Job ID = 8696824 sra ファイルのダウンロード中... Completed: 947985K bytes transferred in 46 seconds (165775K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 14581 0 14581 0 0 1917 0 --:--:-- 0:00:07 --:--:-- 12937 100 31486 0 31486 0 0 3792 0 --:--:-- 0:00:08 --:--:-- 17262 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 40037701 spots for /home/okishinya/chipatlas/results/dm3/SRX110762/SRR388344.sra Written 40037701 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: 00:00:01 Multiseed full-index search: 00:23:30 40037701 reads; of these: 40037701 (100.00%) were unpaired; of these: 4859533 (12.14%) aligned 0 times 32238639 (80.52%) aligned exactly 1 time 2939529 (7.34%) aligned >1 times 87.86% overall alignment rate Time searching: 00:23:31 Overall time: 00:23:31 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 12 files... [bam_rmdupse_core] 11713575 / 35178168 = 0.3330 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 @ Fri, 10 Mar 2017 12:35:07: # Command line: callpeak -t SRX110762.bam -f BAM -g dm -n SRX110762.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX110762.10 # format = BAM # ChIP-seq file = ['SRX110762.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 @ Fri, 10 Mar 2017 12:35:07: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:35:07: # Command line: callpeak -t SRX110762.bam -f BAM -g dm -n SRX110762.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX110762.05 # format = BAM # ChIP-seq file = ['SRX110762.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 @ Fri, 10 Mar 2017 12:35:07: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:35:07: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:35:07: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:35:07: # Command line: callpeak -t SRX110762.bam -f BAM -g dm -n SRX110762.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX110762.20 # format = BAM # ChIP-seq file = ['SRX110762.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 @ Fri, 10 Mar 2017 12:35:07: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:35:07: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:35:17: 1000000 INFO @ Fri, 10 Mar 2017 12:35:20: 1000000 INFO @ Fri, 10 Mar 2017 12:35:22: 1000000 INFO @ Fri, 10 Mar 2017 12:35:25: 2000000 INFO @ Fri, 10 Mar 2017 12:35:32: 3000000 INFO @ Fri, 10 Mar 2017 12:35:33: 2000000 INFO @ Fri, 10 Mar 2017 12:35:37: 2000000 INFO @ Fri, 10 Mar 2017 12:35:40: 4000000 INFO @ Fri, 10 Mar 2017 12:35:40: 3000000 INFO @ Fri, 10 Mar 2017 12:35:47: 5000000 INFO @ Fri, 10 Mar 2017 12:35:48: 4000000 INFO @ Fri, 10 Mar 2017 12:35:53: 3000000 INFO @ Fri, 10 Mar 2017 12:35:55: 6000000 INFO @ Fri, 10 Mar 2017 12:35:56: 5000000 INFO @ Fri, 10 Mar 2017 12:36:03: 7000000 INFO @ Fri, 10 Mar 2017 12:36:05: 6000000 INFO @ Fri, 10 Mar 2017 12:36:08: 4000000 INFO @ Fri, 10 Mar 2017 12:36:10: 8000000 INFO @ Fri, 10 Mar 2017 12:36:13: 7000000 INFO @ Fri, 10 Mar 2017 12:36:18: 9000000 INFO @ Fri, 10 Mar 2017 12:36:21: 8000000 INFO @ Fri, 10 Mar 2017 12:36:24: 5000000 INFO @ Fri, 10 Mar 2017 12:36:26: 10000000 INFO @ Fri, 10 Mar 2017 12:36:29: 9000000 INFO @ Fri, 10 Mar 2017 12:36:33: 11000000 INFO @ Fri, 10 Mar 2017 12:36:37: 10000000 INFO @ Fri, 10 Mar 2017 12:36:40: 6000000 INFO @ Fri, 10 Mar 2017 12:36:41: 12000000 INFO @ Fri, 10 Mar 2017 12:36:46: 11000000 INFO @ Fri, 10 Mar 2017 12:36:49: 13000000 INFO @ Fri, 10 Mar 2017 12:36:54: 12000000 INFO @ Fri, 10 Mar 2017 12:36:54: 7000000 INFO @ Fri, 10 Mar 2017 12:36:56: 14000000 INFO @ Fri, 10 Mar 2017 12:37:02: 13000000 INFO @ Fri, 10 Mar 2017 12:37:04: 8000000 INFO @ Fri, 10 Mar 2017 12:37:04: 15000000 INFO @ Fri, 10 Mar 2017 12:37:10: 14000000 INFO @ Fri, 10 Mar 2017 12:37:12: 16000000 INFO @ Fri, 10 Mar 2017 12:37:13: 9000000 INFO @ Fri, 10 Mar 2017 12:37:18: 15000000 INFO @ Fri, 10 Mar 2017 12:37:20: 17000000 INFO @ Fri, 10 Mar 2017 12:37:21: 10000000 INFO @ Fri, 10 Mar 2017 12:37:26: 16000000 INFO @ Fri, 10 Mar 2017 12:37:27: 18000000 INFO @ Fri, 10 Mar 2017 12:37:30: 11000000 INFO @ Fri, 10 Mar 2017 12:37:35: 17000000 INFO @ Fri, 10 Mar 2017 12:37:35: 19000000 INFO @ Fri, 10 Mar 2017 12:37:39: 12000000 INFO @ Fri, 10 Mar 2017 12:37:43: 18000000 INFO @ Fri, 10 Mar 2017 12:37:43: 20000000 INFO @ Fri, 10 Mar 2017 12:37:48: 13000000 INFO @ Fri, 10 Mar 2017 12:37:51: 19000000 INFO @ Fri, 10 Mar 2017 12:37:51: 21000000 INFO @ Fri, 10 Mar 2017 12:37:57: 14000000 INFO @ Fri, 10 Mar 2017 12:37:58: 22000000 INFO @ Fri, 10 Mar 2017 12:37:59: 20000000 INFO @ Fri, 10 Mar 2017 12:38:06: 15000000 INFO @ Fri, 10 Mar 2017 12:38:06: 23000000 INFO @ Fri, 10 Mar 2017 12:38:07: 21000000 INFO @ Fri, 10 Mar 2017 12:38:10: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 12:38:10: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 12:38:10: #1 total tags in treatment: 23464593 INFO @ Fri, 10 Mar 2017 12:38:10: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:38:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:38:15: 22000000 INFO @ Fri, 10 Mar 2017 12:38:15: 16000000 INFO @ Fri, 10 Mar 2017 12:38:16: #1 tags after filtering in treatment: 23458074 INFO @ Fri, 10 Mar 2017 12:38:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:38:16: #1 finished! INFO @ Fri, 10 Mar 2017 12:38:16: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:38:22: #2 number of paired peaks: 3688 INFO @ Fri, 10 Mar 2017 12:38:22: start model_add_line... INFO @ Fri, 10 Mar 2017 12:38:24: 23000000 INFO @ Fri, 10 Mar 2017 12:38:27: 17000000 INFO @ Fri, 10 Mar 2017 12:38:28: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 12:38:28: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 12:38:28: #1 total tags in treatment: 23464593 INFO @ Fri, 10 Mar 2017 12:38:28: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:38:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:38:34: #1 tags after filtering in treatment: 23458074 INFO @ Fri, 10 Mar 2017 12:38:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:38:34: #1 finished! INFO @ Fri, 10 Mar 2017 12:38:34: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:38:36: 18000000 INFO @ Fri, 10 Mar 2017 12:38:40: #2 number of paired peaks: 3688 INFO @ Fri, 10 Mar 2017 12:38:40: start model_add_line... INFO @ Fri, 10 Mar 2017 12:38:45: 19000000 INFO @ Fri, 10 Mar 2017 12:38:54: 20000000 INFO @ Fri, 10 Mar 2017 12:39:03: 21000000 INFO @ Fri, 10 Mar 2017 12:39:12: 22000000 INFO @ Fri, 10 Mar 2017 12:39:21: 23000000 INFO @ Fri, 10 Mar 2017 12:39:22: start X-correlation... INFO @ Fri, 10 Mar 2017 12:39:22: end of X-cor INFO @ Fri, 10 Mar 2017 12:39:22: #2 finished! INFO @ Fri, 10 Mar 2017 12:39:22: #2 predicted fragment length is 107 bps INFO @ Fri, 10 Mar 2017 12:39:22: #2 alternative fragment length(s) may be 107 bps INFO @ Fri, 10 Mar 2017 12:39:22: #2.2 Generate R script for model : SRX110762.10_model.r INFO @ Fri, 10 Mar 2017 12:39:22: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:39:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:39:26: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 12:39:26: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 12:39:26: #1 total tags in treatment: 23464593 INFO @ Fri, 10 Mar 2017 12:39:26: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:39:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:39:31: #1 tags after filtering in treatment: 23458074 INFO @ Fri, 10 Mar 2017 12:39:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:39:31: #1 finished! INFO @ Fri, 10 Mar 2017 12:39:31: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:39:36: #2 number of paired peaks: 3688 INFO @ Fri, 10 Mar 2017 12:39:36: start model_add_line... INFO @ Fri, 10 Mar 2017 12:39:41: start X-correlation... INFO @ Fri, 10 Mar 2017 12:39:41: end of X-cor INFO @ Fri, 10 Mar 2017 12:39:41: #2 finished! INFO @ Fri, 10 Mar 2017 12:39:41: #2 predicted fragment length is 107 bps INFO @ Fri, 10 Mar 2017 12:39:41: #2 alternative fragment length(s) may be 107 bps INFO @ Fri, 10 Mar 2017 12:39:41: #2.2 Generate R script for model : SRX110762.05_model.r INFO @ Fri, 10 Mar 2017 12:39:41: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:39:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:40:37: start X-correlation... INFO @ Fri, 10 Mar 2017 12:40:37: end of X-cor INFO @ Fri, 10 Mar 2017 12:40:37: #2 finished! INFO @ Fri, 10 Mar 2017 12:40:37: #2 predicted fragment length is 107 bps INFO @ Fri, 10 Mar 2017 12:40:37: #2 alternative fragment length(s) may be 107 bps INFO @ Fri, 10 Mar 2017 12:40:37: #2.2 Generate R script for model : SRX110762.20_model.r INFO @ Fri, 10 Mar 2017 12:40:37: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:40:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:41:48: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:42:03: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:42:59: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:43:47: #4 Write output xls file... SRX110762.10_peaks.xls INFO @ Fri, 10 Mar 2017 12:43:47: #4 Write peak in narrowPeak format file... SRX110762.10_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:43:47: #4 Write summits bed file... SRX110762.10_summits.bed INFO @ Fri, 10 Mar 2017 12:43:47: Done! pass1 - making usageList (13 chroms): 5 millis pass2 - checking and writing primary data (13396 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:44:15: #4 Write output xls file... SRX110762.05_peaks.xls INFO @ Fri, 10 Mar 2017 12:44:15: #4 Write peak in narrowPeak format file... SRX110762.05_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:44:15: #4 Write summits bed file... SRX110762.05_summits.bed INFO @ Fri, 10 Mar 2017 12:44:15: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (19076 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:44:46: #4 Write output xls file... SRX110762.20_peaks.xls INFO @ Fri, 10 Mar 2017 12:44:46: #4 Write peak in narrowPeak format file... SRX110762.20_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:44:47: #4 Write summits bed file... SRX110762.20_summits.bed INFO @ Fri, 10 Mar 2017 12:44:47: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (8486 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。