Job ID = 9029580 sra ファイルのダウンロード中... Completed: 599568K bytes transferred in 10 seconds (462943K 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 1921 0 --:--:-- 0:00:07 --:--:-- 13615 100 40382 0 40382 0 0 4778 0 --:--:-- 0:00:08 --:--:-- 19717 100 74441 0 74441 0 0 8021 0 --:--:-- 0:00:09 --:--:-- 25865 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 18081849 spots for /home/okishinya/chipatlas/results/dm3/SRX1848133/SRR3671296.sra Written 18081849 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: 00:05:16 18081849 reads; of these: 18081849 (100.00%) were unpaired; of these: 4286923 (23.71%) aligned 0 times 10384221 (57.43%) aligned exactly 1 time 3410705 (18.86%) aligned >1 times 76.29% overall alignment rate Time searching: 00:05:16 Overall time: 00:05:16 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] 8653400 / 13794926 = 0.6273 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 14:21:56: # Command line: callpeak -t SRX1848133.bam -f BAM -g dm -n SRX1848133.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1848133.10 # format = BAM # ChIP-seq file = ['SRX1848133.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 14:21:56: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:21:56: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:21:56: # Command line: callpeak -t SRX1848133.bam -f BAM -g dm -n SRX1848133.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1848133.05 # format = BAM # ChIP-seq file = ['SRX1848133.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 14:21:56: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:21:56: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:21:56: # Command line: callpeak -t SRX1848133.bam -f BAM -g dm -n SRX1848133.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1848133.20 # format = BAM # ChIP-seq file = ['SRX1848133.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 14:21:56: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:21:56: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:22:03: 1000000 INFO @ Sat, 03 Jun 2017 14:22:03: 1000000 INFO @ Sat, 03 Jun 2017 14:22:05: 1000000 INFO @ Sat, 03 Jun 2017 14:22:11: 2000000 INFO @ Sat, 03 Jun 2017 14:22:11: 2000000 INFO @ Sat, 03 Jun 2017 14:22:14: 2000000 INFO @ Sat, 03 Jun 2017 14:22:18: 3000000 INFO @ Sat, 03 Jun 2017 14:22:18: 3000000 INFO @ Sat, 03 Jun 2017 14:22:23: 3000000 INFO @ Sat, 03 Jun 2017 14:22:26: 4000000 INFO @ Sat, 03 Jun 2017 14:22:26: 4000000 INFO @ Sat, 03 Jun 2017 14:22:32: 4000000 INFO @ Sat, 03 Jun 2017 14:22:33: 5000000 INFO @ Sat, 03 Jun 2017 14:22:34: 5000000 INFO @ Sat, 03 Jun 2017 14:22:35: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:22:35: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:22:35: #1 total tags in treatment: 5141526 INFO @ Sat, 03 Jun 2017 14:22:35: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:22:35: #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 14:22:35: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:22:35: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:22:35: #1 total tags in treatment: 5141526 INFO @ Sat, 03 Jun 2017 14:22:35: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:22:35: #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 14:22:35: #1 tags after filtering in treatment: 5139744 INFO @ Sat, 03 Jun 2017 14:22:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:22:35: #1 finished! INFO @ Sat, 03 Jun 2017 14:22:35: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:22:36: #1 tags after filtering in treatment: 5139744 INFO @ Sat, 03 Jun 2017 14:22:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:22:36: #1 finished! INFO @ Sat, 03 Jun 2017 14:22:36: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:22:37: #2 number of paired peaks: 1162 INFO @ Sat, 03 Jun 2017 14:22:37: start model_add_line... INFO @ Sat, 03 Jun 2017 14:22:37: #2 number of paired peaks: 1162 INFO @ Sat, 03 Jun 2017 14:22:37: start model_add_line... INFO @ Sat, 03 Jun 2017 14:22:41: 5000000 INFO @ Sat, 03 Jun 2017 14:22:42: start X-correlation... INFO @ Sat, 03 Jun 2017 14:22:42: end of X-cor INFO @ Sat, 03 Jun 2017 14:22:42: #2 finished! INFO @ Sat, 03 Jun 2017 14:22:42: #2 predicted fragment length is 154 bps INFO @ Sat, 03 Jun 2017 14:22:42: #2 alternative fragment length(s) may be 154,575 bps INFO @ Sat, 03 Jun 2017 14:22:42: #2.2 Generate R script for model : SRX1848133.20_model.r INFO @ Sat, 03 Jun 2017 14:22:42: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:22:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:22:42: start X-correlation... INFO @ Sat, 03 Jun 2017 14:22:42: end of X-cor INFO @ Sat, 03 Jun 2017 14:22:42: #2 finished! INFO @ Sat, 03 Jun 2017 14:22:42: #2 predicted fragment length is 154 bps INFO @ Sat, 03 Jun 2017 14:22:42: #2 alternative fragment length(s) may be 154,575 bps INFO @ Sat, 03 Jun 2017 14:22:42: #2.2 Generate R script for model : SRX1848133.10_model.r INFO @ Sat, 03 Jun 2017 14:22:42: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:22:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:22:42: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:22:42: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:22:42: #1 total tags in treatment: 5141526 INFO @ Sat, 03 Jun 2017 14:22:42: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:22:42: #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 14:22:43: #1 tags after filtering in treatment: 5139744 INFO @ Sat, 03 Jun 2017 14:22:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:22:43: #1 finished! INFO @ Sat, 03 Jun 2017 14:22:43: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:22:44: #2 number of paired peaks: 1162 INFO @ Sat, 03 Jun 2017 14:22:44: start model_add_line... INFO @ Sat, 03 Jun 2017 14:22:50: start X-correlation... INFO @ Sat, 03 Jun 2017 14:22:50: end of X-cor INFO @ Sat, 03 Jun 2017 14:22:50: #2 finished! INFO @ Sat, 03 Jun 2017 14:22:50: #2 predicted fragment length is 154 bps INFO @ Sat, 03 Jun 2017 14:22:50: #2 alternative fragment length(s) may be 154,575 bps INFO @ Sat, 03 Jun 2017 14:22:50: #2.2 Generate R script for model : SRX1848133.05_model.r INFO @ Sat, 03 Jun 2017 14:22:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:22:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:23:12: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:23:14: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:23:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:23:33: #4 Write output xls file... SRX1848133.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:23:33: #4 Write peak in narrowPeak format file... SRX1848133.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:23:33: #4 Write summits bed file... SRX1848133.20_summits.bed INFO @ Sat, 03 Jun 2017 14:23:33: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (498 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:23:38: #4 Write output xls file... SRX1848133.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:23:38: #4 Write peak in narrowPeak format file... SRX1848133.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:23:38: #4 Write summits bed file... SRX1848133.10_summits.bed INFO @ Sat, 03 Jun 2017 14:23:38: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1333 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:23:46: #4 Write output xls file... SRX1848133.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:23:46: #4 Write peak in narrowPeak format file... SRX1848133.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:23:46: #4 Write summits bed file... SRX1848133.05_summits.bed INFO @ Sat, 03 Jun 2017 14:23:46: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2821 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。