Job ID = 2161689 sra ファイルのダウンロード中... Completed: 640958K bytes transferred in 9 seconds (566948K 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 44541 0 44541 0 0 47862 0 --:--:-- --:--:-- --:--:-- 60271 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 10425618 spots for /home/okishinya/chipatlas/results/dm3/SRX032125/SRR073951.sra Written 10425618 spots total Written 22745323 spots for /home/okishinya/chipatlas/results/dm3/SRX032125/SRR073950.sra Written 22745323 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: 00:06:45 33170941 reads; of these: 33170941 (100.00%) were unpaired; of these: 3428917 (10.34%) aligned 0 times 26475468 (79.82%) aligned exactly 1 time 3266556 (9.85%) aligned >1 times 89.66% overall alignment rate Time searching: 00:06:45 Overall time: 00:06:45 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] 15717217 / 29742024 = 0.5285 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 13:13:57: # Command line: callpeak -t SRX032125.bam -f BAM -g dm -n SRX032125.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX032125.05 # format = BAM # ChIP-seq file = ['SRX032125.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 13:13:57: # Command line: callpeak -t SRX032125.bam -f BAM -g dm -n SRX032125.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX032125.20 # format = BAM # ChIP-seq file = ['SRX032125.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 13:13:57: # Command line: callpeak -t SRX032125.bam -f BAM -g dm -n SRX032125.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX032125.10 # format = BAM # ChIP-seq file = ['SRX032125.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 13:13:57: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:13:57: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:13:57: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:13:57: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:13:57: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:13:57: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:14:03: 1000000 INFO @ Tue, 21 Apr 2015 13:14:03: 1000000 INFO @ Tue, 21 Apr 2015 13:14:03: 1000000 INFO @ Tue, 21 Apr 2015 13:14:09: 2000000 INFO @ Tue, 21 Apr 2015 13:14:10: 2000000 INFO @ Tue, 21 Apr 2015 13:14:10: 2000000 INFO @ Tue, 21 Apr 2015 13:14:14: 3000000 INFO @ Tue, 21 Apr 2015 13:14:17: 3000000 INFO @ Tue, 21 Apr 2015 13:14:17: 3000000 INFO @ Tue, 21 Apr 2015 13:14:20: 4000000 INFO @ Tue, 21 Apr 2015 13:14:24: 4000000 INFO @ Tue, 21 Apr 2015 13:14:24: 4000000 INFO @ Tue, 21 Apr 2015 13:14:26: 5000000 INFO @ Tue, 21 Apr 2015 13:14:30: 5000000 INFO @ Tue, 21 Apr 2015 13:14:30: 5000000 INFO @ Tue, 21 Apr 2015 13:14:32: 6000000 INFO @ Tue, 21 Apr 2015 13:14:37: 6000000 INFO @ Tue, 21 Apr 2015 13:14:37: 6000000 INFO @ Tue, 21 Apr 2015 13:14:38: 7000000 INFO @ Tue, 21 Apr 2015 13:14:44: 7000000 INFO @ Tue, 21 Apr 2015 13:14:44: 7000000 INFO @ Tue, 21 Apr 2015 13:14:44: 8000000 INFO @ Tue, 21 Apr 2015 13:14:50: 9000000 INFO @ Tue, 21 Apr 2015 13:14:50: 8000000 INFO @ Tue, 21 Apr 2015 13:14:50: 8000000 INFO @ Tue, 21 Apr 2015 13:14:56: 10000000 INFO @ Tue, 21 Apr 2015 13:14:57: 9000000 INFO @ Tue, 21 Apr 2015 13:14:57: 9000000 INFO @ Tue, 21 Apr 2015 13:15:02: 11000000 INFO @ Tue, 21 Apr 2015 13:15:04: 10000000 INFO @ Tue, 21 Apr 2015 13:15:04: 10000000 INFO @ Tue, 21 Apr 2015 13:15:08: 12000000 INFO @ Tue, 21 Apr 2015 13:15:10: 11000000 INFO @ Tue, 21 Apr 2015 13:15:10: 11000000 INFO @ Tue, 21 Apr 2015 13:15:13: 13000000 INFO @ Tue, 21 Apr 2015 13:15:17: 12000000 INFO @ Tue, 21 Apr 2015 13:15:17: 12000000 INFO @ Tue, 21 Apr 2015 13:15:19: 14000000 INFO @ Tue, 21 Apr 2015 13:15:20: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:15:20: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:15:20: #1 total tags in treatment: 14024807 INFO @ Tue, 21 Apr 2015 13:15:20: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:15:20: #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 13:15:22: #1 tags after filtering in treatment: 14023058 INFO @ Tue, 21 Apr 2015 13:15:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:15:22: #1 finished! INFO @ Tue, 21 Apr 2015 13:15:22: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:15:24: 13000000 INFO @ Tue, 21 Apr 2015 13:15:24: 13000000 INFO @ Tue, 21 Apr 2015 13:15:24: #2 number of paired peaks: 276 WARNING @ Tue, 21 Apr 2015 13:15:24: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Tue, 21 Apr 2015 13:15:24: start model_add_line... INFO @ Tue, 21 Apr 2015 13:15:28: start X-correlation... INFO @ Tue, 21 Apr 2015 13:15:28: end of X-cor INFO @ Tue, 21 Apr 2015 13:15:28: #2 finished! INFO @ Tue, 21 Apr 2015 13:15:28: #2 predicted fragment length is 169 bps INFO @ Tue, 21 Apr 2015 13:15:28: #2 alternative fragment length(s) may be 169 bps INFO @ Tue, 21 Apr 2015 13:15:28: #2.2 Generate R script for model : SRX032125.05_model.r INFO @ Tue, 21 Apr 2015 13:15:28: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:15:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:15:31: 14000000 INFO @ Tue, 21 Apr 2015 13:15:31: 14000000 INFO @ Tue, 21 Apr 2015 13:15:31: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:15:31: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:15:31: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:15:31: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:15:31: #1 total tags in treatment: 14024807 INFO @ Tue, 21 Apr 2015 13:15:31: #1 total tags in treatment: 14024807 INFO @ Tue, 21 Apr 2015 13:15:31: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:15:31: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:15:31: #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 13:15:31: #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 13:15:33: #1 tags after filtering in treatment: 14023058 INFO @ Tue, 21 Apr 2015 13:15:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:15:33: #1 finished! INFO @ Tue, 21 Apr 2015 13:15:33: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:15:33: #1 tags after filtering in treatment: 14023058 INFO @ Tue, 21 Apr 2015 13:15:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:15:33: #1 finished! INFO @ Tue, 21 Apr 2015 13:15:33: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:15:36: #2 number of paired peaks: 276 WARNING @ Tue, 21 Apr 2015 13:15:36: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Tue, 21 Apr 2015 13:15:36: start model_add_line... INFO @ Tue, 21 Apr 2015 13:15:36: #2 number of paired peaks: 276 WARNING @ Tue, 21 Apr 2015 13:15:36: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Tue, 21 Apr 2015 13:15:36: start model_add_line... INFO @ Tue, 21 Apr 2015 13:15:39: start X-correlation... INFO @ Tue, 21 Apr 2015 13:15:39: end of X-cor INFO @ Tue, 21 Apr 2015 13:15:39: #2 finished! INFO @ Tue, 21 Apr 2015 13:15:39: #2 predicted fragment length is 169 bps INFO @ Tue, 21 Apr 2015 13:15:39: #2 alternative fragment length(s) may be 169 bps INFO @ Tue, 21 Apr 2015 13:15:39: #2.2 Generate R script for model : SRX032125.20_model.r INFO @ Tue, 21 Apr 2015 13:15:39: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:15:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:15:39: start X-correlation... INFO @ Tue, 21 Apr 2015 13:15:39: end of X-cor INFO @ Tue, 21 Apr 2015 13:15:39: #2 finished! INFO @ Tue, 21 Apr 2015 13:15:39: #2 predicted fragment length is 169 bps INFO @ Tue, 21 Apr 2015 13:15:39: #2 alternative fragment length(s) may be 169 bps INFO @ Tue, 21 Apr 2015 13:15:39: #2.2 Generate R script for model : SRX032125.10_model.r INFO @ Tue, 21 Apr 2015 13:15:39: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:15:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:16:42: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:16:54: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:16:56: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:17:40: #4 Write output xls file... SRX032125.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:17:41: #4 Write peak in narrowPeak format file... SRX032125.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:17:41: #4 Write summits bed file... SRX032125.05_summits.bed INFO @ Tue, 21 Apr 2015 13:17:41: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4274 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:17:49: #4 Write output xls file... SRX032125.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:17:49: #4 Write peak in narrowPeak format file... SRX032125.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:17:49: #4 Write summits bed file... SRX032125.20_summits.bed INFO @ Tue, 21 Apr 2015 13:17:49: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (938 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:17:51: #4 Write output xls file... SRX032125.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:17:51: #4 Write peak in narrowPeak format file... SRX032125.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:17:51: #4 Write summits bed file... SRX032125.10_summits.bed INFO @ Tue, 21 Apr 2015 13:17:51: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2038 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。