Job ID = 9029224 sra ファイルのダウンロード中... Completed: 435175K bytes transferred in 8 seconds (412240K 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 22318 0 22318 0 0 2989 0 --:--:-- 0:00:07 --:--:-- 17969 100 53902 0 53902 0 0 6629 0 --:--:-- 0:00:08 --:--:-- 28280 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 20538046 spots for /home/okishinya/chipatlas/results/dm3/SRX1433364/SRR2919829.sra Written 20538046 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: 00:09:02 20538046 reads; of these: 20538046 (100.00%) were unpaired; of these: 476019 (2.32%) aligned 0 times 14947939 (72.78%) aligned exactly 1 time 5114088 (24.90%) aligned >1 times 97.68% overall alignment rate Time searching: 00:09:02 Overall time: 00:09:02 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] 2915682 / 20062027 = 0.1453 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 13:06:50: # Command line: callpeak -t SRX1433364.bam -f BAM -g dm -n SRX1433364.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1433364.10 # format = BAM # ChIP-seq file = ['SRX1433364.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 13:06:50: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:06:50: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:06:50: # Command line: callpeak -t SRX1433364.bam -f BAM -g dm -n SRX1433364.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1433364.05 # format = BAM # ChIP-seq file = ['SRX1433364.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 13:06:50: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:06:50: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:06:50: # Command line: callpeak -t SRX1433364.bam -f BAM -g dm -n SRX1433364.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1433364.20 # format = BAM # ChIP-seq file = ['SRX1433364.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 13:06:50: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:06:50: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:06:57: 1000000 INFO @ Sat, 03 Jun 2017 13:06:57: 1000000 INFO @ Sat, 03 Jun 2017 13:06:57: 1000000 INFO @ Sat, 03 Jun 2017 13:07:04: 2000000 INFO @ Sat, 03 Jun 2017 13:07:04: 2000000 INFO @ Sat, 03 Jun 2017 13:07:04: 2000000 INFO @ Sat, 03 Jun 2017 13:07:11: 3000000 INFO @ Sat, 03 Jun 2017 13:07:11: 3000000 INFO @ Sat, 03 Jun 2017 13:07:11: 3000000 INFO @ Sat, 03 Jun 2017 13:07:17: 4000000 INFO @ Sat, 03 Jun 2017 13:07:17: 4000000 INFO @ Sat, 03 Jun 2017 13:07:17: 4000000 INFO @ Sat, 03 Jun 2017 13:07:24: 5000000 INFO @ Sat, 03 Jun 2017 13:07:24: 5000000 INFO @ Sat, 03 Jun 2017 13:07:24: 5000000 INFO @ Sat, 03 Jun 2017 13:07:30: 6000000 INFO @ Sat, 03 Jun 2017 13:07:30: 6000000 INFO @ Sat, 03 Jun 2017 13:07:30: 6000000 INFO @ Sat, 03 Jun 2017 13:07:37: 7000000 INFO @ Sat, 03 Jun 2017 13:07:37: 7000000 INFO @ Sat, 03 Jun 2017 13:07:37: 7000000 INFO @ Sat, 03 Jun 2017 13:07:43: 8000000 INFO @ Sat, 03 Jun 2017 13:07:43: 8000000 INFO @ Sat, 03 Jun 2017 13:07:43: 8000000 INFO @ Sat, 03 Jun 2017 13:07:49: 9000000 INFO @ Sat, 03 Jun 2017 13:07:50: 9000000 INFO @ Sat, 03 Jun 2017 13:07:50: 9000000 INFO @ Sat, 03 Jun 2017 13:07:56: 10000000 INFO @ Sat, 03 Jun 2017 13:07:56: 10000000 INFO @ Sat, 03 Jun 2017 13:07:56: 10000000 INFO @ Sat, 03 Jun 2017 13:08:02: 11000000 INFO @ Sat, 03 Jun 2017 13:08:02: 11000000 INFO @ Sat, 03 Jun 2017 13:08:02: 11000000 INFO @ Sat, 03 Jun 2017 13:08:08: 12000000 INFO @ Sat, 03 Jun 2017 13:08:08: 12000000 INFO @ Sat, 03 Jun 2017 13:08:08: 12000000 INFO @ Sat, 03 Jun 2017 13:08:14: 13000000 INFO @ Sat, 03 Jun 2017 13:08:15: 13000000 INFO @ Sat, 03 Jun 2017 13:08:15: 13000000 INFO @ Sat, 03 Jun 2017 13:08:20: 14000000 INFO @ Sat, 03 Jun 2017 13:08:21: 14000000 INFO @ Sat, 03 Jun 2017 13:08:21: 14000000 INFO @ Sat, 03 Jun 2017 13:08:25: 15000000 INFO @ Sat, 03 Jun 2017 13:08:27: 15000000 INFO @ Sat, 03 Jun 2017 13:08:27: 15000000 INFO @ Sat, 03 Jun 2017 13:08:31: 16000000 INFO @ Sat, 03 Jun 2017 13:08:33: 16000000 INFO @ Sat, 03 Jun 2017 13:08:33: 16000000 INFO @ Sat, 03 Jun 2017 13:08:38: 17000000 INFO @ Sat, 03 Jun 2017 13:08:38: 17000000 INFO @ Sat, 03 Jun 2017 13:08:39: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:08:39: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:08:39: #1 total tags in treatment: 17146345 INFO @ Sat, 03 Jun 2017 13:08:39: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:08:39: #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 13:08:39: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:08:39: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:08:39: #1 total tags in treatment: 17146345 INFO @ Sat, 03 Jun 2017 13:08:39: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:08:39: #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 13:08:40: 17000000 INFO @ Sat, 03 Jun 2017 13:08:41: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:08:41: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:08:41: #1 total tags in treatment: 17146345 INFO @ Sat, 03 Jun 2017 13:08:41: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:08:41: #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 13:08:42: #1 tags after filtering in treatment: 17142221 INFO @ Sat, 03 Jun 2017 13:08:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:08:42: #1 finished! INFO @ Sat, 03 Jun 2017 13:08:42: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:08:43: #1 tags after filtering in treatment: 17142221 INFO @ Sat, 03 Jun 2017 13:08:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:08:43: #1 finished! INFO @ Sat, 03 Jun 2017 13:08:43: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:08:44: #1 tags after filtering in treatment: 17142221 INFO @ Sat, 03 Jun 2017 13:08:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:08:44: #1 finished! INFO @ Sat, 03 Jun 2017 13:08:44: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:08:45: #2 number of paired peaks: 255 WARNING @ Sat, 03 Jun 2017 13:08:45: Fewer paired peaks (255) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 255 pairs to build model! INFO @ Sat, 03 Jun 2017 13:08:45: start model_add_line... INFO @ Sat, 03 Jun 2017 13:08:46: #2 number of paired peaks: 255 WARNING @ Sat, 03 Jun 2017 13:08:46: Fewer paired peaks (255) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 255 pairs to build model! INFO @ Sat, 03 Jun 2017 13:08:46: start model_add_line... INFO @ Sat, 03 Jun 2017 13:08:47: #2 number of paired peaks: 255 WARNING @ Sat, 03 Jun 2017 13:08:47: Fewer paired peaks (255) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 255 pairs to build model! INFO @ Sat, 03 Jun 2017 13:08:47: start model_add_line... INFO @ Sat, 03 Jun 2017 13:08:49: start X-correlation... INFO @ Sat, 03 Jun 2017 13:08:49: end of X-cor INFO @ Sat, 03 Jun 2017 13:08:49: #2 finished! INFO @ Sat, 03 Jun 2017 13:08:49: #2 predicted fragment length is 48 bps INFO @ Sat, 03 Jun 2017 13:08:49: #2 alternative fragment length(s) may be 48 bps INFO @ Sat, 03 Jun 2017 13:08:49: #2.2 Generate R script for model : SRX1433364.10_model.r WARNING @ Sat, 03 Jun 2017 13:08:49: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:08:49: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sat, 03 Jun 2017 13:08:49: #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 13:08:49: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:08:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:08:49: start X-correlation... INFO @ Sat, 03 Jun 2017 13:08:49: end of X-cor INFO @ Sat, 03 Jun 2017 13:08:49: #2 finished! INFO @ Sat, 03 Jun 2017 13:08:49: #2 predicted fragment length is 48 bps INFO @ Sat, 03 Jun 2017 13:08:49: #2 alternative fragment length(s) may be 48 bps INFO @ Sat, 03 Jun 2017 13:08:49: #2.2 Generate R script for model : SRX1433364.05_model.r WARNING @ Sat, 03 Jun 2017 13:08:49: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:08:49: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sat, 03 Jun 2017 13:08:49: #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 13:08:49: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:08:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:08:50: start X-correlation... INFO @ Sat, 03 Jun 2017 13:08:50: end of X-cor INFO @ Sat, 03 Jun 2017 13:08:50: #2 finished! INFO @ Sat, 03 Jun 2017 13:08:50: #2 predicted fragment length is 48 bps INFO @ Sat, 03 Jun 2017 13:08:50: #2 alternative fragment length(s) may be 48 bps INFO @ Sat, 03 Jun 2017 13:08:50: #2.2 Generate R script for model : SRX1433364.20_model.r WARNING @ Sat, 03 Jun 2017 13:08:50: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:08:50: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sat, 03 Jun 2017 13:08:50: #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 13:08:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:08:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:10:16: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:10:19: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:10:19: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:11:16: #4 Write output xls file... SRX1433364.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:11:16: #4 Write peak in narrowPeak format file... SRX1433364.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:11:16: #4 Write summits bed file... SRX1433364.20_summits.bed INFO @ Sat, 03 Jun 2017 13:11:16: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (908 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:11:22: #4 Write output xls file... SRX1433364.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:11:22: #4 Write peak in narrowPeak format file... SRX1433364.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:11:22: #4 Write summits bed file... SRX1433364.05_summits.bed INFO @ Sat, 03 Jun 2017 13:11:22: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1840 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:11:23: #4 Write output xls file... SRX1433364.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:11:23: #4 Write peak in narrowPeak format file... SRX1433364.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:11:23: #4 Write summits bed file... SRX1433364.10_summits.bed INFO @ Sat, 03 Jun 2017 13:11:23: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1268 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。