Job ID = 9029568 sra ファイルのダウンロード中... Completed: 1656746K bytes transferred in 21 seconds (639792K 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 7663 0 7663 0 0 1082 0 --:--:-- 0:00:07 --:--:-- 11041 100 24454 0 24454 0 0 3092 0 --:--:-- 0:00:07 --:--:-- 16045 100 56310 0 56310 0 0 6325 0 --:--:-- 0:00:08 --:--:-- 22354 100 67015 0 67015 0 0 7389 0 --:--:-- 0:00:09 --:--:-- 24959 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 38994090 spots for /home/okishinya/chipatlas/results/dm3/SRX1847042/SRR3669859.sra Written 38994090 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: 00:13:18 38994090 reads; of these: 38994090 (100.00%) were unpaired; of these: 765847 (1.96%) aligned 0 times 33799655 (86.68%) aligned exactly 1 time 4428588 (11.36%) aligned >1 times 98.04% overall alignment rate Time searching: 00:13:18 Overall time: 00:13:18 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] 23511383 / 38228243 = 0.6150 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 14:33:46: # Command line: callpeak -t SRX1847042.bam -f BAM -g dm -n SRX1847042.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1847042.05 # format = BAM # ChIP-seq file = ['SRX1847042.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 14:33:46: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:33:46: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:33:46: # Command line: callpeak -t SRX1847042.bam -f BAM -g dm -n SRX1847042.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1847042.10 # format = BAM # ChIP-seq file = ['SRX1847042.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 14:33:46: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:33:46: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:33:46: # Command line: callpeak -t SRX1847042.bam -f BAM -g dm -n SRX1847042.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1847042.20 # format = BAM # ChIP-seq file = ['SRX1847042.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 14:33:46: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:33:46: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:33:51: 1000000 INFO @ Sat, 03 Jun 2017 14:33:51: 1000000 INFO @ Sat, 03 Jun 2017 14:33:51: 1000000 INFO @ Sat, 03 Jun 2017 14:33:57: 2000000 INFO @ Sat, 03 Jun 2017 14:33:57: 2000000 INFO @ Sat, 03 Jun 2017 14:33:57: 2000000 INFO @ Sat, 03 Jun 2017 14:34:02: 3000000 INFO @ Sat, 03 Jun 2017 14:34:02: 3000000 INFO @ Sat, 03 Jun 2017 14:34:02: 3000000 INFO @ Sat, 03 Jun 2017 14:34:08: 4000000 INFO @ Sat, 03 Jun 2017 14:34:08: 4000000 INFO @ Sat, 03 Jun 2017 14:34:08: 4000000 INFO @ Sat, 03 Jun 2017 14:34:13: 5000000 INFO @ Sat, 03 Jun 2017 14:34:14: 5000000 INFO @ Sat, 03 Jun 2017 14:34:14: 5000000 INFO @ Sat, 03 Jun 2017 14:34:19: 6000000 INFO @ Sat, 03 Jun 2017 14:34:19: 6000000 INFO @ Sat, 03 Jun 2017 14:34:19: 6000000 INFO @ Sat, 03 Jun 2017 14:34:25: 7000000 INFO @ Sat, 03 Jun 2017 14:34:25: 7000000 INFO @ Sat, 03 Jun 2017 14:34:25: 7000000 INFO @ Sat, 03 Jun 2017 14:34:31: 8000000 INFO @ Sat, 03 Jun 2017 14:34:31: 8000000 INFO @ Sat, 03 Jun 2017 14:34:31: 8000000 INFO @ Sat, 03 Jun 2017 14:34:36: 9000000 INFO @ Sat, 03 Jun 2017 14:34:37: 9000000 INFO @ Sat, 03 Jun 2017 14:34:38: 9000000 INFO @ Sat, 03 Jun 2017 14:34:42: 10000000 INFO @ Sat, 03 Jun 2017 14:34:43: 10000000 INFO @ Sat, 03 Jun 2017 14:34:44: 10000000 INFO @ Sat, 03 Jun 2017 14:34:48: 11000000 INFO @ Sat, 03 Jun 2017 14:34:48: 11000000 INFO @ Sat, 03 Jun 2017 14:34:49: 11000000 INFO @ Sat, 03 Jun 2017 14:34:53: 12000000 INFO @ Sat, 03 Jun 2017 14:34:54: 12000000 INFO @ Sat, 03 Jun 2017 14:34:55: 12000000 INFO @ Sat, 03 Jun 2017 14:34:59: 13000000 INFO @ Sat, 03 Jun 2017 14:34:59: 13000000 INFO @ Sat, 03 Jun 2017 14:35:01: 13000000 INFO @ Sat, 03 Jun 2017 14:35:04: 14000000 INFO @ Sat, 03 Jun 2017 14:35:05: 14000000 INFO @ Sat, 03 Jun 2017 14:35:06: 14000000 INFO @ Sat, 03 Jun 2017 14:35:08: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 14:35:08: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 14:35:08: #1 total tags in treatment: 14716860 INFO @ Sat, 03 Jun 2017 14:35:08: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:35:08: #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 14:35:09: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 14:35:09: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 14:35:09: #1 total tags in treatment: 14716860 INFO @ Sat, 03 Jun 2017 14:35:09: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:35:09: #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 14:35:11: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 14:35:11: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 14:35:11: #1 total tags in treatment: 14716860 INFO @ Sat, 03 Jun 2017 14:35:11: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:35:11: #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 14:35:11: #1 tags after filtering in treatment: 14706598 INFO @ Sat, 03 Jun 2017 14:35:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:35:11: #1 finished! INFO @ Sat, 03 Jun 2017 14:35:11: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:35:12: #1 tags after filtering in treatment: 14706598 INFO @ Sat, 03 Jun 2017 14:35:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:35:12: #1 finished! INFO @ Sat, 03 Jun 2017 14:35:12: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:35:13: #1 tags after filtering in treatment: 14706598 INFO @ Sat, 03 Jun 2017 14:35:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:35:13: #1 finished! INFO @ Sat, 03 Jun 2017 14:35:13: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:35:14: #2 number of paired peaks: 4904 INFO @ Sat, 03 Jun 2017 14:35:14: start model_add_line... INFO @ Sat, 03 Jun 2017 14:35:15: #2 number of paired peaks: 4904 INFO @ Sat, 03 Jun 2017 14:35:15: start model_add_line... INFO @ Sat, 03 Jun 2017 14:35:16: #2 number of paired peaks: 4904 INFO @ Sat, 03 Jun 2017 14:35:16: start model_add_line... INFO @ Sat, 03 Jun 2017 14:35:57: start X-correlation... INFO @ Sat, 03 Jun 2017 14:35:57: end of X-cor INFO @ Sat, 03 Jun 2017 14:35:57: #2 finished! INFO @ Sat, 03 Jun 2017 14:35:57: #2 predicted fragment length is 115 bps INFO @ Sat, 03 Jun 2017 14:35:57: #2 alternative fragment length(s) may be 4,115 bps INFO @ Sat, 03 Jun 2017 14:35:57: #2.2 Generate R script for model : SRX1847042.10_model.r INFO @ Sat, 03 Jun 2017 14:35:57: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:35:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:35:58: start X-correlation... INFO @ Sat, 03 Jun 2017 14:35:58: end of X-cor INFO @ Sat, 03 Jun 2017 14:35:58: #2 finished! INFO @ Sat, 03 Jun 2017 14:35:58: #2 predicted fragment length is 115 bps INFO @ Sat, 03 Jun 2017 14:35:58: #2 alternative fragment length(s) may be 4,115 bps INFO @ Sat, 03 Jun 2017 14:35:58: #2.2 Generate R script for model : SRX1847042.05_model.r INFO @ Sat, 03 Jun 2017 14:35:58: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:35:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:35:59: start X-correlation... INFO @ Sat, 03 Jun 2017 14:35:59: end of X-cor INFO @ Sat, 03 Jun 2017 14:35:59: #2 finished! INFO @ Sat, 03 Jun 2017 14:35:59: #2 predicted fragment length is 115 bps INFO @ Sat, 03 Jun 2017 14:35:59: #2 alternative fragment length(s) may be 4,115 bps INFO @ Sat, 03 Jun 2017 14:35:59: #2.2 Generate R script for model : SRX1847042.20_model.r INFO @ Sat, 03 Jun 2017 14:35:59: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:35:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:37:13: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:37:16: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:37:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:38:19: #4 Write output xls file... SRX1847042.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:38:19: #4 Write peak in narrowPeak format file... SRX1847042.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:38:19: #4 Write summits bed file... SRX1847042.10_summits.bed INFO @ Sat, 03 Jun 2017 14:38:19: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6572 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:38:20: #4 Write output xls file... SRX1847042.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:38:20: #4 Write peak in narrowPeak format file... SRX1847042.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:38:20: #4 Write summits bed file... SRX1847042.20_summits.bed INFO @ Sat, 03 Jun 2017 14:38:20: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4216 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:38:31: #4 Write output xls file... SRX1847042.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:38:31: #4 Write peak in narrowPeak format file... SRX1847042.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:38:31: #4 Write summits bed file... SRX1847042.05_summits.bed INFO @ Sat, 03 Jun 2017 14:38:31: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7967 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。