Job ID = 9039910 sra ファイルのダウンロード中... Completed: 2659754K bytes transferred in 24 seconds (873259K 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 12695 0 12695 0 0 1699 0 --:--:-- 0:00:07 --:--:-- 14136 100 44109 0 44109 0 0 5210 0 --:--:-- 0:00:08 --:--:-- 23288 100 115k 0 115k 0 0 12545 0 --:--:-- 0:00:09 --:--:-- 41064 100 125k 0 125k 0 0 13541 0 --:--:-- 0:00:09 --:--:-- 44312 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 38399602 spots for /home/okishinya/chipatlas/results/dm3/SRX1084165/SRR2088911.sra Written 38399602 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: 00:10:44 38399602 reads; of these: 38399602 (100.00%) were unpaired; of these: 2013446 (5.24%) aligned 0 times 31395583 (81.76%) aligned exactly 1 time 4990573 (13.00%) aligned >1 times 94.76% overall alignment rate Time searching: 00:10:44 Overall time: 00:10:44 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 16 files... [bam_rmdupse_core] 13794765 / 36386156 = 0.3791 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 @ Sun, 04 Jun 2017 23:33:02: # Command line: callpeak -t SRX1084165.bam -f BAM -g dm -n SRX1084165.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1084165.05 # format = BAM # ChIP-seq file = ['SRX1084165.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 @ Sun, 04 Jun 2017 23:33:02: #1 read tag files... INFO @ Sun, 04 Jun 2017 23:33:02: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 23:33:02: # Command line: callpeak -t SRX1084165.bam -f BAM -g dm -n SRX1084165.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1084165.10 # format = BAM # ChIP-seq file = ['SRX1084165.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 @ Sun, 04 Jun 2017 23:33:02: #1 read tag files... INFO @ Sun, 04 Jun 2017 23:33:02: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 23:33:02: # Command line: callpeak -t SRX1084165.bam -f BAM -g dm -n SRX1084165.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1084165.20 # format = BAM # ChIP-seq file = ['SRX1084165.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 @ Sun, 04 Jun 2017 23:33:02: #1 read tag files... INFO @ Sun, 04 Jun 2017 23:33:02: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 23:33:10: 1000000 INFO @ Sun, 04 Jun 2017 23:33:10: 1000000 INFO @ Sun, 04 Jun 2017 23:33:10: 1000000 INFO @ Sun, 04 Jun 2017 23:33:18: 2000000 INFO @ Sun, 04 Jun 2017 23:33:18: 2000000 INFO @ Sun, 04 Jun 2017 23:33:18: 2000000 INFO @ Sun, 04 Jun 2017 23:33:25: 3000000 INFO @ Sun, 04 Jun 2017 23:33:26: 3000000 INFO @ Sun, 04 Jun 2017 23:33:26: 3000000 INFO @ Sun, 04 Jun 2017 23:33:33: 4000000 INFO @ Sun, 04 Jun 2017 23:33:33: 4000000 INFO @ Sun, 04 Jun 2017 23:33:33: 4000000 INFO @ Sun, 04 Jun 2017 23:33:41: 5000000 INFO @ Sun, 04 Jun 2017 23:33:41: 5000000 INFO @ Sun, 04 Jun 2017 23:33:41: 5000000 INFO @ Sun, 04 Jun 2017 23:33:48: 6000000 INFO @ Sun, 04 Jun 2017 23:33:48: 6000000 INFO @ Sun, 04 Jun 2017 23:33:49: 6000000 INFO @ Sun, 04 Jun 2017 23:33:56: 7000000 INFO @ Sun, 04 Jun 2017 23:33:56: 7000000 INFO @ Sun, 04 Jun 2017 23:33:56: 7000000 INFO @ Sun, 04 Jun 2017 23:34:04: 8000000 INFO @ Sun, 04 Jun 2017 23:34:04: 8000000 INFO @ Sun, 04 Jun 2017 23:34:04: 8000000 INFO @ Sun, 04 Jun 2017 23:34:11: 9000000 INFO @ Sun, 04 Jun 2017 23:34:11: 9000000 INFO @ Sun, 04 Jun 2017 23:34:12: 9000000 INFO @ Sun, 04 Jun 2017 23:34:19: 10000000 INFO @ Sun, 04 Jun 2017 23:34:19: 10000000 INFO @ Sun, 04 Jun 2017 23:34:19: 10000000 INFO @ Sun, 04 Jun 2017 23:34:27: 11000000 INFO @ Sun, 04 Jun 2017 23:34:27: 11000000 INFO @ Sun, 04 Jun 2017 23:34:27: 11000000 INFO @ Sun, 04 Jun 2017 23:34:34: 12000000 INFO @ Sun, 04 Jun 2017 23:34:35: 12000000 INFO @ Sun, 04 Jun 2017 23:34:35: 12000000 INFO @ Sun, 04 Jun 2017 23:34:42: 13000000 INFO @ Sun, 04 Jun 2017 23:34:42: 13000000 INFO @ Sun, 04 Jun 2017 23:34:43: 13000000 INFO @ Sun, 04 Jun 2017 23:34:50: 14000000 INFO @ Sun, 04 Jun 2017 23:34:50: 14000000 INFO @ Sun, 04 Jun 2017 23:34:51: 14000000 INFO @ Sun, 04 Jun 2017 23:34:57: 15000000 INFO @ Sun, 04 Jun 2017 23:34:58: 15000000 INFO @ Sun, 04 Jun 2017 23:34:59: 15000000 INFO @ Sun, 04 Jun 2017 23:35:05: 16000000 INFO @ Sun, 04 Jun 2017 23:35:06: 16000000 INFO @ Sun, 04 Jun 2017 23:35:07: 16000000 INFO @ Sun, 04 Jun 2017 23:35:12: 17000000 INFO @ Sun, 04 Jun 2017 23:35:14: 17000000 INFO @ Sun, 04 Jun 2017 23:35:15: 17000000 INFO @ Sun, 04 Jun 2017 23:35:20: 18000000 INFO @ Sun, 04 Jun 2017 23:35:22: 18000000 INFO @ Sun, 04 Jun 2017 23:35:23: 18000000 INFO @ Sun, 04 Jun 2017 23:35:28: 19000000 INFO @ Sun, 04 Jun 2017 23:35:30: 19000000 INFO @ Sun, 04 Jun 2017 23:35:31: 19000000 INFO @ Sun, 04 Jun 2017 23:35:35: 20000000 INFO @ Sun, 04 Jun 2017 23:35:38: 20000000 INFO @ Sun, 04 Jun 2017 23:35:40: 20000000 INFO @ Sun, 04 Jun 2017 23:35:43: 21000000 INFO @ Sun, 04 Jun 2017 23:35:46: 21000000 INFO @ Sun, 04 Jun 2017 23:35:48: 21000000 INFO @ Sun, 04 Jun 2017 23:35:50: 22000000 INFO @ Sun, 04 Jun 2017 23:35:54: 22000000 INFO @ Sun, 04 Jun 2017 23:35:55: #1 tag size is determined as 100 bps INFO @ Sun, 04 Jun 2017 23:35:55: #1 tag size = 100 INFO @ Sun, 04 Jun 2017 23:35:55: #1 total tags in treatment: 22591391 INFO @ Sun, 04 Jun 2017 23:35:55: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 23:35:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 23:35:56: 22000000 INFO @ Sun, 04 Jun 2017 23:35:59: #1 tag size is determined as 100 bps INFO @ Sun, 04 Jun 2017 23:35:59: #1 tag size = 100 INFO @ Sun, 04 Jun 2017 23:35:59: #1 total tags in treatment: 22591391 INFO @ Sun, 04 Jun 2017 23:35:59: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 23:35:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 23:35:59: #1 tags after filtering in treatment: 22545001 INFO @ Sun, 04 Jun 2017 23:35:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 23:35:59: #1 finished! INFO @ Sun, 04 Jun 2017 23:35:59: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 23:36:00: #1 tag size is determined as 100 bps INFO @ Sun, 04 Jun 2017 23:36:00: #1 tag size = 100 INFO @ Sun, 04 Jun 2017 23:36:00: #1 total tags in treatment: 22591391 INFO @ Sun, 04 Jun 2017 23:36:00: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 23:36:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 23:36:03: #1 tags after filtering in treatment: 22545001 INFO @ Sun, 04 Jun 2017 23:36:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 23:36:03: #1 finished! INFO @ Sun, 04 Jun 2017 23:36:03: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 23:36:04: #2 number of paired peaks: 3816 INFO @ Sun, 04 Jun 2017 23:36:04: start model_add_line... INFO @ Sun, 04 Jun 2017 23:36:05: #1 tags after filtering in treatment: 22545001 INFO @ Sun, 04 Jun 2017 23:36:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 23:36:05: #1 finished! INFO @ Sun, 04 Jun 2017 23:36:05: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 23:36:07: #2 number of paired peaks: 3816 INFO @ Sun, 04 Jun 2017 23:36:07: start model_add_line... INFO @ Sun, 04 Jun 2017 23:36:09: #2 number of paired peaks: 3816 INFO @ Sun, 04 Jun 2017 23:36:09: start model_add_line... INFO @ Sun, 04 Jun 2017 23:36:50: start X-correlation... INFO @ Sun, 04 Jun 2017 23:36:50: end of X-cor INFO @ Sun, 04 Jun 2017 23:36:50: #2 finished! INFO @ Sun, 04 Jun 2017 23:36:50: #2 predicted fragment length is 208 bps INFO @ Sun, 04 Jun 2017 23:36:50: #2 alternative fragment length(s) may be 208 bps INFO @ Sun, 04 Jun 2017 23:36:50: #2.2 Generate R script for model : SRX1084165.05_model.r INFO @ Sun, 04 Jun 2017 23:36:50: #3 Call peaks... INFO @ Sun, 04 Jun 2017 23:36:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 23:36:50: start X-correlation... INFO @ Sun, 04 Jun 2017 23:36:50: end of X-cor INFO @ Sun, 04 Jun 2017 23:36:50: #2 finished! INFO @ Sun, 04 Jun 2017 23:36:50: #2 predicted fragment length is 208 bps INFO @ Sun, 04 Jun 2017 23:36:50: #2 alternative fragment length(s) may be 208 bps INFO @ Sun, 04 Jun 2017 23:36:50: #2.2 Generate R script for model : SRX1084165.20_model.r INFO @ Sun, 04 Jun 2017 23:36:50: #3 Call peaks... INFO @ Sun, 04 Jun 2017 23:36:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 23:36:54: start X-correlation... INFO @ Sun, 04 Jun 2017 23:36:54: end of X-cor INFO @ Sun, 04 Jun 2017 23:36:54: #2 finished! INFO @ Sun, 04 Jun 2017 23:36:54: #2 predicted fragment length is 208 bps INFO @ Sun, 04 Jun 2017 23:36:54: #2 alternative fragment length(s) may be 208 bps INFO @ Sun, 04 Jun 2017 23:36:54: #2.2 Generate R script for model : SRX1084165.10_model.r INFO @ Sun, 04 Jun 2017 23:36:54: #3 Call peaks... INFO @ Sun, 04 Jun 2017 23:36:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 23:38:50: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 23:38:56: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 23:39:03: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 23:40:30: #4 Write output xls file... SRX1084165.20_peaks.xls INFO @ Sun, 04 Jun 2017 23:40:31: #4 Write peak in narrowPeak format file... SRX1084165.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 23:40:31: #4 Write summits bed file... SRX1084165.20_summits.bed INFO @ Sun, 04 Jun 2017 23:40:31: Done! INFO @ Sun, 04 Jun 2017 23:40:31: #4 Write output xls file... SRX1084165.05_peaks.xls pass1 - making usageList (14 chroms): 2 millis INFO @ Sun, 04 Jun 2017 23:40:31: #4 Write peak in narrowPeak format file... SRX1084165.05_peaks.narrowPeak pass2 - checking and writing primary data (6392 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 23:40:31: #4 Write summits bed file... SRX1084165.05_summits.bed INFO @ Sun, 04 Jun 2017 23:40:31: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8290 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 23:40:38: #4 Write output xls file... SRX1084165.10_peaks.xls INFO @ Sun, 04 Jun 2017 23:40:39: #4 Write peak in narrowPeak format file... SRX1084165.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 23:40:39: #4 Write summits bed file... SRX1084165.10_summits.bed INFO @ Sun, 04 Jun 2017 23:40:39: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7398 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。