Job ID = 9029541 sra ファイルのダウンロード中... Completed: 1105871K bytes transferred in 14 seconds (637327K 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 25902 0 25902 0 0 3347 0 --:--:-- 0:00:07 --:--:-- 19387 100 68465 0 68465 0 0 7991 0 --:--:-- 0:00:08 --:--:-- 31623 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 17677079 spots for /home/okishinya/chipatlas/results/dm3/SRX1837981/SRR3658922.sra Written 17677079 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: 00:14:53 17677079 reads; of these: 17677079 (100.00%) were unpaired; of these: 382345 (2.16%) aligned 0 times 14883988 (84.20%) aligned exactly 1 time 2410746 (13.64%) aligned >1 times 97.84% overall alignment rate Time searching: 00:14:53 Overall time: 00:14:53 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 16 files... [bam_rmdupse_core] 3412380 / 17294734 = 0.1973 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 14:28:57: # Command line: callpeak -t SRX1837981.bam -f BAM -g dm -n SRX1837981.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1837981.20 # format = BAM # ChIP-seq file = ['SRX1837981.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 14:28:57: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:28:57: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:28:57: # Command line: callpeak -t SRX1837981.bam -f BAM -g dm -n SRX1837981.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1837981.10 # format = BAM # ChIP-seq file = ['SRX1837981.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 14:28:57: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:28:57: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:28:57: # Command line: callpeak -t SRX1837981.bam -f BAM -g dm -n SRX1837981.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1837981.05 # format = BAM # ChIP-seq file = ['SRX1837981.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 14:28:57: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:28:57: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:29:07: 1000000 INFO @ Sat, 03 Jun 2017 14:29:08: 1000000 INFO @ Sat, 03 Jun 2017 14:29:08: 1000000 INFO @ Sat, 03 Jun 2017 14:29:18: 2000000 INFO @ Sat, 03 Jun 2017 14:29:18: 2000000 INFO @ Sat, 03 Jun 2017 14:29:18: 2000000 INFO @ Sat, 03 Jun 2017 14:29:28: 3000000 INFO @ Sat, 03 Jun 2017 14:29:28: 3000000 INFO @ Sat, 03 Jun 2017 14:29:28: 3000000 INFO @ Sat, 03 Jun 2017 14:29:38: 4000000 INFO @ Sat, 03 Jun 2017 14:29:38: 4000000 INFO @ Sat, 03 Jun 2017 14:29:39: 4000000 INFO @ Sat, 03 Jun 2017 14:29:49: 5000000 INFO @ Sat, 03 Jun 2017 14:29:49: 5000000 INFO @ Sat, 03 Jun 2017 14:29:49: 5000000 INFO @ Sat, 03 Jun 2017 14:29:59: 6000000 INFO @ Sat, 03 Jun 2017 14:29:59: 6000000 INFO @ Sat, 03 Jun 2017 14:30:00: 6000000 INFO @ Sat, 03 Jun 2017 14:30:09: 7000000 INFO @ Sat, 03 Jun 2017 14:30:10: 7000000 INFO @ Sat, 03 Jun 2017 14:30:10: 7000000 INFO @ Sat, 03 Jun 2017 14:30:20: 8000000 INFO @ Sat, 03 Jun 2017 14:30:20: 8000000 INFO @ Sat, 03 Jun 2017 14:30:20: 8000000 INFO @ Sat, 03 Jun 2017 14:30:30: 9000000 INFO @ Sat, 03 Jun 2017 14:30:31: 9000000 INFO @ Sat, 03 Jun 2017 14:30:31: 9000000 INFO @ Sat, 03 Jun 2017 14:30:41: 10000000 INFO @ Sat, 03 Jun 2017 14:30:41: 10000000 INFO @ Sat, 03 Jun 2017 14:30:41: 10000000 INFO @ Sat, 03 Jun 2017 14:30:51: 11000000 INFO @ Sat, 03 Jun 2017 14:30:51: 11000000 INFO @ Sat, 03 Jun 2017 14:30:52: 11000000 INFO @ Sat, 03 Jun 2017 14:31:01: 12000000 INFO @ Sat, 03 Jun 2017 14:31:02: 12000000 INFO @ Sat, 03 Jun 2017 14:31:02: 12000000 INFO @ Sat, 03 Jun 2017 14:31:12: 13000000 INFO @ Sat, 03 Jun 2017 14:31:12: 13000000 INFO @ Sat, 03 Jun 2017 14:31:12: 13000000 INFO @ Sat, 03 Jun 2017 14:31:21: #1 tag size is determined as 149 bps INFO @ Sat, 03 Jun 2017 14:31:21: #1 tag size = 149 INFO @ Sat, 03 Jun 2017 14:31:21: #1 total tags in treatment: 13882354 INFO @ Sat, 03 Jun 2017 14:31:21: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:31:21: #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 14:31:22: #1 tag size is determined as 149 bps INFO @ Sat, 03 Jun 2017 14:31:22: #1 tag size = 149 INFO @ Sat, 03 Jun 2017 14:31:22: #1 total tags in treatment: 13882354 INFO @ Sat, 03 Jun 2017 14:31:22: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:31:22: #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 14:31:22: #1 tag size is determined as 149 bps INFO @ Sat, 03 Jun 2017 14:31:22: #1 tag size = 149 INFO @ Sat, 03 Jun 2017 14:31:22: #1 total tags in treatment: 13882354 INFO @ Sat, 03 Jun 2017 14:31:22: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:31:22: #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 14:31:24: #1 tags after filtering in treatment: 13852657 INFO @ Sat, 03 Jun 2017 14:31:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:31:24: #1 finished! INFO @ Sat, 03 Jun 2017 14:31:24: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:31:24: #1 tags after filtering in treatment: 13852657 INFO @ Sat, 03 Jun 2017 14:31:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:31:24: #1 finished! INFO @ Sat, 03 Jun 2017 14:31:24: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:31:25: #1 tags after filtering in treatment: 13852657 INFO @ Sat, 03 Jun 2017 14:31:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:31:25: #1 finished! INFO @ Sat, 03 Jun 2017 14:31:25: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:31:26: #2 number of paired peaks: 2251 INFO @ Sat, 03 Jun 2017 14:31:26: start model_add_line... INFO @ Sat, 03 Jun 2017 14:31:27: #2 number of paired peaks: 2251 INFO @ Sat, 03 Jun 2017 14:31:27: start model_add_line... INFO @ Sat, 03 Jun 2017 14:31:27: #2 number of paired peaks: 2251 INFO @ Sat, 03 Jun 2017 14:31:27: start model_add_line... INFO @ Sat, 03 Jun 2017 14:31:53: start X-correlation... INFO @ Sat, 03 Jun 2017 14:31:53: end of X-cor INFO @ Sat, 03 Jun 2017 14:31:53: #2 finished! INFO @ Sat, 03 Jun 2017 14:31:53: #2 predicted fragment length is 176 bps INFO @ Sat, 03 Jun 2017 14:31:53: #2 alternative fragment length(s) may be 176 bps INFO @ Sat, 03 Jun 2017 14:31:53: #2.2 Generate R script for model : SRX1837981.20_model.r WARNING @ Sat, 03 Jun 2017 14:31:53: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:31:53: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Sat, 03 Jun 2017 14:31:53: #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 14:31:53: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:31:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:31:53: start X-correlation... INFO @ Sat, 03 Jun 2017 14:31:53: end of X-cor INFO @ Sat, 03 Jun 2017 14:31:53: #2 finished! INFO @ Sat, 03 Jun 2017 14:31:53: #2 predicted fragment length is 176 bps INFO @ Sat, 03 Jun 2017 14:31:53: #2 alternative fragment length(s) may be 176 bps INFO @ Sat, 03 Jun 2017 14:31:53: #2.2 Generate R script for model : SRX1837981.10_model.r WARNING @ Sat, 03 Jun 2017 14:31:53: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:31:53: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Sat, 03 Jun 2017 14:31:53: #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 14:31:53: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:31:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:31:54: start X-correlation... INFO @ Sat, 03 Jun 2017 14:31:54: end of X-cor INFO @ Sat, 03 Jun 2017 14:31:54: #2 finished! INFO @ Sat, 03 Jun 2017 14:31:54: #2 predicted fragment length is 176 bps INFO @ Sat, 03 Jun 2017 14:31:54: #2 alternative fragment length(s) may be 176 bps INFO @ Sat, 03 Jun 2017 14:31:54: #2.2 Generate R script for model : SRX1837981.05_model.r WARNING @ Sat, 03 Jun 2017 14:31:54: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:31:54: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Sat, 03 Jun 2017 14:31:54: #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 14:31:54: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:31:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:33:13: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:33:17: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:33:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:34:08: #4 Write output xls file... SRX1837981.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:34:08: #4 Write peak in narrowPeak format file... SRX1837981.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:34:08: #4 Write summits bed file... SRX1837981.20_summits.bed INFO @ Sat, 03 Jun 2017 14:34:08: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1628 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:34:17: #4 Write output xls file... SRX1837981.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:34:17: #4 Write peak in narrowPeak format file... SRX1837981.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:34:17: #4 Write summits bed file... SRX1837981.05_summits.bed INFO @ Sat, 03 Jun 2017 14:34:17: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6599 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:34:22: #4 Write output xls file... SRX1837981.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:34:22: #4 Write peak in narrowPeak format file... SRX1837981.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:34:22: #4 Write summits bed file... SRX1837981.10_summits.bed INFO @ Sat, 03 Jun 2017 14:34:22: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3494 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。