Job ID = 9029327 sra ファイルのダウンロード中... Completed: 442703K bytes transferred in 5 seconds (609916K 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 --:--:-- 0:00:06 --:--:-- 0 100 22318 0 22318 0 0 2828 0 --:--:-- 0:00:07 --:--:-- 15141 100 73172 0 73172 0 0 8232 0 --:--:-- 0:00:08 --:--:-- 29612 100 75043 0 75043 0 0 8442 0 --:--:-- 0:00:08 --:--:-- 30357 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 14921239 spots for /home/okishinya/chipatlas/results/dm3/SRX1561068/SRR3145071.sra Written 14921239 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: 00:04:11 14921239 reads; of these: 14921239 (100.00%) were unpaired; of these: 1644046 (11.02%) aligned 0 times 11760290 (78.82%) aligned exactly 1 time 1516903 (10.17%) aligned >1 times 88.98% overall alignment rate Time searching: 00:04:11 Overall time: 00:04:11 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] 2753867 / 13277193 = 0.2074 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 13:21:08: # Command line: callpeak -t SRX1561068.bam -f BAM -g dm -n SRX1561068.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1561068.20 # format = BAM # ChIP-seq file = ['SRX1561068.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 13:21:08: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:21:08: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:21:08: # Command line: callpeak -t SRX1561068.bam -f BAM -g dm -n SRX1561068.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1561068.10 # format = BAM # ChIP-seq file = ['SRX1561068.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 13:21:08: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:21:08: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:21:08: # Command line: callpeak -t SRX1561068.bam -f BAM -g dm -n SRX1561068.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1561068.05 # format = BAM # ChIP-seq file = ['SRX1561068.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 13:21:08: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:21:08: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:21:15: 1000000 INFO @ Sat, 03 Jun 2017 13:21:15: 1000000 INFO @ Sat, 03 Jun 2017 13:21:15: 1000000 INFO @ Sat, 03 Jun 2017 13:21:22: 2000000 INFO @ Sat, 03 Jun 2017 13:21:22: 2000000 INFO @ Sat, 03 Jun 2017 13:21:23: 2000000 INFO @ Sat, 03 Jun 2017 13:21:30: 3000000 INFO @ Sat, 03 Jun 2017 13:21:30: 3000000 INFO @ Sat, 03 Jun 2017 13:21:30: 3000000 INFO @ Sat, 03 Jun 2017 13:21:37: 4000000 INFO @ Sat, 03 Jun 2017 13:21:37: 4000000 INFO @ Sat, 03 Jun 2017 13:21:37: 4000000 INFO @ Sat, 03 Jun 2017 13:21:45: 5000000 INFO @ Sat, 03 Jun 2017 13:21:45: 5000000 INFO @ Sat, 03 Jun 2017 13:21:45: 5000000 INFO @ Sat, 03 Jun 2017 13:21:52: 6000000 INFO @ Sat, 03 Jun 2017 13:21:52: 6000000 INFO @ Sat, 03 Jun 2017 13:21:52: 6000000 INFO @ Sat, 03 Jun 2017 13:21:59: 7000000 INFO @ Sat, 03 Jun 2017 13:21:59: 7000000 INFO @ Sat, 03 Jun 2017 13:22:00: 7000000 INFO @ Sat, 03 Jun 2017 13:22:07: 8000000 INFO @ Sat, 03 Jun 2017 13:22:07: 8000000 INFO @ Sat, 03 Jun 2017 13:22:07: 8000000 INFO @ Sat, 03 Jun 2017 13:22:14: 9000000 INFO @ Sat, 03 Jun 2017 13:22:14: 9000000 INFO @ Sat, 03 Jun 2017 13:22:15: 9000000 INFO @ Sat, 03 Jun 2017 13:22:21: 10000000 INFO @ Sat, 03 Jun 2017 13:22:22: 10000000 INFO @ Sat, 03 Jun 2017 13:22:22: 10000000 INFO @ Sat, 03 Jun 2017 13:22:25: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:22:25: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:22:25: #1 total tags in treatment: 10523326 INFO @ Sat, 03 Jun 2017 13:22:25: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:22:25: #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 13:22:25: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:22:25: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:22:25: #1 total tags in treatment: 10523326 INFO @ Sat, 03 Jun 2017 13:22:25: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:22:25: #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 13:22:26: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:22:26: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:22:26: #1 total tags in treatment: 10523326 INFO @ Sat, 03 Jun 2017 13:22:26: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:22:26: #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 13:22:27: #1 tags after filtering in treatment: 10518089 INFO @ Sat, 03 Jun 2017 13:22:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:22:27: #1 finished! INFO @ Sat, 03 Jun 2017 13:22:27: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:22:27: #1 tags after filtering in treatment: 10518089 INFO @ Sat, 03 Jun 2017 13:22:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:22:27: #1 finished! INFO @ Sat, 03 Jun 2017 13:22:27: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:22:29: #1 tags after filtering in treatment: 10518089 INFO @ Sat, 03 Jun 2017 13:22:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:22:29: #1 finished! INFO @ Sat, 03 Jun 2017 13:22:29: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:22:29: #2 number of paired peaks: 4194 INFO @ Sat, 03 Jun 2017 13:22:29: start model_add_line... INFO @ Sat, 03 Jun 2017 13:22:30: #2 number of paired peaks: 4194 INFO @ Sat, 03 Jun 2017 13:22:30: start model_add_line... INFO @ Sat, 03 Jun 2017 13:22:31: #2 number of paired peaks: 4194 INFO @ Sat, 03 Jun 2017 13:22:31: start model_add_line... INFO @ Sat, 03 Jun 2017 13:22:59: start X-correlation... INFO @ Sat, 03 Jun 2017 13:22:59: end of X-cor INFO @ Sat, 03 Jun 2017 13:22:59: #2 finished! INFO @ Sat, 03 Jun 2017 13:22:59: start X-correlation... INFO @ Sat, 03 Jun 2017 13:22:59: #2 predicted fragment length is 121 bps INFO @ Sat, 03 Jun 2017 13:22:59: #2 alternative fragment length(s) may be 121 bps INFO @ Sat, 03 Jun 2017 13:22:59: #2.2 Generate R script for model : SRX1561068.20_model.r INFO @ Sat, 03 Jun 2017 13:22:59: end of X-cor INFO @ Sat, 03 Jun 2017 13:22:59: #2 finished! INFO @ Sat, 03 Jun 2017 13:22:59: #2 predicted fragment length is 121 bps INFO @ Sat, 03 Jun 2017 13:22:59: #2 alternative fragment length(s) may be 121 bps INFO @ Sat, 03 Jun 2017 13:22:59: #2.2 Generate R script for model : SRX1561068.10_model.r INFO @ Sat, 03 Jun 2017 13:22:59: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:22:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:22:59: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:22:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:23:01: start X-correlation... INFO @ Sat, 03 Jun 2017 13:23:01: end of X-cor INFO @ Sat, 03 Jun 2017 13:23:01: #2 finished! INFO @ Sat, 03 Jun 2017 13:23:01: #2 predicted fragment length is 121 bps INFO @ Sat, 03 Jun 2017 13:23:01: #2 alternative fragment length(s) may be 121 bps INFO @ Sat, 03 Jun 2017 13:23:01: #2.2 Generate R script for model : SRX1561068.05_model.r INFO @ Sat, 03 Jun 2017 13:23:01: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:23:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:23:57: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:24:00: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:24:01: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:24:49: #4 Write output xls file... SRX1561068.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:24:49: #4 Write peak in narrowPeak format file... SRX1561068.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:24:50: #4 Write summits bed file... SRX1561068.20_summits.bed INFO @ Sat, 03 Jun 2017 13:24:50: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5758 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:24:55: #4 Write output xls file... SRX1561068.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:24:55: #4 Write peak in narrowPeak format file... SRX1561068.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:24:55: #4 Write summits bed file... SRX1561068.05_summits.bed INFO @ Sat, 03 Jun 2017 13:24:55: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (12516 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:24:56: #4 Write output xls file... SRX1561068.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:24:56: #4 Write peak in narrowPeak format file... SRX1561068.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:24:56: #4 Write summits bed file... SRX1561068.10_summits.bed INFO @ Sat, 03 Jun 2017 13:24:56: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9455 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。