Job ID = 9029238 sra ファイルのダウンロード中... Completed: 590599K bytes transferred in 11 seconds (429365K 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 --:--:-- 0 100 14324 0 14324 0 0 1908 0 --:--:-- 0:00:07 --:--:-- 13852 100 46317 0 46317 0 0 5557 0 --:--:-- 0:00:08 --:--:-- 24834 100 102k 0 102k 0 0 11437 0 --:--:-- 0:00:09 --:--:-- 38909 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 26976055 spots for /home/okishinya/chipatlas/results/dm3/SRX1433378/SRR2919843.sra Written 26976055 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:23 26976055 reads; of these: 26976055 (100.00%) were unpaired; of these: 1854657 (6.88%) aligned 0 times 18388034 (68.16%) aligned exactly 1 time 6733364 (24.96%) aligned >1 times 93.12% overall alignment rate Time searching: 00:11:24 Overall time: 00:11:24 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 12 files... [bam_rmdupse_core] 7544073 / 25121398 = 0.3003 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 @ Sat, 03 Jun 2017 13:11:01: # Command line: callpeak -t SRX1433378.bam -f BAM -g dm -n SRX1433378.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1433378.20 # format = BAM # ChIP-seq file = ['SRX1433378.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 @ Sat, 03 Jun 2017 13:11:01: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:11:01: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:11:01: # Command line: callpeak -t SRX1433378.bam -f BAM -g dm -n SRX1433378.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1433378.05 # format = BAM # ChIP-seq file = ['SRX1433378.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 @ Sat, 03 Jun 2017 13:11:01: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:11:01: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:11:01: # Command line: callpeak -t SRX1433378.bam -f BAM -g dm -n SRX1433378.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1433378.10 # format = BAM # ChIP-seq file = ['SRX1433378.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 @ Sat, 03 Jun 2017 13:11:01: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:11:01: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:11:08: 1000000 INFO @ Sat, 03 Jun 2017 13:11:08: 1000000 INFO @ Sat, 03 Jun 2017 13:11:08: 1000000 INFO @ Sat, 03 Jun 2017 13:11:16: 2000000 INFO @ Sat, 03 Jun 2017 13:11:16: 2000000 INFO @ Sat, 03 Jun 2017 13:11:16: 2000000 INFO @ Sat, 03 Jun 2017 13:11:23: 3000000 INFO @ Sat, 03 Jun 2017 13:11:23: 3000000 INFO @ Sat, 03 Jun 2017 13:11:24: 3000000 INFO @ Sat, 03 Jun 2017 13:11:30: 4000000 INFO @ Sat, 03 Jun 2017 13:11:30: 4000000 INFO @ Sat, 03 Jun 2017 13:11:32: 4000000 INFO @ Sat, 03 Jun 2017 13:11:37: 5000000 INFO @ Sat, 03 Jun 2017 13:11:37: 5000000 INFO @ Sat, 03 Jun 2017 13:11:39: 5000000 INFO @ Sat, 03 Jun 2017 13:11:42: 6000000 INFO @ Sat, 03 Jun 2017 13:11:43: 6000000 INFO @ Sat, 03 Jun 2017 13:11:45: 6000000 INFO @ Sat, 03 Jun 2017 13:11:48: 7000000 INFO @ Sat, 03 Jun 2017 13:11:48: 7000000 INFO @ Sat, 03 Jun 2017 13:11:51: 7000000 INFO @ Sat, 03 Jun 2017 13:11:54: 8000000 INFO @ Sat, 03 Jun 2017 13:11:54: 8000000 INFO @ Sat, 03 Jun 2017 13:11:57: 8000000 INFO @ Sat, 03 Jun 2017 13:12:00: 9000000 INFO @ Sat, 03 Jun 2017 13:12:00: 9000000 INFO @ Sat, 03 Jun 2017 13:12:02: 9000000 INFO @ Sat, 03 Jun 2017 13:12:05: 10000000 INFO @ Sat, 03 Jun 2017 13:12:05: 10000000 INFO @ Sat, 03 Jun 2017 13:12:08: 10000000 INFO @ Sat, 03 Jun 2017 13:12:11: 11000000 INFO @ Sat, 03 Jun 2017 13:12:11: 11000000 INFO @ Sat, 03 Jun 2017 13:12:14: 11000000 INFO @ Sat, 03 Jun 2017 13:12:16: 12000000 INFO @ Sat, 03 Jun 2017 13:12:16: 12000000 INFO @ Sat, 03 Jun 2017 13:12:20: 12000000 INFO @ Sat, 03 Jun 2017 13:12:22: 13000000 INFO @ Sat, 03 Jun 2017 13:12:22: 13000000 INFO @ Sat, 03 Jun 2017 13:12:25: 13000000 INFO @ Sat, 03 Jun 2017 13:12:28: 14000000 INFO @ Sat, 03 Jun 2017 13:12:28: 14000000 INFO @ Sat, 03 Jun 2017 13:12:31: 14000000 INFO @ Sat, 03 Jun 2017 13:12:33: 15000000 INFO @ Sat, 03 Jun 2017 13:12:33: 15000000 INFO @ Sat, 03 Jun 2017 13:12:37: 15000000 INFO @ Sat, 03 Jun 2017 13:12:39: 16000000 INFO @ Sat, 03 Jun 2017 13:12:39: 16000000 INFO @ Sat, 03 Jun 2017 13:12:43: 16000000 INFO @ Sat, 03 Jun 2017 13:12:44: 17000000 INFO @ Sat, 03 Jun 2017 13:12:44: 17000000 INFO @ Sat, 03 Jun 2017 13:12:48: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:12:48: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:12:48: #1 total tags in treatment: 17577325 INFO @ Sat, 03 Jun 2017 13:12:48: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:12:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:12:48: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:12:48: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:12:48: #1 total tags in treatment: 17577325 INFO @ Sat, 03 Jun 2017 13:12:48: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:12:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:12:48: 17000000 INFO @ Sat, 03 Jun 2017 13:12:51: #1 tags after filtering in treatment: 17572650 INFO @ Sat, 03 Jun 2017 13:12:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:12:51: #1 finished! INFO @ Sat, 03 Jun 2017 13:12:51: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:12:51: #1 tags after filtering in treatment: 17572650 INFO @ Sat, 03 Jun 2017 13:12:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:12:51: #1 finished! INFO @ Sat, 03 Jun 2017 13:12:51: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:12:52: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:12:52: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:12:52: #1 total tags in treatment: 17577325 INFO @ Sat, 03 Jun 2017 13:12:52: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:12:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:12:54: #2 number of paired peaks: 575 WARNING @ Sat, 03 Jun 2017 13:12:54: Fewer paired peaks (575) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 575 pairs to build model! INFO @ Sat, 03 Jun 2017 13:12:54: start model_add_line... INFO @ Sat, 03 Jun 2017 13:12:54: #2 number of paired peaks: 575 WARNING @ Sat, 03 Jun 2017 13:12:54: Fewer paired peaks (575) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 575 pairs to build model! INFO @ Sat, 03 Jun 2017 13:12:54: start model_add_line... INFO @ Sat, 03 Jun 2017 13:12:55: #1 tags after filtering in treatment: 17572650 INFO @ Sat, 03 Jun 2017 13:12:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:12:55: #1 finished! INFO @ Sat, 03 Jun 2017 13:12:55: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:12:58: #2 number of paired peaks: 575 WARNING @ Sat, 03 Jun 2017 13:12:58: Fewer paired peaks (575) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 575 pairs to build model! INFO @ Sat, 03 Jun 2017 13:12:58: start model_add_line... INFO @ Sat, 03 Jun 2017 13:13:01: start X-correlation... INFO @ Sat, 03 Jun 2017 13:13:01: end of X-cor INFO @ Sat, 03 Jun 2017 13:13:01: #2 finished! INFO @ Sat, 03 Jun 2017 13:13:01: #2 predicted fragment length is 121 bps INFO @ Sat, 03 Jun 2017 13:13:01: #2 alternative fragment length(s) may be 121 bps INFO @ Sat, 03 Jun 2017 13:13:01: #2.2 Generate R script for model : SRX1433378.20_model.r INFO @ Sat, 03 Jun 2017 13:13:01: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:13:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:13:02: start X-correlation... INFO @ Sat, 03 Jun 2017 13:13:02: end of X-cor INFO @ Sat, 03 Jun 2017 13:13:02: #2 finished! INFO @ Sat, 03 Jun 2017 13:13:02: #2 predicted fragment length is 121 bps INFO @ Sat, 03 Jun 2017 13:13:02: #2 alternative fragment length(s) may be 121 bps INFO @ Sat, 03 Jun 2017 13:13:02: #2.2 Generate R script for model : SRX1433378.10_model.r INFO @ Sat, 03 Jun 2017 13:13:02: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:13:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:13:05: start X-correlation... INFO @ Sat, 03 Jun 2017 13:13:05: end of X-cor INFO @ Sat, 03 Jun 2017 13:13:05: #2 finished! INFO @ Sat, 03 Jun 2017 13:13:05: #2 predicted fragment length is 121 bps INFO @ Sat, 03 Jun 2017 13:13:05: #2 alternative fragment length(s) may be 121 bps INFO @ Sat, 03 Jun 2017 13:13:05: #2.2 Generate R script for model : SRX1433378.05_model.r INFO @ Sat, 03 Jun 2017 13:13:05: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:13:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:14:37: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:14:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:14:45: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:15:46: #4 Write output xls file... SRX1433378.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:15:46: #4 Write peak in narrowPeak format file... SRX1433378.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:15:46: #4 Write summits bed file... SRX1433378.20_summits.bed INFO @ Sat, 03 Jun 2017 13:15:46: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1717 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:15:58: #4 Write output xls file... SRX1433378.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:15:58: #4 Write peak in narrowPeak format file... SRX1433378.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:15:58: #4 Write summits bed file... SRX1433378.10_summits.bed INFO @ Sat, 03 Jun 2017 13:15:58: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3082 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:15:59: #4 Write output xls file... SRX1433378.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:15:59: #4 Write peak in narrowPeak format file... SRX1433378.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:16:00: #4 Write summits bed file... SRX1433378.05_summits.bed INFO @ Sat, 03 Jun 2017 13:16:00: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4989 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。