Job ID = 2161418 sra ファイルのダウンロード中... Completed: 458551K bytes transferred in 7 seconds (533717K bits/sec), in 2 files, 3 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 44495 0 44495 0 0 45447 0 --:--:-- --:--:-- --:--:-- 56465 100 44495 0 44495 0 0 45405 0 --:--:-- --:--:-- --:--:-- 56394 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 11783956 spots for /home/okishinya/chipatlas/results/dm3/SRX025491/SRR063894.sra Written 11783956 spots total Written 20760114 spots for /home/okishinya/chipatlas/results/dm3/SRX025491/SRR063895.sra Written 20760114 spots total 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: 00:31:09 32544070 reads; of these: 32544070 (100.00%) were unpaired; of these: 728661 (2.24%) aligned 0 times 6100910 (18.75%) aligned exactly 1 time 25714499 (79.01%) aligned >1 times 97.76% overall alignment rate Time searching: 00:31:09 Overall time: 00:31:09 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] 22153087 / 31815409 = 0.6963 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 @ Tue, 21 Apr 2015 13:12:09: # Command line: callpeak -t SRX025491.bam -f BAM -g dm -n SRX025491.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX025491.10 # format = BAM # ChIP-seq file = ['SRX025491.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 @ Tue, 21 Apr 2015 13:12:09: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:12:09: # Command line: callpeak -t SRX025491.bam -f BAM -g dm -n SRX025491.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX025491.20 # format = BAM # ChIP-seq file = ['SRX025491.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 @ Tue, 21 Apr 2015 13:12:09: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:12:09: # Command line: callpeak -t SRX025491.bam -f BAM -g dm -n SRX025491.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX025491.05 # format = BAM # ChIP-seq file = ['SRX025491.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 @ Tue, 21 Apr 2015 13:12:09: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:12:09: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:12:09: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:12:09: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:12:14: 1000000 INFO @ Tue, 21 Apr 2015 13:12:14: 1000000 INFO @ Tue, 21 Apr 2015 13:12:14: 1000000 INFO @ Tue, 21 Apr 2015 13:12:19: 2000000 INFO @ Tue, 21 Apr 2015 13:12:19: 2000000 INFO @ Tue, 21 Apr 2015 13:12:19: 2000000 INFO @ Tue, 21 Apr 2015 13:12:24: 3000000 INFO @ Tue, 21 Apr 2015 13:12:24: 3000000 INFO @ Tue, 21 Apr 2015 13:12:24: 3000000 INFO @ Tue, 21 Apr 2015 13:12:29: 4000000 INFO @ Tue, 21 Apr 2015 13:12:29: 4000000 INFO @ Tue, 21 Apr 2015 13:12:29: 4000000 INFO @ Tue, 21 Apr 2015 13:12:34: 5000000 INFO @ Tue, 21 Apr 2015 13:12:34: 5000000 INFO @ Tue, 21 Apr 2015 13:12:34: 5000000 INFO @ Tue, 21 Apr 2015 13:12:39: 6000000 INFO @ Tue, 21 Apr 2015 13:12:39: 6000000 INFO @ Tue, 21 Apr 2015 13:12:39: 6000000 INFO @ Tue, 21 Apr 2015 13:12:44: 7000000 INFO @ Tue, 21 Apr 2015 13:12:44: 7000000 INFO @ Tue, 21 Apr 2015 13:12:44: 7000000 INFO @ Tue, 21 Apr 2015 13:12:49: 8000000 INFO @ Tue, 21 Apr 2015 13:12:49: 8000000 INFO @ Tue, 21 Apr 2015 13:12:49: 8000000 INFO @ Tue, 21 Apr 2015 13:12:54: 9000000 INFO @ Tue, 21 Apr 2015 13:12:54: 9000000 INFO @ Tue, 21 Apr 2015 13:12:54: 9000000 INFO @ Tue, 21 Apr 2015 13:12:57: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:12:57: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:12:57: #1 total tags in treatment: 9662322 INFO @ Tue, 21 Apr 2015 13:12:57: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:12:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 13:12:58: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:12:58: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:12:58: #1 total tags in treatment: 9662322 INFO @ Tue, 21 Apr 2015 13:12:58: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:12:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 13:12:58: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:12:58: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:12:58: #1 total tags in treatment: 9662322 INFO @ Tue, 21 Apr 2015 13:12:58: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:12:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 13:12:59: #1 tags after filtering in treatment: 9660724 INFO @ Tue, 21 Apr 2015 13:12:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:12:59: #1 finished! INFO @ Tue, 21 Apr 2015 13:12:59: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:13:00: #1 tags after filtering in treatment: 9660724 INFO @ Tue, 21 Apr 2015 13:13:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:13:00: #1 finished! INFO @ Tue, 21 Apr 2015 13:13:00: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:13:00: #1 tags after filtering in treatment: 9660724 INFO @ Tue, 21 Apr 2015 13:13:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:13:00: #1 finished! INFO @ Tue, 21 Apr 2015 13:13:00: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:13:02: #2 number of paired peaks: 6591 INFO @ Tue, 21 Apr 2015 13:13:02: start model_add_line... INFO @ Tue, 21 Apr 2015 13:13:02: #2 number of paired peaks: 6591 INFO @ Tue, 21 Apr 2015 13:13:02: start model_add_line... INFO @ Tue, 21 Apr 2015 13:13:03: #2 number of paired peaks: 6591 INFO @ Tue, 21 Apr 2015 13:13:03: start model_add_line... INFO @ Tue, 21 Apr 2015 13:13:39: start X-correlation... INFO @ Tue, 21 Apr 2015 13:13:39: end of X-cor INFO @ Tue, 21 Apr 2015 13:13:39: #2 finished! INFO @ Tue, 21 Apr 2015 13:13:39: #2 predicted fragment length is 30 bps INFO @ Tue, 21 Apr 2015 13:13:39: #2 alternative fragment length(s) may be 30 bps INFO @ Tue, 21 Apr 2015 13:13:39: #2.2 Generate R script for model : SRX025491.05_model.r WARNING @ Tue, 21 Apr 2015 13:13:39: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:13:39: #2 You may need to consider one of the other alternative d(s): 30 WARNING @ Tue, 21 Apr 2015 13:13:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 13:13:39: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:13:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:13:41: start X-correlation... INFO @ Tue, 21 Apr 2015 13:13:41: end of X-cor INFO @ Tue, 21 Apr 2015 13:13:41: #2 finished! INFO @ Tue, 21 Apr 2015 13:13:41: #2 predicted fragment length is 30 bps INFO @ Tue, 21 Apr 2015 13:13:41: #2 alternative fragment length(s) may be 30 bps INFO @ Tue, 21 Apr 2015 13:13:41: #2.2 Generate R script for model : SRX025491.20_model.r WARNING @ Tue, 21 Apr 2015 13:13:41: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:13:41: #2 You may need to consider one of the other alternative d(s): 30 WARNING @ Tue, 21 Apr 2015 13:13:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 13:13:41: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:13:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:13:43: start X-correlation... INFO @ Tue, 21 Apr 2015 13:13:43: end of X-cor INFO @ Tue, 21 Apr 2015 13:13:43: #2 finished! INFO @ Tue, 21 Apr 2015 13:13:43: #2 predicted fragment length is 30 bps INFO @ Tue, 21 Apr 2015 13:13:43: #2 alternative fragment length(s) may be 30 bps INFO @ Tue, 21 Apr 2015 13:13:43: #2.2 Generate R script for model : SRX025491.10_model.r WARNING @ Tue, 21 Apr 2015 13:13:43: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:13:43: #2 You may need to consider one of the other alternative d(s): 30 WARNING @ Tue, 21 Apr 2015 13:13:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 13:13:43: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:13:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:14:24: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:14:28: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:14:35: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:15:01: #4 Write output xls file... SRX025491.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:15:01: #4 Write peak in narrowPeak format file... SRX025491.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:15:01: #4 Write summits bed file... SRX025491.20_summits.bed INFO @ Tue, 21 Apr 2015 13:15:01: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1347 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:15:03: #4 Write output xls file... SRX025491.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:15:03: #4 Write peak in narrowPeak format file... SRX025491.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:15:03: #4 Write summits bed file... SRX025491.05_summits.bed INFO @ Tue, 21 Apr 2015 13:15:03: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (16575 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:15:13: #4 Write output xls file... SRX025491.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:15:14: #4 Write peak in narrowPeak format file... SRX025491.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:15:14: #4 Write summits bed file... SRX025491.10_summits.bed INFO @ Tue, 21 Apr 2015 13:15:14: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4073 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。