Job ID = 8696840 sra ファイルのダウンロード中... Completed: 886867K bytes transferred in 21 seconds (340597K 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 1046 0 --:--:-- 0:00:07 --:--:-- 9926 100 26919 0 26919 0 0 3284 0 --:--:-- 0:00:08 --:--:-- 16384 100 31436 0 31436 0 0 3679 0 --:--:-- 0:00:08 --:--:-- 15781 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 31612277 spots for /home/okishinya/chipatlas/results/dm3/SRX110778/SRR388360.sra Written 31612277 spots total rm: cannot remove `[DSE]RR*.fastq': No such file or directory 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:00 31612277 reads; of these: 31612277 (100.00%) were unpaired; of these: 16199487 (51.24%) aligned 0 times 13018893 (41.18%) aligned exactly 1 time 2393897 (7.57%) aligned >1 times 48.76% overall alignment rate Time searching: 00:11:01 Overall time: 00:11:01 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_rmdupse_core] 3129323 / 15412790 = 0.2030 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 @ Fri, 10 Mar 2017 12:26:25: # Command line: callpeak -t SRX110778.bam -f BAM -g dm -n SRX110778.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX110778.20 # format = BAM # ChIP-seq file = ['SRX110778.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 @ Fri, 10 Mar 2017 12:26:25: # Command line: callpeak -t SRX110778.bam -f BAM -g dm -n SRX110778.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX110778.05 # format = BAM # ChIP-seq file = ['SRX110778.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 @ Fri, 10 Mar 2017 12:26:25: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:26:25: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:26:25: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:26:25: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:26:25: # Command line: callpeak -t SRX110778.bam -f BAM -g dm -n SRX110778.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX110778.10 # format = BAM # ChIP-seq file = ['SRX110778.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 @ Fri, 10 Mar 2017 12:26:25: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:26:25: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:26:32: 1000000 INFO @ Fri, 10 Mar 2017 12:26:39: 1000000 INFO @ Fri, 10 Mar 2017 12:26:39: 2000000 INFO @ Fri, 10 Mar 2017 12:26:43: 1000000 INFO @ Fri, 10 Mar 2017 12:26:46: 3000000 INFO @ Fri, 10 Mar 2017 12:26:53: 4000000 INFO @ Fri, 10 Mar 2017 12:26:53: 2000000 INFO @ Fri, 10 Mar 2017 12:26:57: 2000000 INFO @ Fri, 10 Mar 2017 12:27:00: 5000000 INFO @ Fri, 10 Mar 2017 12:27:07: 6000000 INFO @ Fri, 10 Mar 2017 12:27:08: 3000000 INFO @ Fri, 10 Mar 2017 12:27:09: 3000000 INFO @ Fri, 10 Mar 2017 12:27:14: 7000000 INFO @ Fri, 10 Mar 2017 12:27:25: 4000000 INFO @ Fri, 10 Mar 2017 12:27:27: 4000000 INFO @ Fri, 10 Mar 2017 12:27:27: 8000000 INFO @ Fri, 10 Mar 2017 12:27:45: 5000000 INFO @ Fri, 10 Mar 2017 12:27:48: 5000000 INFO @ Fri, 10 Mar 2017 12:27:50: 9000000 INFO @ Fri, 10 Mar 2017 12:28:05: 6000000 INFO @ Fri, 10 Mar 2017 12:28:07: 6000000 INFO @ Fri, 10 Mar 2017 12:28:13: 10000000 INFO @ Fri, 10 Mar 2017 12:28:26: 7000000 INFO @ Fri, 10 Mar 2017 12:28:31: 7000000 INFO @ Fri, 10 Mar 2017 12:28:37: 11000000 INFO @ Fri, 10 Mar 2017 12:28:48: 8000000 INFO @ Fri, 10 Mar 2017 12:28:56: 8000000 INFO @ Fri, 10 Mar 2017 12:29:02: 12000000 INFO @ Fri, 10 Mar 2017 12:29:08: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 12:29:08: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 12:29:08: #1 total tags in treatment: 12283467 INFO @ Fri, 10 Mar 2017 12:29:08: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:29:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:29:10: 9000000 INFO @ Fri, 10 Mar 2017 12:29:11: #1 tags after filtering in treatment: 12281983 INFO @ Fri, 10 Mar 2017 12:29:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:29:11: #1 finished! INFO @ Fri, 10 Mar 2017 12:29:11: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:29:14: #2 number of paired peaks: 1564 INFO @ Fri, 10 Mar 2017 12:29:14: start model_add_line... INFO @ Fri, 10 Mar 2017 12:29:20: 9000000 INFO @ Fri, 10 Mar 2017 12:29:30: start X-correlation... INFO @ Fri, 10 Mar 2017 12:29:30: end of X-cor INFO @ Fri, 10 Mar 2017 12:29:30: #2 finished! INFO @ Fri, 10 Mar 2017 12:29:30: #2 predicted fragment length is 72 bps INFO @ Fri, 10 Mar 2017 12:29:30: #2 alternative fragment length(s) may be 4,72 bps INFO @ Fri, 10 Mar 2017 12:29:30: #2.2 Generate R script for model : SRX110778.05_model.r WARNING @ Fri, 10 Mar 2017 12:29:30: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Mar 2017 12:29:30: #2 You may need to consider one of the other alternative d(s): 4,72 WARNING @ Fri, 10 Mar 2017 12:29:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Mar 2017 12:29:30: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:29:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:29:30: 10000000 INFO @ Fri, 10 Mar 2017 12:29:41: 10000000 INFO @ Fri, 10 Mar 2017 12:29:51: 11000000 INFO @ Fri, 10 Mar 2017 12:30:03: 11000000 INFO @ Fri, 10 Mar 2017 12:30:11: 12000000 INFO @ Fri, 10 Mar 2017 12:30:17: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 12:30:17: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 12:30:17: #1 total tags in treatment: 12283467 INFO @ Fri, 10 Mar 2017 12:30:17: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:30:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:30:20: #1 tags after filtering in treatment: 12281983 INFO @ Fri, 10 Mar 2017 12:30:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:30:20: #1 finished! INFO @ Fri, 10 Mar 2017 12:30:20: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:30:23: #2 number of paired peaks: 1564 INFO @ Fri, 10 Mar 2017 12:30:23: start model_add_line... INFO @ Fri, 10 Mar 2017 12:30:24: 12000000 INFO @ Fri, 10 Mar 2017 12:30:30: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 12:30:30: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 12:30:30: #1 total tags in treatment: 12283467 INFO @ Fri, 10 Mar 2017 12:30:30: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:30:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:30:33: #1 tags after filtering in treatment: 12281983 INFO @ Fri, 10 Mar 2017 12:30:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:30:33: #1 finished! INFO @ Fri, 10 Mar 2017 12:30:33: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:30:36: #2 number of paired peaks: 1564 INFO @ Fri, 10 Mar 2017 12:30:36: start model_add_line... INFO @ Fri, 10 Mar 2017 12:30:38: start X-correlation... INFO @ Fri, 10 Mar 2017 12:30:38: end of X-cor INFO @ Fri, 10 Mar 2017 12:30:38: #2 finished! INFO @ Fri, 10 Mar 2017 12:30:38: #2 predicted fragment length is 72 bps INFO @ Fri, 10 Mar 2017 12:30:38: #2 alternative fragment length(s) may be 4,72 bps INFO @ Fri, 10 Mar 2017 12:30:38: #2.2 Generate R script for model : SRX110778.10_model.r WARNING @ Fri, 10 Mar 2017 12:30:38: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Mar 2017 12:30:38: #2 You may need to consider one of the other alternative d(s): 4,72 WARNING @ Fri, 10 Mar 2017 12:30:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Mar 2017 12:30:38: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:30:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:30:48: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:30:52: start X-correlation... INFO @ Fri, 10 Mar 2017 12:30:52: end of X-cor INFO @ Fri, 10 Mar 2017 12:30:52: #2 finished! INFO @ Fri, 10 Mar 2017 12:30:52: #2 predicted fragment length is 72 bps INFO @ Fri, 10 Mar 2017 12:30:52: #2 alternative fragment length(s) may be 4,72 bps INFO @ Fri, 10 Mar 2017 12:30:52: #2.2 Generate R script for model : SRX110778.20_model.r WARNING @ Fri, 10 Mar 2017 12:30:52: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Mar 2017 12:30:52: #2 You may need to consider one of the other alternative d(s): 4,72 WARNING @ Fri, 10 Mar 2017 12:30:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Mar 2017 12:30:52: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:30:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:31:45: #4 Write output xls file... SRX110778.05_peaks.xls INFO @ Fri, 10 Mar 2017 12:31:45: #4 Write peak in narrowPeak format file... SRX110778.05_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:31:45: #4 Write summits bed file... SRX110778.05_summits.bed INFO @ Fri, 10 Mar 2017 12:31:45: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1503 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:31:58: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:32:11: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:32:57: #4 Write output xls file... SRX110778.10_peaks.xls INFO @ Fri, 10 Mar 2017 12:32:57: #4 Write peak in narrowPeak format file... SRX110778.10_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:32:57: #4 Write summits bed file... SRX110778.10_summits.bed INFO @ Fri, 10 Mar 2017 12:32:57: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (537 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:33:08: #4 Write output xls file... SRX110778.20_peaks.xls INFO @ Fri, 10 Mar 2017 12:33:08: #4 Write peak in narrowPeak format file... SRX110778.20_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:33:08: #4 Write summits bed file... SRX110778.20_summits.bed INFO @ Fri, 10 Mar 2017 12:33:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (161 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。