Job ID = 9029761 sra ファイルのダウンロード中... Completed: 329774K bytes transferred in 5 seconds (465861K 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 1056 0 --:--:-- 0:00:07 --:--:-- 11121 100 30318 0 30318 0 0 3749 0 --:--:-- 0:00:08 --:--:-- 19959 100 56058 0 56058 0 0 6530 0 --:--:-- 0:00:08 --:--:-- 27806 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 15461190 spots for /home/okishinya/chipatlas/results/dm3/SRX2055945/SRR4069177.sra Written 15461190 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: 00:08:50 15461190 reads; of these: 15461190 (100.00%) were unpaired; of these: 458669 (2.97%) aligned 0 times 8885156 (57.47%) aligned exactly 1 time 6117365 (39.57%) aligned >1 times 97.03% overall alignment rate Time searching: 00:08:50 Overall time: 00:08:50 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] 3783745 / 15002521 = 0.2522 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 15:18:08: # Command line: callpeak -t SRX2055945.bam -f BAM -g dm -n SRX2055945.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2055945.05 # format = BAM # ChIP-seq file = ['SRX2055945.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 15:18:08: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:18:08: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:18:08: # Command line: callpeak -t SRX2055945.bam -f BAM -g dm -n SRX2055945.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2055945.10 # format = BAM # ChIP-seq file = ['SRX2055945.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 15:18:08: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:18:08: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:18:08: # Command line: callpeak -t SRX2055945.bam -f BAM -g dm -n SRX2055945.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2055945.20 # format = BAM # ChIP-seq file = ['SRX2055945.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 15:18:08: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:18:08: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:18:14: 1000000 INFO @ Sat, 03 Jun 2017 15:18:14: 1000000 INFO @ Sat, 03 Jun 2017 15:18:14: 1000000 INFO @ Sat, 03 Jun 2017 15:18:19: 2000000 INFO @ Sat, 03 Jun 2017 15:18:21: 2000000 INFO @ Sat, 03 Jun 2017 15:18:21: 2000000 INFO @ Sat, 03 Jun 2017 15:18:25: 3000000 INFO @ Sat, 03 Jun 2017 15:18:27: 3000000 INFO @ Sat, 03 Jun 2017 15:18:27: 3000000 INFO @ Sat, 03 Jun 2017 15:18:30: 4000000 INFO @ Sat, 03 Jun 2017 15:18:34: 4000000 INFO @ Sat, 03 Jun 2017 15:18:34: 4000000 INFO @ Sat, 03 Jun 2017 15:18:36: 5000000 INFO @ Sat, 03 Jun 2017 15:18:40: 5000000 INFO @ Sat, 03 Jun 2017 15:18:40: 5000000 INFO @ Sat, 03 Jun 2017 15:18:41: 6000000 INFO @ Sat, 03 Jun 2017 15:18:46: 6000000 INFO @ Sat, 03 Jun 2017 15:18:46: 6000000 INFO @ Sat, 03 Jun 2017 15:18:47: 7000000 INFO @ Sat, 03 Jun 2017 15:18:52: 8000000 INFO @ Sat, 03 Jun 2017 15:18:53: 7000000 INFO @ Sat, 03 Jun 2017 15:18:53: 7000000 INFO @ Sat, 03 Jun 2017 15:18:58: 9000000 INFO @ Sat, 03 Jun 2017 15:18:59: 8000000 INFO @ Sat, 03 Jun 2017 15:18:59: 8000000 INFO @ Sat, 03 Jun 2017 15:19:03: 10000000 INFO @ Sat, 03 Jun 2017 15:19:06: 9000000 INFO @ Sat, 03 Jun 2017 15:19:06: 9000000 INFO @ Sat, 03 Jun 2017 15:19:09: 11000000 INFO @ Sat, 03 Jun 2017 15:19:10: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:19:10: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:19:10: #1 total tags in treatment: 11218776 INFO @ Sat, 03 Jun 2017 15:19:10: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:19:10: #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 15:19:12: 10000000 INFO @ Sat, 03 Jun 2017 15:19:12: #1 tags after filtering in treatment: 11216638 INFO @ Sat, 03 Jun 2017 15:19:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:19:12: #1 finished! INFO @ Sat, 03 Jun 2017 15:19:12: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:19:12: 10000000 INFO @ Sat, 03 Jun 2017 15:19:14: #2 number of paired peaks: 1678 INFO @ Sat, 03 Jun 2017 15:19:14: start model_add_line... INFO @ Sat, 03 Jun 2017 15:19:18: 11000000 INFO @ Sat, 03 Jun 2017 15:19:18: 11000000 INFO @ Sat, 03 Jun 2017 15:19:19: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:19:19: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:19:19: #1 total tags in treatment: 11218776 INFO @ Sat, 03 Jun 2017 15:19:19: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:19:19: #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 15:19:20: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:19:20: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:19:20: #1 total tags in treatment: 11218776 INFO @ Sat, 03 Jun 2017 15:19:20: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:19:20: #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 15:19:22: #1 tags after filtering in treatment: 11216638 INFO @ Sat, 03 Jun 2017 15:19:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:19:22: #1 finished! INFO @ Sat, 03 Jun 2017 15:19:22: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:19:22: #1 tags after filtering in treatment: 11216638 INFO @ Sat, 03 Jun 2017 15:19:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:19:22: #1 finished! INFO @ Sat, 03 Jun 2017 15:19:22: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:19:24: #2 number of paired peaks: 1678 INFO @ Sat, 03 Jun 2017 15:19:24: start model_add_line... INFO @ Sat, 03 Jun 2017 15:19:24: #2 number of paired peaks: 1678 INFO @ Sat, 03 Jun 2017 15:19:24: start model_add_line... INFO @ Sat, 03 Jun 2017 15:19:27: start X-correlation... INFO @ Sat, 03 Jun 2017 15:19:27: end of X-cor INFO @ Sat, 03 Jun 2017 15:19:27: #2 finished! INFO @ Sat, 03 Jun 2017 15:19:27: #2 predicted fragment length is 52 bps INFO @ Sat, 03 Jun 2017 15:19:27: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 03 Jun 2017 15:19:27: #2.2 Generate R script for model : SRX2055945.20_model.r WARNING @ Sat, 03 Jun 2017 15:19:27: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:19:27: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 03 Jun 2017 15:19:27: #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 15:19:27: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:19:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:19:37: start X-correlation... INFO @ Sat, 03 Jun 2017 15:19:37: end of X-cor INFO @ Sat, 03 Jun 2017 15:19:37: #2 finished! INFO @ Sat, 03 Jun 2017 15:19:37: #2 predicted fragment length is 52 bps INFO @ Sat, 03 Jun 2017 15:19:37: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 03 Jun 2017 15:19:37: #2.2 Generate R script for model : SRX2055945.05_model.r WARNING @ Sat, 03 Jun 2017 15:19:37: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:19:37: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 03 Jun 2017 15:19:37: #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 15:19:37: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:19:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:19:37: start X-correlation... INFO @ Sat, 03 Jun 2017 15:19:37: end of X-cor INFO @ Sat, 03 Jun 2017 15:19:37: #2 finished! INFO @ Sat, 03 Jun 2017 15:19:37: #2 predicted fragment length is 52 bps INFO @ Sat, 03 Jun 2017 15:19:37: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 03 Jun 2017 15:19:37: #2.2 Generate R script for model : SRX2055945.10_model.r WARNING @ Sat, 03 Jun 2017 15:19:37: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:19:37: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 03 Jun 2017 15:19:37: #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 15:19:37: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:19:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:20:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:20:37: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:20:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:21:11: #4 Write output xls file... SRX2055945.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:21:11: #4 Write peak in narrowPeak format file... SRX2055945.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:21:11: #4 Write summits bed file... SRX2055945.20_summits.bed INFO @ Sat, 03 Jun 2017 15:21:11: Done! pass1 - making usageList (10 chroms): 8 millis pass2 - checking and writing primary data (1337 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:21:22: #4 Write output xls file... SRX2055945.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:21:22: #4 Write peak in narrowPeak format file... SRX2055945.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:21:22: #4 Write summits bed file... SRX2055945.10_summits.bed INFO @ Sat, 03 Jun 2017 15:21:22: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2606 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:21:26: #4 Write output xls file... SRX2055945.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:21:26: #4 Write peak in narrowPeak format file... SRX2055945.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:21:27: #4 Write summits bed file... SRX2055945.05_summits.bed INFO @ Sat, 03 Jun 2017 15:21:27: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3625 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。