Job ID = 2161417 sra ファイルのダウンロード中... Completed: 356157K bytes transferred in 5 seconds (487591K 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 --:--:-- --:--:-- --:--:-- 0 101 5467 0 5467 0 0 9309 0 --:--:-- --:--:-- --:--:-- 13770 100 44506 0 44506 0 0 46035 0 --:--:-- --:--:-- --:--:-- 57353 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 23608065 spots for /home/okishinya/chipatlas/results/dm3/SRX025490/SRR063896.sra Written 23608065 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: 00:12:29 23608065 reads; of these: 23608065 (100.00%) were unpaired; of these: 1063599 (4.51%) aligned 0 times 13744648 (58.22%) aligned exactly 1 time 8799818 (37.27%) aligned >1 times 95.49% overall alignment rate Time searching: 00:12:29 Overall time: 00:12:29 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] 14475762 / 22544466 = 0.6421 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 12:52:01: # Command line: callpeak -t SRX025490.bam -f BAM -g dm -n SRX025490.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX025490.20 # format = BAM # ChIP-seq file = ['SRX025490.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 12:52:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:52:01: # Command line: callpeak -t SRX025490.bam -f BAM -g dm -n SRX025490.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX025490.10 # format = BAM # ChIP-seq file = ['SRX025490.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 12:52:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:52:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:52:01: # Command line: callpeak -t SRX025490.bam -f BAM -g dm -n SRX025490.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX025490.05 # format = BAM # ChIP-seq file = ['SRX025490.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 12:52:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:52:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:52:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:52:06: 1000000 INFO @ Tue, 21 Apr 2015 12:52:06: 1000000 INFO @ Tue, 21 Apr 2015 12:52:06: 1000000 INFO @ Tue, 21 Apr 2015 12:52:11: 2000000 INFO @ Tue, 21 Apr 2015 12:52:11: 2000000 INFO @ Tue, 21 Apr 2015 12:52:11: 2000000 INFO @ Tue, 21 Apr 2015 12:52:16: 3000000 INFO @ Tue, 21 Apr 2015 12:52:16: 3000000 INFO @ Tue, 21 Apr 2015 12:52:17: 3000000 INFO @ Tue, 21 Apr 2015 12:52:21: 4000000 INFO @ Tue, 21 Apr 2015 12:52:21: 4000000 INFO @ Tue, 21 Apr 2015 12:52:22: 4000000 INFO @ Tue, 21 Apr 2015 12:52:26: 5000000 INFO @ Tue, 21 Apr 2015 12:52:26: 5000000 INFO @ Tue, 21 Apr 2015 12:52:27: 5000000 INFO @ Tue, 21 Apr 2015 12:52:31: 6000000 INFO @ Tue, 21 Apr 2015 12:52:31: 6000000 INFO @ Tue, 21 Apr 2015 12:52:33: 6000000 INFO @ Tue, 21 Apr 2015 12:52:35: 7000000 INFO @ Tue, 21 Apr 2015 12:52:36: 7000000 INFO @ Tue, 21 Apr 2015 12:52:38: 7000000 INFO @ Tue, 21 Apr 2015 12:52:40: 8000000 INFO @ Tue, 21 Apr 2015 12:52:41: 8000000 INFO @ Tue, 21 Apr 2015 12:52:41: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:52:41: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:52:41: #1 total tags in treatment: 8068704 INFO @ Tue, 21 Apr 2015 12:52:41: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:52:41: #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 12:52:41: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:52:41: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:52:41: #1 total tags in treatment: 8068704 INFO @ Tue, 21 Apr 2015 12:52:41: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:52:41: #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 12:52:42: #1 tags after filtering in treatment: 8067325 INFO @ Tue, 21 Apr 2015 12:52:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:52:42: #1 finished! INFO @ Tue, 21 Apr 2015 12:52:42: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:52:43: #1 tags after filtering in treatment: 8067325 INFO @ Tue, 21 Apr 2015 12:52:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:52:43: #1 finished! INFO @ Tue, 21 Apr 2015 12:52:43: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:52:43: 8000000 INFO @ Tue, 21 Apr 2015 12:52:44: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:52:44: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:52:44: #1 total tags in treatment: 8068704 INFO @ Tue, 21 Apr 2015 12:52:44: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:52:44: #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 12:52:44: #2 number of paired peaks: 1030 INFO @ Tue, 21 Apr 2015 12:52:44: start model_add_line... INFO @ Tue, 21 Apr 2015 12:52:44: #2 number of paired peaks: 1030 INFO @ Tue, 21 Apr 2015 12:52:44: start model_add_line... INFO @ Tue, 21 Apr 2015 12:52:45: #1 tags after filtering in treatment: 8067325 INFO @ Tue, 21 Apr 2015 12:52:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:52:45: #1 finished! INFO @ Tue, 21 Apr 2015 12:52:45: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:52:47: #2 number of paired peaks: 1030 INFO @ Tue, 21 Apr 2015 12:52:47: start model_add_line... INFO @ Tue, 21 Apr 2015 12:52:51: start X-correlation... INFO @ Tue, 21 Apr 2015 12:52:51: end of X-cor INFO @ Tue, 21 Apr 2015 12:52:51: #2 finished! INFO @ Tue, 21 Apr 2015 12:52:51: #2 predicted fragment length is 35 bps INFO @ Tue, 21 Apr 2015 12:52:51: #2 alternative fragment length(s) may be 35 bps INFO @ Tue, 21 Apr 2015 12:52:51: #2.2 Generate R script for model : SRX025490.10_model.r WARNING @ Tue, 21 Apr 2015 12:52:51: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:52:51: #2 You may need to consider one of the other alternative d(s): 35 WARNING @ Tue, 21 Apr 2015 12:52:51: #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 12:52:51: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:52:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:52:51: start X-correlation... INFO @ Tue, 21 Apr 2015 12:52:51: end of X-cor INFO @ Tue, 21 Apr 2015 12:52:51: #2 finished! INFO @ Tue, 21 Apr 2015 12:52:51: #2 predicted fragment length is 35 bps INFO @ Tue, 21 Apr 2015 12:52:51: #2 alternative fragment length(s) may be 35 bps INFO @ Tue, 21 Apr 2015 12:52:51: #2.2 Generate R script for model : SRX025490.05_model.r WARNING @ Tue, 21 Apr 2015 12:52:51: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:52:51: #2 You may need to consider one of the other alternative d(s): 35 WARNING @ Tue, 21 Apr 2015 12:52:51: #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 12:52:51: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:52:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:52:54: start X-correlation... INFO @ Tue, 21 Apr 2015 12:52:54: end of X-cor INFO @ Tue, 21 Apr 2015 12:52:54: #2 finished! INFO @ Tue, 21 Apr 2015 12:52:54: #2 predicted fragment length is 35 bps INFO @ Tue, 21 Apr 2015 12:52:54: #2 alternative fragment length(s) may be 35 bps INFO @ Tue, 21 Apr 2015 12:52:54: #2.2 Generate R script for model : SRX025490.20_model.r WARNING @ Tue, 21 Apr 2015 12:52:54: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:52:54: #2 You may need to consider one of the other alternative d(s): 35 WARNING @ Tue, 21 Apr 2015 12:52:54: #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 12:52:54: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:52:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:53:34: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:53:35: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:53:38: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:54:06: #4 Write output xls file... SRX025490.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:54:06: #4 Write peak in narrowPeak format file... SRX025490.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:54:06: #4 Write summits bed file... SRX025490.10_summits.bed INFO @ Tue, 21 Apr 2015 12:54:06: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1813 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:54:07: #4 Write output xls file... SRX025490.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:54:07: #4 Write peak in narrowPeak format file... SRX025490.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:54:07: #4 Write summits bed file... SRX025490.05_summits.bed INFO @ Tue, 21 Apr 2015 12:54:07: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2397 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:54:09: #4 Write output xls file... SRX025490.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:54:09: #4 Write peak in narrowPeak format file... SRX025490.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:54:09: #4 Write summits bed file... SRX025490.20_summits.bed INFO @ Tue, 21 Apr 2015 12:54:09: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (1175 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。