... INFO @ Thu, 30 Apr 2015 11:35:41: start X-correlation... INFO @ Thu, 30 Apr 2015 11:35:41: end of X-cor INFO @ Thu, 30 Apr 2015 11:35:41: #2 finished! INFO @ Thu, 30 Apr 2015 11:35:41: #2 predicted fragment length is 160 bps INFO @ Thu, 30 Apr 2015 11:35:41: #2 alternative fragment length(s) may be 1,160 bps INFO @ Thu, 30 Apr 2015 11:35:41: #2.2 Generate R script for model : SRX113611.20_model.r INFO @ Thu, 30 Apr 2015 11:35:41: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:35:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:35:41: start X-correlation... INFO @ Thu, 30 Apr 2015 11:35:41: end of X-cor INFO @ Thu, 30 Apr 2015 11:35:41: #2 finished! INFO @ Thu, 30 Apr 2015 11:35:41: #2 predicted fragment length is 160 bps INFO @ Thu, 30 Apr 2015 11:35:41: #2 alternative fragment length(s) may be 1,160 bps INFO @ Thu, 30 Apr 2015 11:35:41: #2.2 Generate R script for model : SRX113611.05_model.r INFO @ Thu, 30 Apr 2015 11:35:41: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:35:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:35:41: start X-correlation... INFO @ Thu, 30 Apr 2015 11:35:41: end of X-cor INFO @ Thu, 30 Apr 2015 11:35:41: #2 finished! INFO @ Thu, 30 Apr 2015 11:35:41: #2 predicted fragment length is 160 bps INFO @ Thu, 30 Apr 2015 11:35:41: #2 alternative fragment length(s) may be 1,160 bps INFO @ Thu, 30 Apr 2015 11:35:41: #2.2 Generate R script for model : SRX113611.10_model.r INFO @ Thu, 30 Apr 2015 11:35:41: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:35:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:36:22: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:36:24: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:36:25: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:36:50: #4 Write output xls file... SRX113611.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:36:50: #4 Write peak in narrowPeak format file... SRX113611.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:36:50: #4 Write summits bed file... SRX113611.20_summits.bed INFO @ Thu, 30 Apr 2015 11:36:50: Done! INFO @ Thu, 30 Apr 2015 11:36:50: #4 Write output xls file... SRX113611.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:36:50: #4 Write peak in narrowPeak format file... SRX113611.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:36:50: #4 Write summits bed file... SRX113611.10_summits.bed pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (235 records, 4 fields): 2 millis INFO @ Thu, 30 Apr 2015 11:36:50: Done! CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1039 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 30 Apr 2015 11:36:56: #4 Write output xls file... SRX113611.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:36:56: #4 Write peak in narrowPeak format file... SRX113611.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:36:56: #4 Write summits bed file... SRX113611.05_summits.bed INFO @ Thu, 30 Apr 2015 11:36:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3185 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。