Job ID = 2161287 sra ファイルのダウンロード中... Completed: 606060K bytes transferred in 8 seconds (610859K bits/sec), in 2 files, 3 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 20748 0 20748 0 0 29281 0 --:--:-- --:--:-- --:--:-- 40131 100 34350 0 34350 0 0 48416 0 --:--:-- --:--:-- --:--:-- 66312 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 10331119 spots for /home/okishinya/chipatlas/results/dm3/SRX016153/SRR034714.sra Written 10331119 spots total Written 15512177 spots for /home/okishinya/chipatlas/results/dm3/SRX016153/SRR034715.sra Written 15512177 spots total 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: 00:06:52 25843296 reads; of these: 25843296 (100.00%) were unpaired; of these: 1536812 (5.95%) aligned 0 times 19498224 (75.45%) aligned exactly 1 time 4808260 (18.61%) aligned >1 times 94.05% overall alignment rate Time searching: 00:06:52 Overall time: 00:06:52 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] 13987714 / 24306484 = 0.5755 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 12:25:04: # Command line: callpeak -t SRX016153.bam -f BAM -g dm -n SRX016153.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX016153.20 # format = BAM # ChIP-seq file = ['SRX016153.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 12:25:04: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:25:04: # Command line: callpeak -t SRX016153.bam -f BAM -g dm -n SRX016153.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX016153.05 # format = BAM # ChIP-seq file = ['SRX016153.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 12:25:04: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:25:04: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:25:04: # Command line: callpeak -t SRX016153.bam -f BAM -g dm -n SRX016153.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX016153.10 # format = BAM # ChIP-seq file = ['SRX016153.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 12:25:04: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:25:04: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:25:04: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:25:09: 1000000 INFO @ Tue, 21 Apr 2015 12:25:09: 1000000 INFO @ Tue, 21 Apr 2015 12:25:09: 1000000 INFO @ Tue, 21 Apr 2015 12:25:14: 2000000 INFO @ Tue, 21 Apr 2015 12:25:14: 2000000 INFO @ Tue, 21 Apr 2015 12:25:15: 2000000 INFO @ Tue, 21 Apr 2015 12:25:19: 3000000 INFO @ Tue, 21 Apr 2015 12:25:19: 3000000 INFO @ Tue, 21 Apr 2015 12:25:20: 3000000 INFO @ Tue, 21 Apr 2015 12:25:24: 4000000 INFO @ Tue, 21 Apr 2015 12:25:24: 4000000 INFO @ Tue, 21 Apr 2015 12:25:26: 4000000 INFO @ Tue, 21 Apr 2015 12:25:29: 5000000 INFO @ Tue, 21 Apr 2015 12:25:29: 5000000 INFO @ Tue, 21 Apr 2015 12:25:31: 5000000 INFO @ Tue, 21 Apr 2015 12:25:34: 6000000 INFO @ Tue, 21 Apr 2015 12:25:34: 6000000 INFO @ Tue, 21 Apr 2015 12:25:37: 6000000 INFO @ Tue, 21 Apr 2015 12:25:39: 7000000 INFO @ Tue, 21 Apr 2015 12:25:39: 7000000 INFO @ Tue, 21 Apr 2015 12:25:42: 7000000 INFO @ Tue, 21 Apr 2015 12:25:44: 8000000 INFO @ Tue, 21 Apr 2015 12:25:45: 8000000 INFO @ Tue, 21 Apr 2015 12:25:47: 8000000 INFO @ Tue, 21 Apr 2015 12:25:49: 9000000 INFO @ Tue, 21 Apr 2015 12:25:50: 9000000 INFO @ Tue, 21 Apr 2015 12:25:52: 9000000 INFO @ Tue, 21 Apr 2015 12:25:54: 10000000 INFO @ Tue, 21 Apr 2015 12:25:55: 10000000 INFO @ Tue, 21 Apr 2015 12:25:56: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:25:56: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:25:56: #1 total tags in treatment: 10318770 INFO @ Tue, 21 Apr 2015 12:25:56: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:25:56: #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 12:25:56: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:25:56: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:25:56: #1 total tags in treatment: 10318770 INFO @ Tue, 21 Apr 2015 12:25:56: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:25:56: #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 12:25:57: 10000000 INFO @ Tue, 21 Apr 2015 12:25:58: #1 tags after filtering in treatment: 10317427 INFO @ Tue, 21 Apr 2015 12:25:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:25:58: #1 finished! INFO @ Tue, 21 Apr 2015 12:25:58: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:25:58: #1 tags after filtering in treatment: 10317427 INFO @ Tue, 21 Apr 2015 12:25:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:25:58: #1 finished! INFO @ Tue, 21 Apr 2015 12:25:58: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:25:59: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:25:59: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:25:59: #1 total tags in treatment: 10318770 INFO @ Tue, 21 Apr 2015 12:25:59: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:25:59: #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 12:26:00: #2 number of paired peaks: 532 WARNING @ Tue, 21 Apr 2015 12:26:00: Fewer paired peaks (532) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 532 pairs to build model! INFO @ Tue, 21 Apr 2015 12:26:00: start model_add_line... INFO @ Tue, 21 Apr 2015 12:26:00: #2 number of paired peaks: 532 WARNING @ Tue, 21 Apr 2015 12:26:00: Fewer paired peaks (532) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 532 pairs to build model! INFO @ Tue, 21 Apr 2015 12:26:00: start model_add_line... INFO @ Tue, 21 Apr 2015 12:26:01: #1 tags after filtering in treatment: 10317427 INFO @ Tue, 21 Apr 2015 12:26:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:26:01: #1 finished! INFO @ Tue, 21 Apr 2015 12:26:01: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:26:03: #2 number of paired peaks: 532 WARNING @ Tue, 21 Apr 2015 12:26:03: Fewer paired peaks (532) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 532 pairs to build model! INFO @ Tue, 21 Apr 2015 12:26:03: start model_add_line... INFO @ Tue, 21 Apr 2015 12:26:04: start X-correlation... INFO @ Tue, 21 Apr 2015 12:26:04: end of X-cor INFO @ Tue, 21 Apr 2015 12:26:04: #2 finished! INFO @ Tue, 21 Apr 2015 12:26:04: #2 predicted fragment length is 90 bps INFO @ Tue, 21 Apr 2015 12:26:04: #2 alternative fragment length(s) may be 90 bps INFO @ Tue, 21 Apr 2015 12:26:04: #2.2 Generate R script for model : SRX016153.20_model.r INFO @ Tue, 21 Apr 2015 12:26:04: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:26:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:26:04: start X-correlation... INFO @ Tue, 21 Apr 2015 12:26:04: end of X-cor INFO @ Tue, 21 Apr 2015 12:26:04: #2 finished! INFO @ Tue, 21 Apr 2015 12:26:04: #2 predicted fragment length is 90 bps INFO @ Tue, 21 Apr 2015 12:26:04: #2 alternative fragment length(s) may be 90 bps INFO @ Tue, 21 Apr 2015 12:26:04: #2.2 Generate R script for model : SRX016153.10_model.r INFO @ Tue, 21 Apr 2015 12:26:04: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:26:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:26:07: start X-correlation... INFO @ Tue, 21 Apr 2015 12:26:07: end of X-cor INFO @ Tue, 21 Apr 2015 12:26:07: #2 finished! INFO @ Tue, 21 Apr 2015 12:26:07: #2 predicted fragment length is 90 bps INFO @ Tue, 21 Apr 2015 12:26:07: #2 alternative fragment length(s) may be 90 bps INFO @ Tue, 21 Apr 2015 12:26:07: #2.2 Generate R script for model : SRX016153.05_model.r INFO @ Tue, 21 Apr 2015 12:26:07: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:26:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:27:00: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:27:02: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:27:05: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:27:42: #4 Write output xls file... SRX016153.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:27:42: #4 Write peak in narrowPeak format file... SRX016153.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:27:42: #4 Write summits bed file... SRX016153.20_summits.bed INFO @ Tue, 21 Apr 2015 12:27:42: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1006 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:27:45: #4 Write output xls file... SRX016153.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:27:45: #4 Write peak in narrowPeak format file... SRX016153.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:27:45: #4 Write summits bed file... SRX016153.05_summits.bed INFO @ Tue, 21 Apr 2015 12:27:45: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3089 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:27:50: #4 Write output xls file... SRX016153.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:27:50: #4 Write peak in narrowPeak format file... SRX016153.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:27:50: #4 Write summits bed file... SRX016153.10_summits.bed INFO @ Tue, 21 Apr 2015 12:27:50: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1802 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。