Job ID = 9041708 sra ファイルのダウンロード中... Completed: 1804087K bytes transferred in 17 seconds (863466K 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 9111 0 9111 0 0 1250 0 --:--:-- 0:00:07 --:--:-- 10769 100 23765 0 23765 0 0 2990 0 --:--:-- 0:00:07 --:--:-- 15738 100 51965 0 51965 0 0 5784 0 --:--:-- 0:00:08 --:--:-- 20418 100 110k 0 110k 0 0 11359 0 --:--:-- 0:00:09 --:--:-- 32249 100 112k 0 112k 0 0 11500 0 --:--:-- 0:00:09 --:--:-- 32404 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 53867255 spots for /home/okishinya/chipatlas/results/dm3/SRX1361356/SRR2749794.sra Written 53867255 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: 00:08:54 53867255 reads; of these: 53867255 (100.00%) were unpaired; of these: 4907238 (9.11%) aligned 0 times 38134587 (70.79%) aligned exactly 1 time 10825430 (20.10%) aligned >1 times 90.89% overall alignment rate Time searching: 00:08:54 Overall time: 00:08:54 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] 26235888 / 48960017 = 0.5359 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 @ Mon, 05 Jun 2017 01:53:07: # Command line: callpeak -t SRX1361356.bam -f BAM -g dm -n SRX1361356.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1361356.20 # format = BAM # ChIP-seq file = ['SRX1361356.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 @ Mon, 05 Jun 2017 01:53:07: #1 read tag files... INFO @ Mon, 05 Jun 2017 01:53:07: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 01:53:07: # Command line: callpeak -t SRX1361356.bam -f BAM -g dm -n SRX1361356.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1361356.05 # format = BAM # ChIP-seq file = ['SRX1361356.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 @ Mon, 05 Jun 2017 01:53:07: #1 read tag files... INFO @ Mon, 05 Jun 2017 01:53:07: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 01:53:07: # Command line: callpeak -t SRX1361356.bam -f BAM -g dm -n SRX1361356.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1361356.10 # format = BAM # ChIP-seq file = ['SRX1361356.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 @ Mon, 05 Jun 2017 01:53:07: #1 read tag files... INFO @ Mon, 05 Jun 2017 01:53:07: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 01:53:12: 1000000 INFO @ Mon, 05 Jun 2017 01:53:12: 1000000 INFO @ Mon, 05 Jun 2017 01:53:12: 1000000 INFO @ Mon, 05 Jun 2017 01:53:18: 2000000 INFO @ Mon, 05 Jun 2017 01:53:18: 2000000 INFO @ Mon, 05 Jun 2017 01:53:18: 2000000 INFO @ Mon, 05 Jun 2017 01:53:24: 3000000 INFO @ Mon, 05 Jun 2017 01:53:24: 3000000 INFO @ Mon, 05 Jun 2017 01:53:24: 3000000 INFO @ Mon, 05 Jun 2017 01:53:31: 4000000 INFO @ Mon, 05 Jun 2017 01:53:31: 4000000 INFO @ Mon, 05 Jun 2017 01:53:32: 4000000 INFO @ Mon, 05 Jun 2017 01:53:36: 5000000 INFO @ Mon, 05 Jun 2017 01:53:37: 5000000 INFO @ Mon, 05 Jun 2017 01:53:38: 5000000 INFO @ Mon, 05 Jun 2017 01:53:42: 6000000 INFO @ Mon, 05 Jun 2017 01:53:43: 6000000 INFO @ Mon, 05 Jun 2017 01:53:43: 6000000 INFO @ Mon, 05 Jun 2017 01:53:48: 7000000 INFO @ Mon, 05 Jun 2017 01:53:48: 7000000 INFO @ Mon, 05 Jun 2017 01:53:49: 7000000 INFO @ Mon, 05 Jun 2017 01:53:54: 8000000 INFO @ Mon, 05 Jun 2017 01:53:54: 8000000 INFO @ Mon, 05 Jun 2017 01:53:55: 8000000 INFO @ Mon, 05 Jun 2017 01:53:59: 9000000 INFO @ Mon, 05 Jun 2017 01:53:59: 9000000 INFO @ Mon, 05 Jun 2017 01:54:00: 9000000 INFO @ Mon, 05 Jun 2017 01:54:05: 10000000 INFO @ Mon, 05 Jun 2017 01:54:06: 10000000 INFO @ Mon, 05 Jun 2017 01:54:07: 10000000 INFO @ Mon, 05 Jun 2017 01:54:12: 11000000 INFO @ Mon, 05 Jun 2017 01:54:13: 11000000 INFO @ Mon, 05 Jun 2017 01:54:13: 11000000 INFO @ Mon, 05 Jun 2017 01:54:18: 12000000 INFO @ Mon, 05 Jun 2017 01:54:19: 12000000 INFO @ Mon, 05 Jun 2017 01:54:19: 12000000 INFO @ Mon, 05 Jun 2017 01:54:24: 13000000 INFO @ Mon, 05 Jun 2017 01:54:25: 13000000 INFO @ Mon, 05 Jun 2017 01:54:25: 13000000 INFO @ Mon, 05 Jun 2017 01:54:31: 14000000 INFO @ Mon, 05 Jun 2017 01:54:31: 14000000 INFO @ Mon, 05 Jun 2017 01:54:31: 14000000 INFO @ Mon, 05 Jun 2017 01:54:37: 15000000 INFO @ Mon, 05 Jun 2017 01:54:37: 15000000 INFO @ Mon, 05 Jun 2017 01:54:37: 15000000 INFO @ Mon, 05 Jun 2017 01:54:42: 16000000 INFO @ Mon, 05 Jun 2017 01:54:42: 16000000 INFO @ Mon, 05 Jun 2017 01:54:43: 16000000 INFO @ Mon, 05 Jun 2017 01:54:48: 17000000 INFO @ Mon, 05 Jun 2017 01:54:49: 17000000 INFO @ Mon, 05 Jun 2017 01:54:50: 17000000 INFO @ Mon, 05 Jun 2017 01:54:56: 18000000 INFO @ Mon, 05 Jun 2017 01:54:56: 18000000 INFO @ Mon, 05 Jun 2017 01:54:57: 18000000 INFO @ Mon, 05 Jun 2017 01:55:02: 19000000 INFO @ Mon, 05 Jun 2017 01:55:03: 19000000 INFO @ Mon, 05 Jun 2017 01:55:05: 19000000 INFO @ Mon, 05 Jun 2017 01:55:08: 20000000 INFO @ Mon, 05 Jun 2017 01:55:09: 20000000 INFO @ Mon, 05 Jun 2017 01:55:12: 20000000 INFO @ Mon, 05 Jun 2017 01:55:14: 21000000 INFO @ Mon, 05 Jun 2017 01:55:15: 21000000 INFO @ Mon, 05 Jun 2017 01:55:18: 21000000 INFO @ Mon, 05 Jun 2017 01:55:20: 22000000 INFO @ Mon, 05 Jun 2017 01:55:21: 22000000 INFO @ Mon, 05 Jun 2017 01:55:25: 22000000 INFO @ Mon, 05 Jun 2017 01:55:25: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 01:55:25: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 01:55:25: #1 total tags in treatment: 22724129 INFO @ Mon, 05 Jun 2017 01:55:25: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 01:55:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 01:55:26: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 01:55:26: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 01:55:26: #1 total tags in treatment: 22724129 INFO @ Mon, 05 Jun 2017 01:55:26: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 01:55:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 01:55:29: #1 tags after filtering in treatment: 22712239 INFO @ Mon, 05 Jun 2017 01:55:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 01:55:29: #1 finished! INFO @ Mon, 05 Jun 2017 01:55:29: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 01:55:30: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 01:55:30: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 01:55:30: #1 total tags in treatment: 22724129 INFO @ Mon, 05 Jun 2017 01:55:30: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 01:55:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 01:55:30: #1 tags after filtering in treatment: 22712239 INFO @ Mon, 05 Jun 2017 01:55:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 01:55:30: #1 finished! INFO @ Mon, 05 Jun 2017 01:55:30: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 01:55:33: #2 number of paired peaks: 2156 INFO @ Mon, 05 Jun 2017 01:55:33: start model_add_line... INFO @ Mon, 05 Jun 2017 01:55:34: #1 tags after filtering in treatment: 22712239 INFO @ Mon, 05 Jun 2017 01:55:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 01:55:34: #1 finished! INFO @ Mon, 05 Jun 2017 01:55:34: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 01:55:34: #2 number of paired peaks: 2156 INFO @ Mon, 05 Jun 2017 01:55:34: start model_add_line... INFO @ Mon, 05 Jun 2017 01:55:38: #2 number of paired peaks: 2156 INFO @ Mon, 05 Jun 2017 01:55:38: start model_add_line... INFO @ Mon, 05 Jun 2017 01:56:01: start X-correlation... INFO @ Mon, 05 Jun 2017 01:56:01: end of X-cor INFO @ Mon, 05 Jun 2017 01:56:01: #2 finished! INFO @ Mon, 05 Jun 2017 01:56:01: #2 predicted fragment length is 237 bps INFO @ Mon, 05 Jun 2017 01:56:01: #2 alternative fragment length(s) may be 237 bps INFO @ Mon, 05 Jun 2017 01:56:01: #2.2 Generate R script for model : SRX1361356.20_model.r INFO @ Mon, 05 Jun 2017 01:56:01: #3 Call peaks... INFO @ Mon, 05 Jun 2017 01:56:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 01:56:02: start X-correlation... INFO @ Mon, 05 Jun 2017 01:56:02: end of X-cor INFO @ Mon, 05 Jun 2017 01:56:02: #2 finished! INFO @ Mon, 05 Jun 2017 01:56:02: #2 predicted fragment length is 237 bps INFO @ Mon, 05 Jun 2017 01:56:02: #2 alternative fragment length(s) may be 237 bps INFO @ Mon, 05 Jun 2017 01:56:02: #2.2 Generate R script for model : SRX1361356.05_model.r INFO @ Mon, 05 Jun 2017 01:56:02: #3 Call peaks... INFO @ Mon, 05 Jun 2017 01:56:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 01:56:07: start X-correlation... INFO @ Mon, 05 Jun 2017 01:56:07: end of X-cor INFO @ Mon, 05 Jun 2017 01:56:07: #2 finished! INFO @ Mon, 05 Jun 2017 01:56:07: #2 predicted fragment length is 237 bps INFO @ Mon, 05 Jun 2017 01:56:07: #2 alternative fragment length(s) may be 237 bps INFO @ Mon, 05 Jun 2017 01:56:07: #2.2 Generate R script for model : SRX1361356.10_model.r INFO @ Mon, 05 Jun 2017 01:56:07: #3 Call peaks... INFO @ Mon, 05 Jun 2017 01:56:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 01:58:15: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 01:58:15: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 01:58:21: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 01:59:48: #4 Write output xls file... SRX1361356.20_peaks.xls INFO @ Mon, 05 Jun 2017 01:59:48: #4 Write peak in narrowPeak format file... SRX1361356.20_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 01:59:48: #4 Write summits bed file... SRX1361356.20_summits.bed INFO @ Mon, 05 Jun 2017 01:59:48: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6027 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 01:59:53: #4 Write output xls file... SRX1361356.05_peaks.xls INFO @ Mon, 05 Jun 2017 01:59:54: #4 Write peak in narrowPeak format file... SRX1361356.05_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 01:59:54: #4 Write summits bed file... SRX1361356.05_summits.bed INFO @ Mon, 05 Jun 2017 01:59:54: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9080 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 02:00:00: #4 Write output xls file... SRX1361356.10_peaks.xls INFO @ Mon, 05 Jun 2017 02:00:00: #4 Write peak in narrowPeak format file... SRX1361356.10_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 02:00:01: #4 Write summits bed file... SRX1361356.10_summits.bed INFO @ Mon, 05 Jun 2017 02:00:01: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7508 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。