Job ID = 9032373 sra ファイルのダウンロード中... Completed: 259792K bytes transferred in 5 seconds (395021K 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 14324 0 14324 0 0 1885 0 --:--:-- 0:00:07 --:--:-- 13411 100 31773 0 31773 0 0 3847 0 --:--:-- 0:00:08 --:--:-- 18344 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 18096495 spots for /home/okishinya/chipatlas/results/dm3/SRX858995/SRR1779551.sra Written 18096495 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: 00:03:55 18096495 reads; of these: 18096495 (100.00%) were unpaired; of these: 81721 (0.45%) aligned 0 times 17417224 (96.25%) aligned exactly 1 time 597550 (3.30%) aligned >1 times 99.55% overall alignment rate Time searching: 00:03:55 Overall time: 00:03:55 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] 1530 / 18014774 = 0.0001 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 23:52:59: # Command line: callpeak -t SRX858995.bam -f BAM -g dm -n SRX858995.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX858995.20 # format = BAM # ChIP-seq file = ['SRX858995.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 23:52:59: #1 read tag files... INFO @ Sat, 03 Jun 2017 23:52:59: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 23:52:59: # Command line: callpeak -t SRX858995.bam -f BAM -g dm -n SRX858995.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX858995.10 # format = BAM # ChIP-seq file = ['SRX858995.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 23:52:59: #1 read tag files... INFO @ Sat, 03 Jun 2017 23:52:59: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 23:52:59: # Command line: callpeak -t SRX858995.bam -f BAM -g dm -n SRX858995.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX858995.05 # format = BAM # ChIP-seq file = ['SRX858995.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 23:52:59: #1 read tag files... INFO @ Sat, 03 Jun 2017 23:52:59: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 23:53:05: 1000000 INFO @ Sat, 03 Jun 2017 23:53:07: 1000000 INFO @ Sat, 03 Jun 2017 23:53:07: 1000000 INFO @ Sat, 03 Jun 2017 23:53:12: 2000000 INFO @ Sat, 03 Jun 2017 23:53:16: 2000000 INFO @ Sat, 03 Jun 2017 23:53:16: 2000000 INFO @ Sat, 03 Jun 2017 23:53:19: 3000000 INFO @ Sat, 03 Jun 2017 23:53:24: 3000000 INFO @ Sat, 03 Jun 2017 23:53:24: 3000000 INFO @ Sat, 03 Jun 2017 23:53:25: 4000000 INFO @ Sat, 03 Jun 2017 23:53:32: 5000000 INFO @ Sat, 03 Jun 2017 23:53:32: 4000000 INFO @ Sat, 03 Jun 2017 23:53:32: 4000000 INFO @ Sat, 03 Jun 2017 23:53:37: 6000000 INFO @ Sat, 03 Jun 2017 23:53:39: 5000000 INFO @ Sat, 03 Jun 2017 23:53:39: 5000000 INFO @ Sat, 03 Jun 2017 23:53:43: 7000000 INFO @ Sat, 03 Jun 2017 23:53:45: 6000000 INFO @ Sat, 03 Jun 2017 23:53:45: 6000000 INFO @ Sat, 03 Jun 2017 23:53:49: 8000000 INFO @ Sat, 03 Jun 2017 23:53:52: 7000000 INFO @ Sat, 03 Jun 2017 23:53:52: 7000000 INFO @ Sat, 03 Jun 2017 23:53:54: 9000000 INFO @ Sat, 03 Jun 2017 23:53:59: 8000000 INFO @ Sat, 03 Jun 2017 23:53:59: 8000000 INFO @ Sat, 03 Jun 2017 23:54:00: 10000000 INFO @ Sat, 03 Jun 2017 23:54:05: 11000000 INFO @ Sat, 03 Jun 2017 23:54:06: 9000000 INFO @ Sat, 03 Jun 2017 23:54:06: 9000000 INFO @ Sat, 03 Jun 2017 23:54:11: 12000000 INFO @ Sat, 03 Jun 2017 23:54:13: 10000000 INFO @ Sat, 03 Jun 2017 23:54:13: 10000000 INFO @ Sat, 03 Jun 2017 23:54:17: 13000000 INFO @ Sat, 03 Jun 2017 23:54:20: 11000000 INFO @ Sat, 03 Jun 2017 23:54:20: 11000000 INFO @ Sat, 03 Jun 2017 23:54:23: 14000000 INFO @ Sat, 03 Jun 2017 23:54:27: 12000000 INFO @ Sat, 03 Jun 2017 23:54:27: 12000000 INFO @ Sat, 03 Jun 2017 23:54:28: 15000000 INFO @ Sat, 03 Jun 2017 23:54:34: 13000000 INFO @ Sat, 03 Jun 2017 23:54:34: 13000000 INFO @ Sat, 03 Jun 2017 23:54:34: 16000000 INFO @ Sat, 03 Jun 2017 23:54:40: 17000000 INFO @ Sat, 03 Jun 2017 23:54:41: 14000000 INFO @ Sat, 03 Jun 2017 23:54:41: 14000000 INFO @ Sat, 03 Jun 2017 23:54:45: 18000000 INFO @ Sat, 03 Jun 2017 23:54:46: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 23:54:46: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 23:54:46: #1 total tags in treatment: 18013244 INFO @ Sat, 03 Jun 2017 23:54:46: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 23:54:46: #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 23:54:48: 15000000 INFO @ Sat, 03 Jun 2017 23:54:48: 15000000 INFO @ Sat, 03 Jun 2017 23:54:49: #1 tags after filtering in treatment: 18012864 INFO @ Sat, 03 Jun 2017 23:54:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 23:54:49: #1 finished! INFO @ Sat, 03 Jun 2017 23:54:49: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 23:54:53: #2 number of paired peaks: 3450 INFO @ Sat, 03 Jun 2017 23:54:53: start model_add_line... INFO @ Sat, 03 Jun 2017 23:54:55: 16000000 INFO @ Sat, 03 Jun 2017 23:54:55: 16000000 INFO @ Sat, 03 Jun 2017 23:55:02: 17000000 INFO @ Sat, 03 Jun 2017 23:55:02: 17000000 INFO @ Sat, 03 Jun 2017 23:55:08: 18000000 INFO @ Sat, 03 Jun 2017 23:55:08: 18000000 INFO @ Sat, 03 Jun 2017 23:55:09: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 23:55:09: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 23:55:09: #1 total tags in treatment: 18013244 INFO @ Sat, 03 Jun 2017 23:55:09: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 23:55:09: #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 23:55:09: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 23:55:09: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 23:55:09: #1 total tags in treatment: 18013244 INFO @ Sat, 03 Jun 2017 23:55:09: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 23:55:09: #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 23:55:12: #1 tags after filtering in treatment: 18012864 INFO @ Sat, 03 Jun 2017 23:55:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 23:55:12: #1 finished! INFO @ Sat, 03 Jun 2017 23:55:12: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 23:55:12: #1 tags after filtering in treatment: 18012864 INFO @ Sat, 03 Jun 2017 23:55:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 23:55:12: #1 finished! INFO @ Sat, 03 Jun 2017 23:55:12: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 23:55:16: #2 number of paired peaks: 3450 INFO @ Sat, 03 Jun 2017 23:55:16: start model_add_line... INFO @ Sat, 03 Jun 2017 23:55:16: #2 number of paired peaks: 3450 INFO @ Sat, 03 Jun 2017 23:55:16: start model_add_line... INFO @ Sat, 03 Jun 2017 23:55:33: start X-correlation... INFO @ Sat, 03 Jun 2017 23:55:33: end of X-cor INFO @ Sat, 03 Jun 2017 23:55:33: #2 finished! INFO @ Sat, 03 Jun 2017 23:55:33: #2 predicted fragment length is 90 bps INFO @ Sat, 03 Jun 2017 23:55:33: #2 alternative fragment length(s) may be 90 bps INFO @ Sat, 03 Jun 2017 23:55:33: #2.2 Generate R script for model : SRX858995.10_model.r WARNING @ Sat, 03 Jun 2017 23:55:33: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 23:55:33: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Sat, 03 Jun 2017 23:55:33: #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 23:55:33: #3 Call peaks... INFO @ Sat, 03 Jun 2017 23:55:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 23:55:57: start X-correlation... INFO @ Sat, 03 Jun 2017 23:55:57: end of X-cor INFO @ Sat, 03 Jun 2017 23:55:57: #2 finished! INFO @ Sat, 03 Jun 2017 23:55:57: #2 predicted fragment length is 90 bps INFO @ Sat, 03 Jun 2017 23:55:57: #2 alternative fragment length(s) may be 90 bps INFO @ Sat, 03 Jun 2017 23:55:57: #2.2 Generate R script for model : SRX858995.20_model.r WARNING @ Sat, 03 Jun 2017 23:55:57: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 23:55:57: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Sat, 03 Jun 2017 23:55:57: #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 23:55:57: #3 Call peaks... INFO @ Sat, 03 Jun 2017 23:55:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 23:55:57: start X-correlation... INFO @ Sat, 03 Jun 2017 23:55:57: end of X-cor INFO @ Sat, 03 Jun 2017 23:55:57: #2 finished! INFO @ Sat, 03 Jun 2017 23:55:57: #2 predicted fragment length is 90 bps INFO @ Sat, 03 Jun 2017 23:55:57: #2 alternative fragment length(s) may be 90 bps INFO @ Sat, 03 Jun 2017 23:55:57: #2.2 Generate R script for model : SRX858995.05_model.r WARNING @ Sat, 03 Jun 2017 23:55:57: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 23:55:57: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Sat, 03 Jun 2017 23:55:57: #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 23:55:57: #3 Call peaks... INFO @ Sat, 03 Jun 2017 23:55:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 23:57:03: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 23:57:24: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 23:57:29: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 23:58:20: #4 Write output xls file... SRX858995.10_peaks.xls INFO @ Sat, 03 Jun 2017 23:58:20: #4 Write peak in narrowPeak format file... SRX858995.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 23:58:20: #4 Write summits bed file... SRX858995.10_summits.bed INFO @ Sat, 03 Jun 2017 23:58:20: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10914 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 23:58:30: #4 Write output xls file... SRX858995.20_peaks.xls INFO @ Sat, 03 Jun 2017 23:58:31: #4 Write peak in narrowPeak format file... SRX858995.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 23:58:31: #4 Write summits bed file... SRX858995.20_summits.bed INFO @ Sat, 03 Jun 2017 23:58:31: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6831 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 23:58:53: #4 Write output xls file... SRX858995.05_peaks.xls INFO @ Sat, 03 Jun 2017 23:58:53: #4 Write peak in narrowPeak format file... SRX858995.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 23:58:53: #4 Write summits bed file... SRX858995.05_summits.bed INFO @ Sat, 03 Jun 2017 23:58:53: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (14641 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。