Job ID = 8696841 sra ファイルのダウンロード中... Completed: 468227K bytes transferred in 8 seconds (432254K 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 --:--:-- 0:00:06 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 100 28367 0 28367 0 0 3366 0 --:--:-- 0:00:08 --:--:-- 16706 100 31438 0 31438 0 0 3729 0 --:--:-- 0:00:08 --:--:-- 18503 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 39316019 spots for /home/okishinya/chipatlas/results/dm3/SRX110779/SRR388361.sra Written 39316019 spots total rm: cannot remove `[DSE]RR*.fastq': No such file or directory 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: 00:31:20 39316019 reads; of these: 39316019 (100.00%) were unpaired; of these: 8270215 (21.04%) aligned 0 times 16320331 (41.51%) aligned exactly 1 time 14725473 (37.45%) aligned >1 times 78.96% overall alignment rate Time searching: 00:31:20 Overall time: 00:31:20 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_sort_core] merging from 8 files... [bam_rmdupse_core] 12617358 / 31045804 = 0.4064 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 @ Fri, 10 Mar 2017 12:52:39: # Command line: callpeak -t SRX110779.bam -f BAM -g dm -n SRX110779.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX110779.05 # format = BAM # ChIP-seq file = ['SRX110779.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 @ Fri, 10 Mar 2017 12:52:39: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:52:39: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:52:39: # Command line: callpeak -t SRX110779.bam -f BAM -g dm -n SRX110779.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX110779.20 # format = BAM # ChIP-seq file = ['SRX110779.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 @ Fri, 10 Mar 2017 12:52:39: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:52:39: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:52:39: # Command line: callpeak -t SRX110779.bam -f BAM -g dm -n SRX110779.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX110779.10 # format = BAM # ChIP-seq file = ['SRX110779.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 @ Fri, 10 Mar 2017 12:52:39: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:52:39: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:52:47: 1000000 INFO @ Fri, 10 Mar 2017 12:52:48: 1000000 INFO @ Fri, 10 Mar 2017 12:52:50: 1000000 INFO @ Fri, 10 Mar 2017 12:52:55: 2000000 INFO @ Fri, 10 Mar 2017 12:52:59: 2000000 INFO @ Fri, 10 Mar 2017 12:53:01: 2000000 INFO @ Fri, 10 Mar 2017 12:53:02: 3000000 INFO @ Fri, 10 Mar 2017 12:53:08: 3000000 INFO @ Fri, 10 Mar 2017 12:53:10: 4000000 INFO @ Fri, 10 Mar 2017 12:53:14: 3000000 INFO @ Fri, 10 Mar 2017 12:53:14: 4000000 INFO @ Fri, 10 Mar 2017 12:53:17: 5000000 INFO @ Fri, 10 Mar 2017 12:53:21: 5000000 INFO @ Fri, 10 Mar 2017 12:53:24: 6000000 INFO @ Fri, 10 Mar 2017 12:53:26: 4000000 INFO @ Fri, 10 Mar 2017 12:53:27: 6000000 INFO @ Fri, 10 Mar 2017 12:53:30: 7000000 INFO @ Fri, 10 Mar 2017 12:53:33: 7000000 INFO @ Fri, 10 Mar 2017 12:53:37: 8000000 INFO @ Fri, 10 Mar 2017 12:53:39: 5000000 INFO @ Fri, 10 Mar 2017 12:53:39: 8000000 INFO @ Fri, 10 Mar 2017 12:53:44: 9000000 INFO @ Fri, 10 Mar 2017 12:53:45: 9000000 INFO @ Fri, 10 Mar 2017 12:53:51: 10000000 INFO @ Fri, 10 Mar 2017 12:53:52: 6000000 INFO @ Fri, 10 Mar 2017 12:53:52: 10000000 INFO @ Fri, 10 Mar 2017 12:53:57: 11000000 INFO @ Fri, 10 Mar 2017 12:53:59: 11000000 INFO @ Fri, 10 Mar 2017 12:54:03: 12000000 INFO @ Fri, 10 Mar 2017 12:54:05: 7000000 INFO @ Fri, 10 Mar 2017 12:54:05: 12000000 INFO @ Fri, 10 Mar 2017 12:54:09: 13000000 INFO @ Fri, 10 Mar 2017 12:54:12: 13000000 INFO @ Fri, 10 Mar 2017 12:54:15: 14000000 INFO @ Fri, 10 Mar 2017 12:54:18: 8000000 INFO @ Fri, 10 Mar 2017 12:54:19: 14000000 INFO @ Fri, 10 Mar 2017 12:54:21: 15000000 INFO @ Fri, 10 Mar 2017 12:54:26: 15000000 INFO @ Fri, 10 Mar 2017 12:54:27: 16000000 INFO @ Fri, 10 Mar 2017 12:54:31: 9000000 INFO @ Fri, 10 Mar 2017 12:54:32: 16000000 INFO @ Fri, 10 Mar 2017 12:54:33: 17000000 INFO @ Fri, 10 Mar 2017 12:54:39: 17000000 INFO @ Fri, 10 Mar 2017 12:54:39: 18000000 INFO @ Fri, 10 Mar 2017 12:54:43: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:54:43: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:54:43: #1 total tags in treatment: 18428446 INFO @ Fri, 10 Mar 2017 12:54:43: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:54:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:54:44: 10000000 INFO @ Fri, 10 Mar 2017 12:54:46: 18000000 INFO @ Fri, 10 Mar 2017 12:54:47: #1 tags after filtering in treatment: 18428446 INFO @ Fri, 10 Mar 2017 12:54:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:54:47: #1 finished! INFO @ Fri, 10 Mar 2017 12:54:47: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:54:49: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:54:49: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:54:49: #1 total tags in treatment: 18428446 INFO @ Fri, 10 Mar 2017 12:54:49: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:54:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:54:51: #2 number of paired peaks: 243 WARNING @ Fri, 10 Mar 2017 12:54:51: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Fri, 10 Mar 2017 12:54:51: start model_add_line... INFO @ Fri, 10 Mar 2017 12:54:54: #1 tags after filtering in treatment: 18428446 INFO @ Fri, 10 Mar 2017 12:54:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:54:54: #1 finished! INFO @ Fri, 10 Mar 2017 12:54:54: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:54:56: start X-correlation... INFO @ Fri, 10 Mar 2017 12:54:56: end of X-cor INFO @ Fri, 10 Mar 2017 12:54:56: #2 finished! INFO @ Fri, 10 Mar 2017 12:54:56: #2 predicted fragment length is 49 bps INFO @ Fri, 10 Mar 2017 12:54:56: #2 alternative fragment length(s) may be 3,49 bps INFO @ Fri, 10 Mar 2017 12:54:56: #2.2 Generate R script for model : SRX110779.05_model.r INFO @ Fri, 10 Mar 2017 12:54:56: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:54:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:54:57: 11000000 INFO @ Fri, 10 Mar 2017 12:54:58: #2 number of paired peaks: 243 WARNING @ Fri, 10 Mar 2017 12:54:58: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Fri, 10 Mar 2017 12:54:58: start model_add_line... INFO @ Fri, 10 Mar 2017 12:55:03: start X-correlation... INFO @ Fri, 10 Mar 2017 12:55:03: end of X-cor INFO @ Fri, 10 Mar 2017 12:55:03: #2 finished! INFO @ Fri, 10 Mar 2017 12:55:03: #2 predicted fragment length is 49 bps INFO @ Fri, 10 Mar 2017 12:55:03: #2 alternative fragment length(s) may be 3,49 bps INFO @ Fri, 10 Mar 2017 12:55:03: #2.2 Generate R script for model : SRX110779.10_model.r INFO @ Fri, 10 Mar 2017 12:55:03: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:55:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:55:11: 12000000 INFO @ Fri, 10 Mar 2017 12:55:25: 13000000 INFO @ Fri, 10 Mar 2017 12:55:39: 14000000 INFO @ Fri, 10 Mar 2017 12:55:53: 15000000 INFO @ Fri, 10 Mar 2017 12:56:08: 16000000 INFO @ Fri, 10 Mar 2017 12:56:24: 17000000 INFO @ Fri, 10 Mar 2017 12:56:40: 18000000 INFO @ Fri, 10 Mar 2017 12:56:47: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:56:47: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:56:47: #1 total tags in treatment: 18428446 INFO @ Fri, 10 Mar 2017 12:56:47: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:56:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:56:48: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:56:52: #1 tags after filtering in treatment: 18428446 INFO @ Fri, 10 Mar 2017 12:56:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:56:52: #1 finished! INFO @ Fri, 10 Mar 2017 12:56:52: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:56:56: #2 number of paired peaks: 243 WARNING @ Fri, 10 Mar 2017 12:56:56: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Fri, 10 Mar 2017 12:56:56: start model_add_line... INFO @ Fri, 10 Mar 2017 12:56:57: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:57:01: start X-correlation... INFO @ Fri, 10 Mar 2017 12:57:01: end of X-cor INFO @ Fri, 10 Mar 2017 12:57:01: #2 finished! INFO @ Fri, 10 Mar 2017 12:57:01: #2 predicted fragment length is 49 bps INFO @ Fri, 10 Mar 2017 12:57:01: #2 alternative fragment length(s) may be 3,49 bps INFO @ Fri, 10 Mar 2017 12:57:01: #2.2 Generate R script for model : SRX110779.20_model.r INFO @ Fri, 10 Mar 2017 12:57:01: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:57:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:58:10: #4 Write output xls file... SRX110779.05_peaks.xls INFO @ Fri, 10 Mar 2017 12:58:10: #4 Write peak in narrowPeak format file... SRX110779.05_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:58:10: #4 Write summits bed file... SRX110779.05_summits.bed INFO @ Fri, 10 Mar 2017 12:58:10: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1720 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:58:23: #4 Write output xls file... SRX110779.10_peaks.xls INFO @ Fri, 10 Mar 2017 12:58:23: #4 Write peak in narrowPeak format file... SRX110779.10_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:58:23: #4 Write summits bed file... SRX110779.10_summits.bed INFO @ Fri, 10 Mar 2017 12:58:23: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1060 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:58:58: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 13:00:23: #4 Write output xls file... SRX110779.20_peaks.xls INFO @ Fri, 10 Mar 2017 13:00:23: #4 Write peak in narrowPeak format file... SRX110779.20_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 13:00:23: #4 Write summits bed file... SRX110779.20_summits.bed INFO @ Fri, 10 Mar 2017 13:00:23: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (516 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。