Job ID = 9030568 sra ファイルのダウンロード中... Completed: 530395K bytes transferred in 6 seconds (693565K 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 14323 0 14323 0 0 1871 0 --:--:-- 0:00:07 --:--:-- 13104 100 38317 0 38317 0 0 4429 0 --:--:-- 0:00:08 --:--:-- 18351 100 59649 0 59649 0 0 6519 0 --:--:-- 0:00:09 --:--:-- 23057 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 16267419 spots for /home/okishinya/chipatlas/results/dm3/SRX288009/SRR870198.sra Written 16267419 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: 00:05:25 16267419 reads; of these: 16267419 (100.00%) were unpaired; of these: 1454653 (8.94%) aligned 0 times 12187883 (74.92%) aligned exactly 1 time 2624883 (16.14%) aligned >1 times 91.06% overall alignment rate Time searching: 00:05:25 Overall time: 00:05:25 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] 2830649 / 14812766 = 0.1911 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 17:55:33: # Command line: callpeak -t SRX288009.bam -f BAM -g dm -n SRX288009.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX288009.05 # format = BAM # ChIP-seq file = ['SRX288009.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 17:55:33: #1 read tag files... INFO @ Sat, 03 Jun 2017 17:55:33: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 17:55:33: # Command line: callpeak -t SRX288009.bam -f BAM -g dm -n SRX288009.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX288009.20 # format = BAM # ChIP-seq file = ['SRX288009.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 17:55:33: #1 read tag files... INFO @ Sat, 03 Jun 2017 17:55:33: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 17:55:33: # Command line: callpeak -t SRX288009.bam -f BAM -g dm -n SRX288009.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX288009.10 # format = BAM # ChIP-seq file = ['SRX288009.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 17:55:33: #1 read tag files... INFO @ Sat, 03 Jun 2017 17:55:33: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 17:55:39: 1000000 INFO @ Sat, 03 Jun 2017 17:55:40: 1000000 INFO @ Sat, 03 Jun 2017 17:55:40: 1000000 INFO @ Sat, 03 Jun 2017 17:55:45: 2000000 INFO @ Sat, 03 Jun 2017 17:55:47: 2000000 INFO @ Sat, 03 Jun 2017 17:55:47: 2000000 INFO @ Sat, 03 Jun 2017 17:55:52: 3000000 INFO @ Sat, 03 Jun 2017 17:55:54: 3000000 INFO @ Sat, 03 Jun 2017 17:55:54: 3000000 INFO @ Sat, 03 Jun 2017 17:55:58: 4000000 INFO @ Sat, 03 Jun 2017 17:56:01: 4000000 INFO @ Sat, 03 Jun 2017 17:56:01: 4000000 INFO @ Sat, 03 Jun 2017 17:56:04: 5000000 INFO @ Sat, 03 Jun 2017 17:56:08: 5000000 INFO @ Sat, 03 Jun 2017 17:56:08: 5000000 INFO @ Sat, 03 Jun 2017 17:56:10: 6000000 INFO @ Sat, 03 Jun 2017 17:56:14: 6000000 INFO @ Sat, 03 Jun 2017 17:56:14: 6000000 INFO @ Sat, 03 Jun 2017 17:56:16: 7000000 INFO @ Sat, 03 Jun 2017 17:56:21: 7000000 INFO @ Sat, 03 Jun 2017 17:56:21: 7000000 INFO @ Sat, 03 Jun 2017 17:56:22: 8000000 INFO @ Sat, 03 Jun 2017 17:56:28: 8000000 INFO @ Sat, 03 Jun 2017 17:56:28: 8000000 INFO @ Sat, 03 Jun 2017 17:56:28: 9000000 INFO @ Sat, 03 Jun 2017 17:56:35: 10000000 INFO @ Sat, 03 Jun 2017 17:56:35: 9000000 INFO @ Sat, 03 Jun 2017 17:56:35: 9000000 INFO @ Sat, 03 Jun 2017 17:56:41: 11000000 INFO @ Sat, 03 Jun 2017 17:56:42: 10000000 INFO @ Sat, 03 Jun 2017 17:56:42: 10000000 INFO @ Sat, 03 Jun 2017 17:56:47: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 17:56:47: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 17:56:47: #1 total tags in treatment: 11982117 INFO @ Sat, 03 Jun 2017 17:56:47: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 17:56:47: #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 17:56:49: 11000000 INFO @ Sat, 03 Jun 2017 17:56:49: 11000000 INFO @ Sat, 03 Jun 2017 17:56:50: #1 tags after filtering in treatment: 11978820 INFO @ Sat, 03 Jun 2017 17:56:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 17:56:50: #1 finished! INFO @ Sat, 03 Jun 2017 17:56:50: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 17:56:52: #2 number of paired peaks: 3386 INFO @ Sat, 03 Jun 2017 17:56:52: start model_add_line... INFO @ Sat, 03 Jun 2017 17:56:56: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 17:56:56: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 17:56:56: #1 total tags in treatment: 11982117 INFO @ Sat, 03 Jun 2017 17:56:56: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 17:56:56: #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 17:56:56: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 17:56:56: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 17:56:56: #1 total tags in treatment: 11982117 INFO @ Sat, 03 Jun 2017 17:56:56: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 17:56:56: #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 17:56:58: #1 tags after filtering in treatment: 11978820 INFO @ Sat, 03 Jun 2017 17:56:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 17:56:58: #1 finished! INFO @ Sat, 03 Jun 2017 17:56:58: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 17:56:59: #1 tags after filtering in treatment: 11978820 INFO @ Sat, 03 Jun 2017 17:56:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 17:56:59: #1 finished! INFO @ Sat, 03 Jun 2017 17:56:59: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 17:57:01: #2 number of paired peaks: 3386 INFO @ Sat, 03 Jun 2017 17:57:01: start model_add_line... INFO @ Sat, 03 Jun 2017 17:57:02: #2 number of paired peaks: 3386 INFO @ Sat, 03 Jun 2017 17:57:02: start model_add_line... INFO @ Sat, 03 Jun 2017 17:57:19: start X-correlation... INFO @ Sat, 03 Jun 2017 17:57:19: end of X-cor INFO @ Sat, 03 Jun 2017 17:57:19: #2 finished! INFO @ Sat, 03 Jun 2017 17:57:19: #2 predicted fragment length is 245 bps INFO @ Sat, 03 Jun 2017 17:57:19: #2 alternative fragment length(s) may be 245 bps INFO @ Sat, 03 Jun 2017 17:57:19: #2.2 Generate R script for model : SRX288009.10_model.r INFO @ Sat, 03 Jun 2017 17:57:19: #3 Call peaks... INFO @ Sat, 03 Jun 2017 17:57:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 17:57:28: start X-correlation... INFO @ Sat, 03 Jun 2017 17:57:28: end of X-cor INFO @ Sat, 03 Jun 2017 17:57:28: #2 finished! INFO @ Sat, 03 Jun 2017 17:57:28: #2 predicted fragment length is 245 bps INFO @ Sat, 03 Jun 2017 17:57:28: #2 alternative fragment length(s) may be 245 bps INFO @ Sat, 03 Jun 2017 17:57:28: #2.2 Generate R script for model : SRX288009.20_model.r INFO @ Sat, 03 Jun 2017 17:57:28: #3 Call peaks... INFO @ Sat, 03 Jun 2017 17:57:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 17:57:28: start X-correlation... INFO @ Sat, 03 Jun 2017 17:57:28: end of X-cor INFO @ Sat, 03 Jun 2017 17:57:28: #2 finished! INFO @ Sat, 03 Jun 2017 17:57:28: #2 predicted fragment length is 245 bps INFO @ Sat, 03 Jun 2017 17:57:28: #2 alternative fragment length(s) may be 245 bps INFO @ Sat, 03 Jun 2017 17:57:28: #2.2 Generate R script for model : SRX288009.05_model.r INFO @ Sat, 03 Jun 2017 17:57:28: #3 Call peaks... INFO @ Sat, 03 Jun 2017 17:57:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 17:58:32: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 17:58:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 17:58:45: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 17:59:34: #4 Write output xls file... SRX288009.10_peaks.xls INFO @ Sat, 03 Jun 2017 17:59:35: #4 Write peak in narrowPeak format file... SRX288009.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 17:59:35: #4 Write summits bed file... SRX288009.10_summits.bed INFO @ Sat, 03 Jun 2017 17:59:35: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6631 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 17:59:44: #4 Write output xls file... SRX288009.20_peaks.xls INFO @ Sat, 03 Jun 2017 17:59:45: #4 Write peak in narrowPeak format file... SRX288009.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 17:59:45: #4 Write summits bed file... SRX288009.20_summits.bed INFO @ Sat, 03 Jun 2017 17:59:45: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4807 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 17:59:48: #4 Write output xls file... SRX288009.05_peaks.xls INFO @ Sat, 03 Jun 2017 17:59:48: #4 Write peak in narrowPeak format file... SRX288009.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 17:59:48: #4 Write summits bed file... SRX288009.05_summits.bed INFO @ Sat, 03 Jun 2017 17:59:48: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8439 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。