Job ID = 2161226 sra ファイルのダウンロード中... Completed: 170615K bytes transferred in 4 seconds (284759K 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 19281 0 19281 0 0 26471 0 --:--:-- --:--:-- --:--:-- 35838 100 34563 0 34563 0 0 47395 0 --:--:-- --:--:-- --:--:-- 64124 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 6873870 spots for /home/okishinya/chipatlas/results/dm3/SRX013074/SRR030340.sra Written 6873870 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: 00:01:35 6873870 reads; of these: 6873870 (100.00%) were unpaired; of these: 547635 (7.97%) aligned 0 times 5479155 (79.71%) aligned exactly 1 time 847080 (12.32%) aligned >1 times 92.03% overall alignment rate Time searching: 00:01:35 Overall time: 00:01:35 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] 259387 / 6326235 = 0.0410 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 12:07:20: # Command line: callpeak -t SRX013074.bam -f BAM -g dm -n SRX013074.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013074.20 # format = BAM # ChIP-seq file = ['SRX013074.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 12:07:20: # Command line: callpeak -t SRX013074.bam -f BAM -g dm -n SRX013074.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013074.10 # format = BAM # ChIP-seq file = ['SRX013074.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 12:07:20: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:07:20: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:07:20: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:07:20: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:07:20: # Command line: callpeak -t SRX013074.bam -f BAM -g dm -n SRX013074.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013074.05 # format = BAM # ChIP-seq file = ['SRX013074.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 12:07:20: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:07:20: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:07:27: 1000000 INFO @ Tue, 21 Apr 2015 12:07:27: 1000000 INFO @ Tue, 21 Apr 2015 12:07:27: 1000000 INFO @ Tue, 21 Apr 2015 12:07:34: 2000000 INFO @ Tue, 21 Apr 2015 12:07:35: 2000000 INFO @ Tue, 21 Apr 2015 12:07:35: 2000000 INFO @ Tue, 21 Apr 2015 12:07:41: 3000000 INFO @ Tue, 21 Apr 2015 12:07:42: 3000000 INFO @ Tue, 21 Apr 2015 12:07:42: 3000000 INFO @ Tue, 21 Apr 2015 12:07:46: 4000000 INFO @ Tue, 21 Apr 2015 12:07:48: 4000000 INFO @ Tue, 21 Apr 2015 12:07:48: 4000000 INFO @ Tue, 21 Apr 2015 12:07:52: 5000000 INFO @ Tue, 21 Apr 2015 12:07:54: 5000000 INFO @ Tue, 21 Apr 2015 12:07:54: 5000000 INFO @ Tue, 21 Apr 2015 12:07:58: 6000000 INFO @ Tue, 21 Apr 2015 12:07:58: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:07:58: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:07:58: #1 total tags in treatment: 6066848 INFO @ Tue, 21 Apr 2015 12:07:58: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:07:58: #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 12:08:00: #1 tags after filtering in treatment: 6066669 INFO @ Tue, 21 Apr 2015 12:08:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:08:00: #1 finished! INFO @ Tue, 21 Apr 2015 12:08:00: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:08:00: 6000000 INFO @ Tue, 21 Apr 2015 12:08:00: 6000000 INFO @ Tue, 21 Apr 2015 12:08:01: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:08:01: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:08:01: #1 total tags in treatment: 6066848 INFO @ Tue, 21 Apr 2015 12:08:01: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:08:01: #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 12:08:01: #2 number of paired peaks: 522 WARNING @ Tue, 21 Apr 2015 12:08:01: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Tue, 21 Apr 2015 12:08:01: start model_add_line... INFO @ Tue, 21 Apr 2015 12:08:01: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:08:01: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:08:01: #1 total tags in treatment: 6066848 INFO @ Tue, 21 Apr 2015 12:08:01: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:08:01: #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 12:08:02: #1 tags after filtering in treatment: 6066669 INFO @ Tue, 21 Apr 2015 12:08:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:08:02: #1 finished! INFO @ Tue, 21 Apr 2015 12:08:02: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:08:02: #1 tags after filtering in treatment: 6066669 INFO @ Tue, 21 Apr 2015 12:08:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:08:02: #1 finished! INFO @ Tue, 21 Apr 2015 12:08:02: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:08:03: start X-correlation... INFO @ Tue, 21 Apr 2015 12:08:03: end of X-cor INFO @ Tue, 21 Apr 2015 12:08:03: #2 finished! INFO @ Tue, 21 Apr 2015 12:08:03: #2 predicted fragment length is 141 bps INFO @ Tue, 21 Apr 2015 12:08:03: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 21 Apr 2015 12:08:03: #2.2 Generate R script for model : SRX013074.05_model.r INFO @ Tue, 21 Apr 2015 12:08:03: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:08:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:08:03: #2 number of paired peaks: 522 WARNING @ Tue, 21 Apr 2015 12:08:03: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Tue, 21 Apr 2015 12:08:03: start model_add_line... INFO @ Tue, 21 Apr 2015 12:08:03: #2 number of paired peaks: 522 WARNING @ Tue, 21 Apr 2015 12:08:03: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Tue, 21 Apr 2015 12:08:03: start model_add_line... INFO @ Tue, 21 Apr 2015 12:08:05: start X-correlation... INFO @ Tue, 21 Apr 2015 12:08:05: end of X-cor INFO @ Tue, 21 Apr 2015 12:08:05: #2 finished! INFO @ Tue, 21 Apr 2015 12:08:05: #2 predicted fragment length is 141 bps INFO @ Tue, 21 Apr 2015 12:08:05: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 21 Apr 2015 12:08:05: #2.2 Generate R script for model : SRX013074.10_model.r INFO @ Tue, 21 Apr 2015 12:08:05: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:08:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:08:05: start X-correlation... INFO @ Tue, 21 Apr 2015 12:08:05: end of X-cor INFO @ Tue, 21 Apr 2015 12:08:05: #2 finished! INFO @ Tue, 21 Apr 2015 12:08:05: #2 predicted fragment length is 141 bps INFO @ Tue, 21 Apr 2015 12:08:05: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 21 Apr 2015 12:08:05: #2.2 Generate R script for model : SRX013074.20_model.r INFO @ Tue, 21 Apr 2015 12:08:05: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:08:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:08:36: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:08:41: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:08:41: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:09:05: #4 Write output xls file... SRX013074.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:09:05: #4 Write peak in narrowPeak format file... SRX013074.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:09:05: #4 Write summits bed file... SRX013074.05_summits.bed INFO @ Tue, 21 Apr 2015 12:09:06: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5655 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:09:07: #4 Write output xls file... SRX013074.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:09:07: #4 Write peak in narrowPeak format file... SRX013074.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:09:07: #4 Write summits bed file... SRX013074.20_summits.bed INFO @ Tue, 21 Apr 2015 12:09:07: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (292 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:09:08: #4 Write output xls file... SRX013074.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:09:08: #4 Write peak in narrowPeak format file... SRX013074.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:09:08: #4 Write summits bed file... SRX013074.10_summits.bed INFO @ Tue, 21 Apr 2015 12:09:08: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1935 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。