Job ID = 9029539 sra ファイルのダウンロード中... Completed: 1015138K bytes transferred in 14 seconds (560399K 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 14324 0 14324 0 0 1915 0 --:--:-- 0:00:07 --:--:-- 13551 100 36110 0 36110 0 0 4346 0 --:--:-- 0:00:08 --:--:-- 19115 100 64869 0 64869 0 0 7098 0 --:--:-- 0:00:09 --:--:-- 23866 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 16868459 spots for /home/okishinya/chipatlas/results/dm3/SRX1837979/SRR3658920.sra Written 16868459 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: 00:13:37 16868459 reads; of these: 16868459 (100.00%) were unpaired; of these: 424230 (2.51%) aligned 0 times 14477736 (85.83%) aligned exactly 1 time 1966493 (11.66%) aligned >1 times 97.49% overall alignment rate Time searching: 00:13:37 Overall time: 00:13:37 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] 4149949 / 16444229 = 0.2524 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 14:26:31: # Command line: callpeak -t SRX1837979.bam -f BAM -g dm -n SRX1837979.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1837979.20 # format = BAM # ChIP-seq file = ['SRX1837979.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 14:26:31: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:26:31: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:26:31: # Command line: callpeak -t SRX1837979.bam -f BAM -g dm -n SRX1837979.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1837979.10 # format = BAM # ChIP-seq file = ['SRX1837979.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 14:26:31: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:26:31: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:26:31: # Command line: callpeak -t SRX1837979.bam -f BAM -g dm -n SRX1837979.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1837979.05 # format = BAM # ChIP-seq file = ['SRX1837979.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 14:26:31: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:26:31: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:26:44: 1000000 INFO @ Sat, 03 Jun 2017 14:26:44: 1000000 INFO @ Sat, 03 Jun 2017 14:26:45: 1000000 INFO @ Sat, 03 Jun 2017 14:26:56: 2000000 INFO @ Sat, 03 Jun 2017 14:26:56: 2000000 INFO @ Sat, 03 Jun 2017 14:26:59: 2000000 INFO @ Sat, 03 Jun 2017 14:27:07: 3000000 INFO @ Sat, 03 Jun 2017 14:27:07: 3000000 INFO @ Sat, 03 Jun 2017 14:27:13: 3000000 INFO @ Sat, 03 Jun 2017 14:27:18: 4000000 INFO @ Sat, 03 Jun 2017 14:27:19: 4000000 INFO @ Sat, 03 Jun 2017 14:27:27: 4000000 INFO @ Sat, 03 Jun 2017 14:27:30: 5000000 INFO @ Sat, 03 Jun 2017 14:27:30: 5000000 INFO @ Sat, 03 Jun 2017 14:27:40: 5000000 INFO @ Sat, 03 Jun 2017 14:27:42: 6000000 INFO @ Sat, 03 Jun 2017 14:27:42: 6000000 INFO @ Sat, 03 Jun 2017 14:27:53: 7000000 INFO @ Sat, 03 Jun 2017 14:27:53: 7000000 INFO @ Sat, 03 Jun 2017 14:27:54: 6000000 INFO @ Sat, 03 Jun 2017 14:28:04: 8000000 INFO @ Sat, 03 Jun 2017 14:28:05: 8000000 INFO @ Sat, 03 Jun 2017 14:28:08: 7000000 INFO @ Sat, 03 Jun 2017 14:28:16: 9000000 INFO @ Sat, 03 Jun 2017 14:28:16: 9000000 INFO @ Sat, 03 Jun 2017 14:28:22: 8000000 INFO @ Sat, 03 Jun 2017 14:28:27: 10000000 INFO @ Sat, 03 Jun 2017 14:28:28: 10000000 INFO @ Sat, 03 Jun 2017 14:28:35: 9000000 INFO @ Sat, 03 Jun 2017 14:28:39: 11000000 INFO @ Sat, 03 Jun 2017 14:28:39: 11000000 INFO @ Sat, 03 Jun 2017 14:28:49: 10000000 INFO @ Sat, 03 Jun 2017 14:28:51: 12000000 INFO @ Sat, 03 Jun 2017 14:28:51: 12000000 INFO @ Sat, 03 Jun 2017 14:28:54: #1 tag size is determined as 149 bps INFO @ Sat, 03 Jun 2017 14:28:54: #1 tag size = 149 INFO @ Sat, 03 Jun 2017 14:28:54: #1 total tags in treatment: 12294280 INFO @ Sat, 03 Jun 2017 14:28:54: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:28:54: #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 14:28:54: #1 tag size is determined as 149 bps INFO @ Sat, 03 Jun 2017 14:28:54: #1 tag size = 149 INFO @ Sat, 03 Jun 2017 14:28:54: #1 total tags in treatment: 12294280 INFO @ Sat, 03 Jun 2017 14:28:54: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:28:54: #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 14:28:57: #1 tags after filtering in treatment: 12263719 INFO @ Sat, 03 Jun 2017 14:28:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:28:57: #1 finished! INFO @ Sat, 03 Jun 2017 14:28:57: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:28:57: #1 tags after filtering in treatment: 12263719 INFO @ Sat, 03 Jun 2017 14:28:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:28:57: #1 finished! INFO @ Sat, 03 Jun 2017 14:28:57: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:28:59: #2 number of paired peaks: 2654 INFO @ Sat, 03 Jun 2017 14:28:59: start model_add_line... INFO @ Sat, 03 Jun 2017 14:29:00: #2 number of paired peaks: 2654 INFO @ Sat, 03 Jun 2017 14:29:00: start model_add_line... INFO @ Sat, 03 Jun 2017 14:29:00: 11000000 INFO @ Sat, 03 Jun 2017 14:29:10: 12000000 INFO @ Sat, 03 Jun 2017 14:29:13: #1 tag size is determined as 149 bps INFO @ Sat, 03 Jun 2017 14:29:13: #1 tag size = 149 INFO @ Sat, 03 Jun 2017 14:29:13: #1 total tags in treatment: 12294280 INFO @ Sat, 03 Jun 2017 14:29:13: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:29:13: #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 14:29:15: #1 tags after filtering in treatment: 12263719 INFO @ Sat, 03 Jun 2017 14:29:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:29:15: #1 finished! INFO @ Sat, 03 Jun 2017 14:29:15: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:29:18: #2 number of paired peaks: 2654 INFO @ Sat, 03 Jun 2017 14:29:18: start model_add_line... INFO @ Sat, 03 Jun 2017 14:29:25: start X-correlation... INFO @ Sat, 03 Jun 2017 14:29:25: end of X-cor INFO @ Sat, 03 Jun 2017 14:29:25: #2 finished! INFO @ Sat, 03 Jun 2017 14:29:25: #2 predicted fragment length is 168 bps INFO @ Sat, 03 Jun 2017 14:29:25: #2 alternative fragment length(s) may be 168 bps INFO @ Sat, 03 Jun 2017 14:29:25: #2.2 Generate R script for model : SRX1837979.20_model.r WARNING @ Sat, 03 Jun 2017 14:29:25: #2 Since the d (168) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:29:25: #2 You may need to consider one of the other alternative d(s): 168 WARNING @ Sat, 03 Jun 2017 14:29:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 14:29:25: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:29:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:29:26: start X-correlation... INFO @ Sat, 03 Jun 2017 14:29:26: end of X-cor INFO @ Sat, 03 Jun 2017 14:29:26: #2 finished! INFO @ Sat, 03 Jun 2017 14:29:26: #2 predicted fragment length is 168 bps INFO @ Sat, 03 Jun 2017 14:29:26: #2 alternative fragment length(s) may be 168 bps INFO @ Sat, 03 Jun 2017 14:29:26: #2.2 Generate R script for model : SRX1837979.10_model.r WARNING @ Sat, 03 Jun 2017 14:29:26: #2 Since the d (168) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:29:26: #2 You may need to consider one of the other alternative d(s): 168 WARNING @ Sat, 03 Jun 2017 14:29:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 14:29:26: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:29:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:29:46: start X-correlation... INFO @ Sat, 03 Jun 2017 14:29:46: end of X-cor INFO @ Sat, 03 Jun 2017 14:29:46: #2 finished! INFO @ Sat, 03 Jun 2017 14:29:46: #2 predicted fragment length is 168 bps INFO @ Sat, 03 Jun 2017 14:29:46: #2 alternative fragment length(s) may be 168 bps INFO @ Sat, 03 Jun 2017 14:29:46: #2.2 Generate R script for model : SRX1837979.05_model.r WARNING @ Sat, 03 Jun 2017 14:29:46: #2 Since the d (168) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:29:46: #2 You may need to consider one of the other alternative d(s): 168 WARNING @ Sat, 03 Jun 2017 14:29:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 14:29:46: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:29:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:30:40: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:30:44: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:31:02: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:31:32: #4 Write output xls file... SRX1837979.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:31:32: #4 Write peak in narrowPeak format file... SRX1837979.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:31:32: #4 Write summits bed file... SRX1837979.20_summits.bed INFO @ Sat, 03 Jun 2017 14:31:32: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (2554 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:31:38: #4 Write output xls file... SRX1837979.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:31:38: #4 Write peak in narrowPeak format file... SRX1837979.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:31:38: #4 Write summits bed file... SRX1837979.10_summits.bed INFO @ Sat, 03 Jun 2017 14:31:39: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (5223 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 14:32:04: #4 Write output xls file... SRX1837979.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:32:04: #4 Write peak in narrowPeak format file... SRX1837979.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:32:04: #4 Write summits bed file... SRX1837979.05_summits.bed INFO @ Sat, 03 Jun 2017 14:32:04: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8978 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。