Job ID = 9029542 sra ファイルのダウンロード中... Completed: 1248683K bytes transferred in 15 seconds (680384K 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 22317 0 22317 0 0 2937 0 --:--:-- 0:00:07 --:--:-- 18738 100 62317 0 62317 0 0 7251 0 --:--:-- 0:00:08 --:--:-- 28494 100 94300 0 94300 0 0 10563 0 --:--:-- 0:00:08 --:--:-- 37420 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 18924419 spots for /home/okishinya/chipatlas/results/dm3/SRX1837982/SRR3658923.sra Written 18924419 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: 00:28:23 18924419 reads; of these: 18924419 (100.00%) were unpaired; of these: 588143 (3.11%) aligned 0 times 14638364 (77.35%) aligned exactly 1 time 3697912 (19.54%) aligned >1 times 96.89% overall alignment rate Time searching: 00:28:23 Overall time: 00:28:23 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] 4143261 / 18336276 = 0.2260 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 14:42:58: # Command line: callpeak -t SRX1837982.bam -f BAM -g dm -n SRX1837982.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1837982.10 # format = BAM # ChIP-seq file = ['SRX1837982.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 14:42:58: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:42:58: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:42:58: # Command line: callpeak -t SRX1837982.bam -f BAM -g dm -n SRX1837982.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1837982.05 # format = BAM # ChIP-seq file = ['SRX1837982.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 14:42:58: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:42:58: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:42:58: # Command line: callpeak -t SRX1837982.bam -f BAM -g dm -n SRX1837982.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1837982.20 # format = BAM # ChIP-seq file = ['SRX1837982.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 14:42:58: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:42:58: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:43:06: 1000000 INFO @ Sat, 03 Jun 2017 14:43:07: 1000000 INFO @ Sat, 03 Jun 2017 14:43:07: 1000000 INFO @ Sat, 03 Jun 2017 14:43:15: 2000000 INFO @ Sat, 03 Jun 2017 14:43:15: 2000000 INFO @ Sat, 03 Jun 2017 14:43:16: 2000000 INFO @ Sat, 03 Jun 2017 14:43:24: 3000000 INFO @ Sat, 03 Jun 2017 14:43:24: 3000000 INFO @ Sat, 03 Jun 2017 14:43:25: 3000000 INFO @ Sat, 03 Jun 2017 14:43:33: 4000000 INFO @ Sat, 03 Jun 2017 14:43:33: 4000000 INFO @ Sat, 03 Jun 2017 14:43:34: 4000000 INFO @ Sat, 03 Jun 2017 14:43:42: 5000000 INFO @ Sat, 03 Jun 2017 14:43:42: 5000000 INFO @ Sat, 03 Jun 2017 14:43:43: 5000000 INFO @ Sat, 03 Jun 2017 14:43:51: 6000000 INFO @ Sat, 03 Jun 2017 14:43:52: 6000000 INFO @ Sat, 03 Jun 2017 14:43:53: 6000000 INFO @ Sat, 03 Jun 2017 14:44:00: 7000000 INFO @ Sat, 03 Jun 2017 14:44:01: 7000000 INFO @ Sat, 03 Jun 2017 14:44:02: 7000000 INFO @ Sat, 03 Jun 2017 14:44:10: 8000000 INFO @ Sat, 03 Jun 2017 14:44:11: 8000000 INFO @ Sat, 03 Jun 2017 14:44:12: 8000000 INFO @ Sat, 03 Jun 2017 14:44:18: 9000000 INFO @ Sat, 03 Jun 2017 14:44:19: 9000000 INFO @ Sat, 03 Jun 2017 14:44:21: 9000000 INFO @ Sat, 03 Jun 2017 14:44:25: 10000000 INFO @ Sat, 03 Jun 2017 14:44:28: 10000000 INFO @ Sat, 03 Jun 2017 14:44:29: 10000000 INFO @ Sat, 03 Jun 2017 14:44:33: 11000000 INFO @ Sat, 03 Jun 2017 14:44:36: 11000000 INFO @ Sat, 03 Jun 2017 14:44:38: 11000000 INFO @ Sat, 03 Jun 2017 14:44:40: 12000000 INFO @ Sat, 03 Jun 2017 14:44:45: 12000000 INFO @ Sat, 03 Jun 2017 14:44:46: 12000000 INFO @ Sat, 03 Jun 2017 14:44:48: 13000000 INFO @ Sat, 03 Jun 2017 14:44:53: 13000000 INFO @ Sat, 03 Jun 2017 14:44:55: 13000000 INFO @ Sat, 03 Jun 2017 14:44:55: 14000000 INFO @ Sat, 03 Jun 2017 14:44:57: #1 tag size is determined as 149 bps INFO @ Sat, 03 Jun 2017 14:44:57: #1 tag size = 149 INFO @ Sat, 03 Jun 2017 14:44:57: #1 total tags in treatment: 14193015 INFO @ Sat, 03 Jun 2017 14:44:57: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:44:57: #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 14:44:59: #1 tags after filtering in treatment: 14155702 INFO @ Sat, 03 Jun 2017 14:44:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:44:59: #1 finished! INFO @ Sat, 03 Jun 2017 14:44:59: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:45:01: 14000000 INFO @ Sat, 03 Jun 2017 14:45:02: #2 number of paired peaks: 2103 INFO @ Sat, 03 Jun 2017 14:45:02: start model_add_line... INFO @ Sat, 03 Jun 2017 14:45:03: 14000000 INFO @ Sat, 03 Jun 2017 14:45:03: #1 tag size is determined as 149 bps INFO @ Sat, 03 Jun 2017 14:45:03: #1 tag size = 149 INFO @ Sat, 03 Jun 2017 14:45:03: #1 total tags in treatment: 14193015 INFO @ Sat, 03 Jun 2017 14:45:03: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:45:03: #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 14:45:04: #1 tag size is determined as 149 bps INFO @ Sat, 03 Jun 2017 14:45:04: #1 tag size = 149 INFO @ Sat, 03 Jun 2017 14:45:04: #1 total tags in treatment: 14193015 INFO @ Sat, 03 Jun 2017 14:45:04: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:45:04: #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 14:45:06: #1 tags after filtering in treatment: 14155702 INFO @ Sat, 03 Jun 2017 14:45:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:45:06: #1 finished! INFO @ Sat, 03 Jun 2017 14:45:06: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:45:07: #1 tags after filtering in treatment: 14155702 INFO @ Sat, 03 Jun 2017 14:45:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:45:07: #1 finished! INFO @ Sat, 03 Jun 2017 14:45:07: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:45:09: #2 number of paired peaks: 2103 INFO @ Sat, 03 Jun 2017 14:45:09: start model_add_line... INFO @ Sat, 03 Jun 2017 14:45:10: #2 number of paired peaks: 2103 INFO @ Sat, 03 Jun 2017 14:45:10: start model_add_line... INFO @ Sat, 03 Jun 2017 14:45:18: start X-correlation... INFO @ Sat, 03 Jun 2017 14:45:18: end of X-cor INFO @ Sat, 03 Jun 2017 14:45:18: #2 finished! INFO @ Sat, 03 Jun 2017 14:45:18: #2 predicted fragment length is 156 bps INFO @ Sat, 03 Jun 2017 14:45:18: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 03 Jun 2017 14:45:18: #2.2 Generate R script for model : SRX1837982.20_model.r WARNING @ Sat, 03 Jun 2017 14:45:18: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:45:18: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Sat, 03 Jun 2017 14:45:18: #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 14:45:18: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:45:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:45:23: start X-correlation... INFO @ Sat, 03 Jun 2017 14:45:23: end of X-cor INFO @ Sat, 03 Jun 2017 14:45:23: #2 finished! INFO @ Sat, 03 Jun 2017 14:45:23: #2 predicted fragment length is 156 bps INFO @ Sat, 03 Jun 2017 14:45:23: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 03 Jun 2017 14:45:23: #2.2 Generate R script for model : SRX1837982.05_model.r WARNING @ Sat, 03 Jun 2017 14:45:23: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:45:23: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Sat, 03 Jun 2017 14:45:23: #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 14:45:23: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:45:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:45:25: start X-correlation... INFO @ Sat, 03 Jun 2017 14:45:25: end of X-cor INFO @ Sat, 03 Jun 2017 14:45:25: #2 finished! INFO @ Sat, 03 Jun 2017 14:45:25: #2 predicted fragment length is 156 bps INFO @ Sat, 03 Jun 2017 14:45:25: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 03 Jun 2017 14:45:25: #2.2 Generate R script for model : SRX1837982.10_model.r WARNING @ Sat, 03 Jun 2017 14:45:25: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:45:25: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Sat, 03 Jun 2017 14:45:25: #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 14:45:25: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:45:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:46:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:46:37: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:46:42: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:47:39: #4 Write output xls file... SRX1837982.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:47:40: #4 Write peak in narrowPeak format file... SRX1837982.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:47:40: #4 Write summits bed file... SRX1837982.20_summits.bed INFO @ Sat, 03 Jun 2017 14:47:40: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10312 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:48:06: #4 Write output xls file... SRX1837982.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:48:06: #4 Write peak in narrowPeak format file... SRX1837982.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:48:06: #4 Write summits bed file... SRX1837982.10_summits.bed INFO @ Sat, 03 Jun 2017 14:48:06: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (20672 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:48:15: #4 Write output xls file... SRX1837982.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:48:15: #4 Write peak in narrowPeak format file... SRX1837982.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:48:16: #4 Write summits bed file... SRX1837982.05_summits.bed INFO @ Sat, 03 Jun 2017 14:48:16: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (31421 records, 4 fields): 35 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。