Job ID = 8696834 sra ファイルのダウンロード中... Completed: 385082K bytes transferred in 7 seconds (428055K 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 --:--:-- 0:00:07 --:--:-- 0 100 14581 0 14581 0 0 1872 0 --:--:-- 0:00:07 --:--:-- 12903 100 31498 0 31498 0 0 3790 0 --:--:-- 0:00:08 --:--:-- 19055 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 14101314 spots for /home/okishinya/chipatlas/results/dm3/SRX110772/SRR388354.sra Written 14101314 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: 00:08:58 14101314 reads; of these: 14101314 (100.00%) were unpaired; of these: 1621084 (11.50%) aligned 0 times 9487397 (67.28%) aligned exactly 1 time 2992833 (21.22%) aligned >1 times 88.50% overall alignment rate Time searching: 00:08:58 Overall time: 00:08:58 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] 2979653 / 12480230 = 0.2387 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 12:12:50: # Command line: callpeak -t SRX110772.bam -f BAM -g dm -n SRX110772.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX110772.05 # format = BAM # ChIP-seq file = ['SRX110772.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 12:12:50: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:12:50: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:12:50: # Command line: callpeak -t SRX110772.bam -f BAM -g dm -n SRX110772.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX110772.10 # format = BAM # ChIP-seq file = ['SRX110772.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 12:12:50: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:12:50: # Command line: callpeak -t SRX110772.bam -f BAM -g dm -n SRX110772.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX110772.20 # format = BAM # ChIP-seq file = ['SRX110772.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 12:12:50: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:12:50: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:12:50: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:12:57: 1000000 INFO @ Fri, 10 Mar 2017 12:12:57: 1000000 INFO @ Fri, 10 Mar 2017 12:12:57: 1000000 INFO @ Fri, 10 Mar 2017 12:13:05: 2000000 INFO @ Fri, 10 Mar 2017 12:13:05: 2000000 INFO @ Fri, 10 Mar 2017 12:13:05: 2000000 INFO @ Fri, 10 Mar 2017 12:13:12: 3000000 INFO @ Fri, 10 Mar 2017 12:13:12: 3000000 INFO @ Fri, 10 Mar 2017 12:13:12: 3000000 INFO @ Fri, 10 Mar 2017 12:13:20: 4000000 INFO @ Fri, 10 Mar 2017 12:13:20: 4000000 INFO @ Fri, 10 Mar 2017 12:13:20: 4000000 INFO @ Fri, 10 Mar 2017 12:13:31: 5000000 INFO @ Fri, 10 Mar 2017 12:13:31: 5000000 INFO @ Fri, 10 Mar 2017 12:13:31: 5000000 INFO @ Fri, 10 Mar 2017 12:13:39: 6000000 INFO @ Fri, 10 Mar 2017 12:13:39: 6000000 INFO @ Fri, 10 Mar 2017 12:13:39: 6000000 INFO @ Fri, 10 Mar 2017 12:13:47: 7000000 INFO @ Fri, 10 Mar 2017 12:13:47: 7000000 INFO @ Fri, 10 Mar 2017 12:13:48: 7000000 INFO @ Fri, 10 Mar 2017 12:13:57: 8000000 INFO @ Fri, 10 Mar 2017 12:13:57: 8000000 INFO @ Fri, 10 Mar 2017 12:13:57: 8000000 INFO @ Fri, 10 Mar 2017 12:14:04: 9000000 INFO @ Fri, 10 Mar 2017 12:14:04: 9000000 INFO @ Fri, 10 Mar 2017 12:14:06: 9000000 INFO @ Fri, 10 Mar 2017 12:14:08: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 12:14:08: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 12:14:08: #1 total tags in treatment: 9500577 INFO @ Fri, 10 Mar 2017 12:14:08: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:14:08: #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 12:14:08: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 12:14:08: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 12:14:08: #1 total tags in treatment: 9500577 INFO @ Fri, 10 Mar 2017 12:14:08: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:14:08: #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 12:14:10: #1 tags after filtering in treatment: 9497571 INFO @ Fri, 10 Mar 2017 12:14:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:14:10: #1 finished! INFO @ Fri, 10 Mar 2017 12:14:10: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:14:10: #1 tags after filtering in treatment: 9497571 INFO @ Fri, 10 Mar 2017 12:14:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:14:10: #1 finished! INFO @ Fri, 10 Mar 2017 12:14:10: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:14:11: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 12:14:11: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 12:14:11: #1 total tags in treatment: 9500577 INFO @ Fri, 10 Mar 2017 12:14:11: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:14:11: #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 12:14:13: #1 tags after filtering in treatment: 9497571 INFO @ Fri, 10 Mar 2017 12:14:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:14:13: #1 finished! INFO @ Fri, 10 Mar 2017 12:14:13: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:14:13: #2 number of paired peaks: 3928 INFO @ Fri, 10 Mar 2017 12:14:13: start model_add_line... INFO @ Fri, 10 Mar 2017 12:14:13: #2 number of paired peaks: 3928 INFO @ Fri, 10 Mar 2017 12:14:13: start model_add_line... INFO @ Fri, 10 Mar 2017 12:14:16: #2 number of paired peaks: 3928 INFO @ Fri, 10 Mar 2017 12:14:16: start model_add_line... INFO @ Fri, 10 Mar 2017 12:14:48: start X-correlation... INFO @ Fri, 10 Mar 2017 12:14:48: end of X-cor INFO @ Fri, 10 Mar 2017 12:14:48: #2 finished! INFO @ Fri, 10 Mar 2017 12:14:48: #2 predicted fragment length is 76 bps INFO @ Fri, 10 Mar 2017 12:14:48: #2 alternative fragment length(s) may be 76 bps INFO @ Fri, 10 Mar 2017 12:14:48: #2.2 Generate R script for model : SRX110772.05_model.r WARNING @ Fri, 10 Mar 2017 12:14:48: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Mar 2017 12:14:48: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Fri, 10 Mar 2017 12:14:48: #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 12:14:48: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:14:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:14:48: start X-correlation... INFO @ Fri, 10 Mar 2017 12:14:48: end of X-cor INFO @ Fri, 10 Mar 2017 12:14:48: #2 finished! INFO @ Fri, 10 Mar 2017 12:14:48: #2 predicted fragment length is 76 bps INFO @ Fri, 10 Mar 2017 12:14:48: #2 alternative fragment length(s) may be 76 bps INFO @ Fri, 10 Mar 2017 12:14:48: #2.2 Generate R script for model : SRX110772.20_model.r WARNING @ Fri, 10 Mar 2017 12:14:48: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Mar 2017 12:14:48: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Fri, 10 Mar 2017 12:14:48: #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 12:14:48: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:14:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:14:50: start X-correlation... INFO @ Fri, 10 Mar 2017 12:14:50: end of X-cor INFO @ Fri, 10 Mar 2017 12:14:50: #2 finished! INFO @ Fri, 10 Mar 2017 12:14:50: #2 predicted fragment length is 76 bps INFO @ Fri, 10 Mar 2017 12:14:50: #2 alternative fragment length(s) may be 76 bps INFO @ Fri, 10 Mar 2017 12:14:50: #2.2 Generate R script for model : SRX110772.10_model.r WARNING @ Fri, 10 Mar 2017 12:14:50: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Mar 2017 12:14:50: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Fri, 10 Mar 2017 12:14:50: #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 12:14:50: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:14:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:15:54: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:15:54: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:16:00: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:16:44: #4 Write output xls file... SRX110772.10_peaks.xls INFO @ Fri, 10 Mar 2017 12:16:44: #4 Write peak in narrowPeak format file... SRX110772.10_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:16:44: #4 Write summits bed file... SRX110772.10_summits.bed INFO @ Fri, 10 Mar 2017 12:16:44: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5634 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:16:46: #4 Write output xls file... SRX110772.20_peaks.xls INFO @ Fri, 10 Mar 2017 12:16:46: #4 Write peak in narrowPeak format file... SRX110772.20_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:16:46: #4 Write summits bed file... SRX110772.20_summits.bed INFO @ Fri, 10 Mar 2017 12:16:46: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3672 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:16:58: #4 Write output xls file... SRX110772.05_peaks.xls INFO @ Fri, 10 Mar 2017 12:16:58: #4 Write peak in narrowPeak format file... SRX110772.05_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:16:58: #4 Write summits bed file... SRX110772.05_summits.bed INFO @ Fri, 10 Mar 2017 12:16:58: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (8185 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。