Job ID = 9029400 sra ファイルのダウンロード中... Completed: 2376786K bytes transferred in 20 seconds (937182K 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 --:--:-- 0 101 5455 0 5455 0 0 790 0 --:--:-- 0:00:06 --:--:-- 10997 100 28788 0 28788 0 0 3569 0 --:--:-- 0:00:08 --:--:-- 17352 100 30659 0 30659 0 0 3801 0 --:--:-- 0:00:08 --:--:-- 18469 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 55708155 spots for /home/okishinya/chipatlas/results/dm3/SRX1715673/SRR3405214.sra Written 55708155 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: 00:19:04 55708155 reads; of these: 55708155 (100.00%) were unpaired; of these: 952303 (1.71%) aligned 0 times 48599929 (87.24%) aligned exactly 1 time 6155923 (11.05%) aligned >1 times 98.29% overall alignment rate Time searching: 00:19:04 Overall time: 00:19:04 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 24 files... [bam_rmdupse_core] 35813112 / 54755852 = 0.6541 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 13:58:34: # Command line: callpeak -t SRX1715673.bam -f BAM -g dm -n SRX1715673.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1715673.20 # format = BAM # ChIP-seq file = ['SRX1715673.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 13:58:34: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:58:34: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:58:34: # Command line: callpeak -t SRX1715673.bam -f BAM -g dm -n SRX1715673.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1715673.05 # format = BAM # ChIP-seq file = ['SRX1715673.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 13:58:34: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:58:34: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:58:34: # Command line: callpeak -t SRX1715673.bam -f BAM -g dm -n SRX1715673.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1715673.10 # format = BAM # ChIP-seq file = ['SRX1715673.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 13:58:34: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:58:34: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:58:41: 1000000 INFO @ Sat, 03 Jun 2017 13:58:41: 1000000 INFO @ Sat, 03 Jun 2017 13:58:41: 1000000 INFO @ Sat, 03 Jun 2017 13:58:48: 2000000 INFO @ Sat, 03 Jun 2017 13:58:48: 2000000 INFO @ Sat, 03 Jun 2017 13:58:48: 2000000 INFO @ Sat, 03 Jun 2017 13:58:55: 3000000 INFO @ Sat, 03 Jun 2017 13:58:55: 3000000 INFO @ Sat, 03 Jun 2017 13:58:55: 3000000 INFO @ Sat, 03 Jun 2017 13:59:02: 4000000 INFO @ Sat, 03 Jun 2017 13:59:02: 4000000 INFO @ Sat, 03 Jun 2017 13:59:02: 4000000 INFO @ Sat, 03 Jun 2017 13:59:09: 5000000 INFO @ Sat, 03 Jun 2017 13:59:09: 5000000 INFO @ Sat, 03 Jun 2017 13:59:09: 5000000 INFO @ Sat, 03 Jun 2017 13:59:16: 6000000 INFO @ Sat, 03 Jun 2017 13:59:16: 6000000 INFO @ Sat, 03 Jun 2017 13:59:16: 6000000 INFO @ Sat, 03 Jun 2017 13:59:23: 7000000 INFO @ Sat, 03 Jun 2017 13:59:23: 7000000 INFO @ Sat, 03 Jun 2017 13:59:23: 7000000 INFO @ Sat, 03 Jun 2017 13:59:30: 8000000 INFO @ Sat, 03 Jun 2017 13:59:30: 8000000 INFO @ Sat, 03 Jun 2017 13:59:30: 8000000 INFO @ Sat, 03 Jun 2017 13:59:37: 9000000 INFO @ Sat, 03 Jun 2017 13:59:37: 9000000 INFO @ Sat, 03 Jun 2017 13:59:37: 9000000 INFO @ Sat, 03 Jun 2017 13:59:44: 10000000 INFO @ Sat, 03 Jun 2017 13:59:44: 10000000 INFO @ Sat, 03 Jun 2017 13:59:44: 10000000 INFO @ Sat, 03 Jun 2017 13:59:51: 11000000 INFO @ Sat, 03 Jun 2017 13:59:51: 11000000 INFO @ Sat, 03 Jun 2017 13:59:51: 11000000 INFO @ Sat, 03 Jun 2017 13:59:59: 12000000 INFO @ Sat, 03 Jun 2017 13:59:59: 12000000 INFO @ Sat, 03 Jun 2017 13:59:59: 12000000 INFO @ Sat, 03 Jun 2017 14:00:06: 13000000 INFO @ Sat, 03 Jun 2017 14:00:06: 13000000 INFO @ Sat, 03 Jun 2017 14:00:06: 13000000 INFO @ Sat, 03 Jun 2017 14:00:13: 14000000 INFO @ Sat, 03 Jun 2017 14:00:13: 14000000 INFO @ Sat, 03 Jun 2017 14:00:13: 14000000 INFO @ Sat, 03 Jun 2017 14:00:21: 15000000 INFO @ Sat, 03 Jun 2017 14:00:21: 15000000 INFO @ Sat, 03 Jun 2017 14:00:21: 15000000 INFO @ Sat, 03 Jun 2017 14:00:28: 16000000 INFO @ Sat, 03 Jun 2017 14:00:28: 16000000 INFO @ Sat, 03 Jun 2017 14:00:28: 16000000 INFO @ Sat, 03 Jun 2017 14:00:35: 17000000 INFO @ Sat, 03 Jun 2017 14:00:35: 17000000 INFO @ Sat, 03 Jun 2017 14:00:35: 17000000 INFO @ Sat, 03 Jun 2017 14:00:42: 18000000 INFO @ Sat, 03 Jun 2017 14:00:42: 18000000 INFO @ Sat, 03 Jun 2017 14:00:42: 18000000 INFO @ Sat, 03 Jun 2017 14:00:49: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 14:00:49: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 14:00:49: #1 total tags in treatment: 18942740 INFO @ Sat, 03 Jun 2017 14:00:49: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:00:49: #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 14:00:49: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 14:00:49: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 14:00:49: #1 total tags in treatment: 18942740 INFO @ Sat, 03 Jun 2017 14:00:49: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:00:49: #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 14:00:49: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 14:00:49: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 14:00:49: #1 total tags in treatment: 18942740 INFO @ Sat, 03 Jun 2017 14:00:49: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:00:49: #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 14:00:52: #1 tags after filtering in treatment: 18933446 INFO @ Sat, 03 Jun 2017 14:00:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:00:52: #1 finished! INFO @ Sat, 03 Jun 2017 14:00:52: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:00:53: #1 tags after filtering in treatment: 18933446 INFO @ Sat, 03 Jun 2017 14:00:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:00:53: #1 finished! INFO @ Sat, 03 Jun 2017 14:00:53: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:00:54: #1 tags after filtering in treatment: 18933446 INFO @ Sat, 03 Jun 2017 14:00:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:00:54: #1 finished! INFO @ Sat, 03 Jun 2017 14:00:54: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:00:56: #2 number of paired peaks: 2575 INFO @ Sat, 03 Jun 2017 14:00:56: start model_add_line... INFO @ Sat, 03 Jun 2017 14:00:56: #2 number of paired peaks: 2575 INFO @ Sat, 03 Jun 2017 14:00:56: start model_add_line... INFO @ Sat, 03 Jun 2017 14:00:58: #2 number of paired peaks: 2575 INFO @ Sat, 03 Jun 2017 14:00:58: start model_add_line... INFO @ Sat, 03 Jun 2017 14:01:22: start X-correlation... INFO @ Sat, 03 Jun 2017 14:01:22: end of X-cor INFO @ Sat, 03 Jun 2017 14:01:22: #2 finished! INFO @ Sat, 03 Jun 2017 14:01:22: #2 predicted fragment length is 105 bps INFO @ Sat, 03 Jun 2017 14:01:22: #2 alternative fragment length(s) may be 4,105 bps INFO @ Sat, 03 Jun 2017 14:01:22: #2.2 Generate R script for model : SRX1715673.10_model.r INFO @ Sat, 03 Jun 2017 14:01:22: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:01:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:01:23: start X-correlation... INFO @ Sat, 03 Jun 2017 14:01:23: end of X-cor INFO @ Sat, 03 Jun 2017 14:01:23: #2 finished! INFO @ Sat, 03 Jun 2017 14:01:23: #2 predicted fragment length is 105 bps INFO @ Sat, 03 Jun 2017 14:01:23: #2 alternative fragment length(s) may be 4,105 bps INFO @ Sat, 03 Jun 2017 14:01:23: #2.2 Generate R script for model : SRX1715673.05_model.r INFO @ Sat, 03 Jun 2017 14:01:23: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:01:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:01:24: start X-correlation... INFO @ Sat, 03 Jun 2017 14:01:24: end of X-cor INFO @ Sat, 03 Jun 2017 14:01:24: #2 finished! INFO @ Sat, 03 Jun 2017 14:01:24: #2 predicted fragment length is 105 bps INFO @ Sat, 03 Jun 2017 14:01:24: #2 alternative fragment length(s) may be 4,105 bps INFO @ Sat, 03 Jun 2017 14:01:24: #2.2 Generate R script for model : SRX1715673.20_model.r INFO @ Sat, 03 Jun 2017 14:01:24: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:01:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:03:00: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:03:01: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:03:08: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:04:19: #4 Write output xls file... SRX1715673.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:04:19: #4 Write peak in narrowPeak format file... SRX1715673.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:04:19: #4 Write summits bed file... SRX1715673.20_summits.bed INFO @ Sat, 03 Jun 2017 14:04:19: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3629 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:04:20: #4 Write output xls file... SRX1715673.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:04:20: #4 Write peak in narrowPeak format file... SRX1715673.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:04:20: #4 Write summits bed file... SRX1715673.10_summits.bed INFO @ Sat, 03 Jun 2017 14:04:20: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6500 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:04:32: #4 Write output xls file... SRX1715673.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:04:32: #4 Write peak in narrowPeak format file... SRX1715673.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:04:32: #4 Write summits bed file... SRX1715673.05_summits.bed INFO @ Sat, 03 Jun 2017 14:04:32: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8423 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。