Job ID = 2161195 sra ファイルのダウンロード中... Completed: 148034K bytes transferred in 5 seconds (240645K 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 34373 0 34373 0 0 47205 0 --:--:-- --:--:-- --:--:-- 64128 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 6611764 spots for /home/okishinya/chipatlas/results/dm3/SRX013043/SRR030309.sra Written 6611764 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: 00:01:13 6611764 reads; of these: 6611764 (100.00%) were unpaired; of these: 1388458 (21.00%) aligned 0 times 4751253 (71.86%) aligned exactly 1 time 472053 (7.14%) aligned >1 times 79.00% overall alignment rate Time searching: 00:01:13 Overall time: 00:01:13 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] 306774 / 5223306 = 0.0587 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 12:03:06: # Command line: callpeak -t SRX013043.bam -f BAM -g dm -n SRX013043.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013043.05 # format = BAM # ChIP-seq file = ['SRX013043.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 12:03:06: # Command line: callpeak -t SRX013043.bam -f BAM -g dm -n SRX013043.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013043.10 # format = BAM # ChIP-seq file = ['SRX013043.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 12:03:06: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:03:06: # Command line: callpeak -t SRX013043.bam -f BAM -g dm -n SRX013043.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013043.20 # format = BAM # ChIP-seq file = ['SRX013043.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 12:03:06: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:03:06: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:03:06: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:03:06: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:03:06: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:03:13: 1000000 INFO @ Tue, 21 Apr 2015 12:03:13: 1000000 INFO @ Tue, 21 Apr 2015 12:03:13: 1000000 INFO @ Tue, 21 Apr 2015 12:03:20: 2000000 INFO @ Tue, 21 Apr 2015 12:03:20: 2000000 INFO @ Tue, 21 Apr 2015 12:03:20: 2000000 INFO @ Tue, 21 Apr 2015 12:03:26: 3000000 INFO @ Tue, 21 Apr 2015 12:03:26: 3000000 INFO @ Tue, 21 Apr 2015 12:03:26: 3000000 INFO @ Tue, 21 Apr 2015 12:03:33: 4000000 INFO @ Tue, 21 Apr 2015 12:03:33: 4000000 INFO @ Tue, 21 Apr 2015 12:03:33: 4000000 INFO @ Tue, 21 Apr 2015 12:03:39: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:03:39: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:03:39: #1 total tags in treatment: 4916532 INFO @ Tue, 21 Apr 2015 12:03:39: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:03:39: #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 12:03:39: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:03:39: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:03:39: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:03:39: #1 total tags in treatment: 4916532 INFO @ Tue, 21 Apr 2015 12:03:39: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:03:39: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:03:39: #1 total tags in treatment: 4916532 INFO @ Tue, 21 Apr 2015 12:03:39: #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 12:03:39: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:03:39: #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 12:03:39: #1 tags after filtering in treatment: 4916173 INFO @ Tue, 21 Apr 2015 12:03:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:03:39: #1 finished! INFO @ Tue, 21 Apr 2015 12:03:39: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:03:40: #1 tags after filtering in treatment: 4916173 INFO @ Tue, 21 Apr 2015 12:03:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:03:40: #1 finished! INFO @ Tue, 21 Apr 2015 12:03:40: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:03:40: #1 tags after filtering in treatment: 4916173 INFO @ Tue, 21 Apr 2015 12:03:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:03:40: #1 finished! INFO @ Tue, 21 Apr 2015 12:03:40: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:03:40: #2 number of paired peaks: 1000 INFO @ Tue, 21 Apr 2015 12:03:40: start model_add_line... INFO @ Tue, 21 Apr 2015 12:03:41: #2 number of paired peaks: 1000 INFO @ Tue, 21 Apr 2015 12:03:41: start model_add_line... INFO @ Tue, 21 Apr 2015 12:03:41: #2 number of paired peaks: 1000 INFO @ Tue, 21 Apr 2015 12:03:41: start model_add_line... INFO @ Tue, 21 Apr 2015 12:03:43: start X-correlation... INFO @ Tue, 21 Apr 2015 12:03:43: end of X-cor INFO @ Tue, 21 Apr 2015 12:03:43: #2 finished! INFO @ Tue, 21 Apr 2015 12:03:43: #2 predicted fragment length is 125 bps INFO @ Tue, 21 Apr 2015 12:03:43: #2 alternative fragment length(s) may be 125 bps INFO @ Tue, 21 Apr 2015 12:03:43: #2.2 Generate R script for model : SRX013043.10_model.r INFO @ Tue, 21 Apr 2015 12:03:43: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:03:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:03:43: start X-correlation... INFO @ Tue, 21 Apr 2015 12:03:43: end of X-cor INFO @ Tue, 21 Apr 2015 12:03:43: #2 finished! INFO @ Tue, 21 Apr 2015 12:03:43: #2 predicted fragment length is 125 bps INFO @ Tue, 21 Apr 2015 12:03:43: #2 alternative fragment length(s) may be 125 bps INFO @ Tue, 21 Apr 2015 12:03:43: #2.2 Generate R script for model : SRX013043.05_model.r INFO @ Tue, 21 Apr 2015 12:03:43: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:03:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:03:43: start X-correlation... INFO @ Tue, 21 Apr 2015 12:03:43: end of X-cor INFO @ Tue, 21 Apr 2015 12:03:43: #2 finished! INFO @ Tue, 21 Apr 2015 12:03:43: #2 predicted fragment length is 125 bps INFO @ Tue, 21 Apr 2015 12:03:43: #2 alternative fragment length(s) may be 125 bps INFO @ Tue, 21 Apr 2015 12:03:43: #2.2 Generate R script for model : SRX013043.20_model.r INFO @ Tue, 21 Apr 2015 12:03:43: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:03:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:04:11: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:04:11: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:04:12: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:04:32: #4 Write output xls file... SRX013043.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:04:32: #4 Write peak in narrowPeak format file... SRX013043.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:04:32: #4 Write summits bed file... SRX013043.10_summits.bed INFO @ Tue, 21 Apr 2015 12:04:32: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1001 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:04:33: #4 Write output xls file... SRX013043.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:04:33: #4 Write peak in narrowPeak format file... SRX013043.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:04:33: #4 Write summits bed file... SRX013043.20_summits.bed INFO @ Tue, 21 Apr 2015 12:04:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (86 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:04:34: #4 Write output xls file... SRX013043.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:04:34: #4 Write peak in narrowPeak format file... SRX013043.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:04:34: #4 Write summits bed file... SRX013043.05_summits.bed INFO @ Tue, 21 Apr 2015 12:04:34: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (4642 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。