Job ID = 9029239 sra ファイルのダウンロード中... Completed: 868781K bytes transferred in 13 seconds (508519K 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 30317 0 30317 0 0 3881 0 --:--:-- 0:00:07 --:--:-- 19815 100 76581 0 76581 0 0 8863 0 --:--:-- 0:00:08 --:--:-- 32449 100 159k 0 159k 0 0 17001 0 --:--:-- 0:00:09 --:--:-- 48814 100 165k 0 165k 0 0 17616 0 --:--:-- 0:00:09 --:--:-- 50570 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 35885621 spots for /home/okishinya/chipatlas/results/dm3/SRX1433379/SRR2919844.sra Written 35885621 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: 00:11:05 35885621 reads; of these: 35885621 (100.00%) were unpaired; of these: 17593278 (49.03%) aligned 0 times 13318597 (37.11%) aligned exactly 1 time 4973746 (13.86%) aligned >1 times 50.97% overall alignment rate Time searching: 00:11:05 Overall time: 00:11:05 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 8 files... [bam_rmdupse_core] 6643353 / 18292343 = 0.3632 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 13:10:09: # Command line: callpeak -t SRX1433379.bam -f BAM -g dm -n SRX1433379.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1433379.20 # format = BAM # ChIP-seq file = ['SRX1433379.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 13:10:09: # Command line: callpeak -t SRX1433379.bam -f BAM -g dm -n SRX1433379.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1433379.05 # format = BAM # ChIP-seq file = ['SRX1433379.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 13:10:09: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:10:09: # Command line: callpeak -t SRX1433379.bam -f BAM -g dm -n SRX1433379.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1433379.10 # format = BAM # ChIP-seq file = ['SRX1433379.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 13:10:09: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:10:09: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:10:09: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:10:09: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:10:09: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:10:17: 1000000 INFO @ Sat, 03 Jun 2017 13:10:17: 1000000 INFO @ Sat, 03 Jun 2017 13:10:17: 1000000 INFO @ Sat, 03 Jun 2017 13:10:23: 2000000 INFO @ Sat, 03 Jun 2017 13:10:24: 2000000 INFO @ Sat, 03 Jun 2017 13:10:24: 2000000 INFO @ Sat, 03 Jun 2017 13:10:30: 3000000 INFO @ Sat, 03 Jun 2017 13:10:32: 3000000 INFO @ Sat, 03 Jun 2017 13:10:32: 3000000 INFO @ Sat, 03 Jun 2017 13:10:37: 4000000 INFO @ Sat, 03 Jun 2017 13:10:39: 4000000 INFO @ Sat, 03 Jun 2017 13:10:39: 4000000 INFO @ Sat, 03 Jun 2017 13:10:44: 5000000 INFO @ Sat, 03 Jun 2017 13:10:45: 5000000 INFO @ Sat, 03 Jun 2017 13:10:47: 5000000 INFO @ Sat, 03 Jun 2017 13:10:52: 6000000 INFO @ Sat, 03 Jun 2017 13:10:52: 6000000 INFO @ Sat, 03 Jun 2017 13:10:54: 6000000 INFO @ Sat, 03 Jun 2017 13:10:58: 7000000 INFO @ Sat, 03 Jun 2017 13:10:59: 7000000 INFO @ Sat, 03 Jun 2017 13:11:01: 7000000 INFO @ Sat, 03 Jun 2017 13:11:05: 8000000 INFO @ Sat, 03 Jun 2017 13:11:07: 8000000 INFO @ Sat, 03 Jun 2017 13:11:11: 8000000 INFO @ Sat, 03 Jun 2017 13:11:12: 9000000 INFO @ Sat, 03 Jun 2017 13:11:16: 9000000 INFO @ Sat, 03 Jun 2017 13:11:19: 10000000 INFO @ Sat, 03 Jun 2017 13:11:21: 9000000 INFO @ Sat, 03 Jun 2017 13:11:24: 10000000 INFO @ Sat, 03 Jun 2017 13:11:27: 11000000 INFO @ Sat, 03 Jun 2017 13:11:29: 10000000 INFO @ Sat, 03 Jun 2017 13:11:32: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:11:32: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:11:32: #1 total tags in treatment: 11648990 INFO @ Sat, 03 Jun 2017 13:11:32: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:11:32: #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 13:11:33: 11000000 INFO @ Sat, 03 Jun 2017 13:11:34: #1 tags after filtering in treatment: 11646389 INFO @ Sat, 03 Jun 2017 13:11:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:11:34: #1 finished! INFO @ Sat, 03 Jun 2017 13:11:34: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:11:36: #2 number of paired peaks: 561 WARNING @ Sat, 03 Jun 2017 13:11:36: Fewer paired peaks (561) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 561 pairs to build model! INFO @ Sat, 03 Jun 2017 13:11:36: start model_add_line... INFO @ Sat, 03 Jun 2017 13:11:37: 11000000 INFO @ Sat, 03 Jun 2017 13:11:38: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:11:38: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:11:38: #1 total tags in treatment: 11648990 INFO @ Sat, 03 Jun 2017 13:11:38: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:11:38: #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 13:11:40: #1 tags after filtering in treatment: 11646389 INFO @ Sat, 03 Jun 2017 13:11:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:11:40: #1 finished! INFO @ Sat, 03 Jun 2017 13:11:40: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:11:41: start X-correlation... INFO @ Sat, 03 Jun 2017 13:11:41: end of X-cor INFO @ Sat, 03 Jun 2017 13:11:41: #2 finished! INFO @ Sat, 03 Jun 2017 13:11:41: #2 predicted fragment length is 68 bps INFO @ Sat, 03 Jun 2017 13:11:41: #2 alternative fragment length(s) may be 68 bps INFO @ Sat, 03 Jun 2017 13:11:41: #2.2 Generate R script for model : SRX1433379.20_model.r WARNING @ Sat, 03 Jun 2017 13:11:41: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:11:41: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sat, 03 Jun 2017 13:11:41: #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 13:11:41: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:11:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:11:42: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:11:42: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:11:42: #1 total tags in treatment: 11648990 INFO @ Sat, 03 Jun 2017 13:11:42: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:11:42: #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 13:11:42: #2 number of paired peaks: 561 WARNING @ Sat, 03 Jun 2017 13:11:42: Fewer paired peaks (561) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 561 pairs to build model! INFO @ Sat, 03 Jun 2017 13:11:42: start model_add_line... INFO @ Sat, 03 Jun 2017 13:11:44: #1 tags after filtering in treatment: 11646389 INFO @ Sat, 03 Jun 2017 13:11:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:11:44: #1 finished! INFO @ Sat, 03 Jun 2017 13:11:44: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:11:46: #2 number of paired peaks: 561 WARNING @ Sat, 03 Jun 2017 13:11:46: Fewer paired peaks (561) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 561 pairs to build model! INFO @ Sat, 03 Jun 2017 13:11:46: start model_add_line... INFO @ Sat, 03 Jun 2017 13:11:47: start X-correlation... INFO @ Sat, 03 Jun 2017 13:11:47: end of X-cor INFO @ Sat, 03 Jun 2017 13:11:47: #2 finished! INFO @ Sat, 03 Jun 2017 13:11:47: #2 predicted fragment length is 68 bps INFO @ Sat, 03 Jun 2017 13:11:47: #2 alternative fragment length(s) may be 68 bps INFO @ Sat, 03 Jun 2017 13:11:47: #2.2 Generate R script for model : SRX1433379.05_model.r WARNING @ Sat, 03 Jun 2017 13:11:47: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:11:47: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sat, 03 Jun 2017 13:11:47: #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 13:11:47: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:11:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:11:50: start X-correlation... INFO @ Sat, 03 Jun 2017 13:11:50: end of X-cor INFO @ Sat, 03 Jun 2017 13:11:50: #2 finished! INFO @ Sat, 03 Jun 2017 13:11:50: #2 predicted fragment length is 68 bps INFO @ Sat, 03 Jun 2017 13:11:50: #2 alternative fragment length(s) may be 68 bps INFO @ Sat, 03 Jun 2017 13:11:50: #2.2 Generate R script for model : SRX1433379.10_model.r WARNING @ Sat, 03 Jun 2017 13:11:50: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:11:50: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sat, 03 Jun 2017 13:11:50: #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 13:11:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:11:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:12:47: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:12:52: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:12:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:13:32: #4 Write output xls file... SRX1433379.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:13:32: #4 Write peak in narrowPeak format file... SRX1433379.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:13:32: #4 Write summits bed file... SRX1433379.20_summits.bed INFO @ Sat, 03 Jun 2017 13:13:32: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1275 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:13:37: #4 Write output xls file... SRX1433379.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:13:37: #4 Write peak in narrowPeak format file... SRX1433379.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:13:37: #4 Write summits bed file... SRX1433379.10_summits.bed INFO @ Sat, 03 Jun 2017 13:13:37: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2384 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:13:45: #4 Write output xls file... SRX1433379.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:13:45: #4 Write peak in narrowPeak format file... SRX1433379.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:13:45: #4 Write summits bed file... SRX1433379.05_summits.bed INFO @ Sat, 03 Jun 2017 13:13:45: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3816 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。