Job ID = 2162403 sra ファイルのダウンロード中... Completed: 508664K bytes transferred in 6 seconds (609019K 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 --:--:-- --:--:-- --:--:-- 0 100 35540 0 35540 0 0 47613 0 --:--:-- --:--:-- --:--:-- 64036 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 21362116 spots for /home/okishinya/chipatlas/results/dm3/SRX085400/SRR317178.sra Written 21362116 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: 00:05:59 21362116 reads; of these: 21362116 (100.00%) were unpaired; of these: 11329254 (53.03%) aligned 0 times 8484452 (39.72%) aligned exactly 1 time 1548410 (7.25%) aligned >1 times 46.97% overall alignment rate Time searching: 00:05:59 Overall time: 00:06:00 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] 5954391 / 10032862 = 0.5935 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 13:55:16: # Command line: callpeak -t SRX085400.bam -f BAM -g dm -n SRX085400.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX085400.20 # format = BAM # ChIP-seq file = ['SRX085400.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 13:55:16: # Command line: callpeak -t SRX085400.bam -f BAM -g dm -n SRX085400.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX085400.10 # format = BAM # ChIP-seq file = ['SRX085400.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 13:55:16: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:55:16: # Command line: callpeak -t SRX085400.bam -f BAM -g dm -n SRX085400.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX085400.05 # format = BAM # ChIP-seq file = ['SRX085400.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 13:55:16: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:55:16: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:55:16: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:55:16: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:55:16: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:55:22: 1000000 INFO @ Tue, 21 Apr 2015 13:55:22: 1000000 INFO @ Tue, 21 Apr 2015 13:55:22: 1000000 INFO @ Tue, 21 Apr 2015 13:55:27: 2000000 INFO @ Tue, 21 Apr 2015 13:55:28: 2000000 INFO @ Tue, 21 Apr 2015 13:55:28: 2000000 INFO @ Tue, 21 Apr 2015 13:55:33: 3000000 INFO @ Tue, 21 Apr 2015 13:55:34: 3000000 INFO @ Tue, 21 Apr 2015 13:55:34: 3000000 INFO @ Tue, 21 Apr 2015 13:55:38: 4000000 INFO @ Tue, 21 Apr 2015 13:55:38: #1 tag size is determined as 54 bps INFO @ Tue, 21 Apr 2015 13:55:38: #1 tag size = 54 INFO @ Tue, 21 Apr 2015 13:55:38: #1 total tags in treatment: 4078471 INFO @ Tue, 21 Apr 2015 13:55:38: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:55:38: #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 13:55:39: #1 tags after filtering in treatment: 4002660 INFO @ Tue, 21 Apr 2015 13:55:39: #1 Redundant rate of treatment: 0.02 INFO @ Tue, 21 Apr 2015 13:55:39: #1 finished! INFO @ Tue, 21 Apr 2015 13:55:39: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:55:40: 4000000 INFO @ Tue, 21 Apr 2015 13:55:40: 4000000 INFO @ Tue, 21 Apr 2015 13:55:40: #1 tag size is determined as 54 bps INFO @ Tue, 21 Apr 2015 13:55:40: #1 tag size = 54 INFO @ Tue, 21 Apr 2015 13:55:40: #1 total tags in treatment: 4078471 INFO @ Tue, 21 Apr 2015 13:55:40: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:55:40: #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 13:55:40: #1 tag size is determined as 54 bps INFO @ Tue, 21 Apr 2015 13:55:40: #1 tag size = 54 INFO @ Tue, 21 Apr 2015 13:55:40: #1 total tags in treatment: 4078471 INFO @ Tue, 21 Apr 2015 13:55:40: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:55:40: #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 13:55:41: #2 number of paired peaks: 4936 INFO @ Tue, 21 Apr 2015 13:55:41: start model_add_line... INFO @ Tue, 21 Apr 2015 13:55:41: #1 tags after filtering in treatment: 4002660 INFO @ Tue, 21 Apr 2015 13:55:41: #1 Redundant rate of treatment: 0.02 INFO @ Tue, 21 Apr 2015 13:55:41: #1 finished! INFO @ Tue, 21 Apr 2015 13:55:41: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:55:41: #1 tags after filtering in treatment: 4002660 INFO @ Tue, 21 Apr 2015 13:55:41: #1 Redundant rate of treatment: 0.02 INFO @ Tue, 21 Apr 2015 13:55:41: #1 finished! INFO @ Tue, 21 Apr 2015 13:55:41: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:55:42: #2 number of paired peaks: 4936 INFO @ Tue, 21 Apr 2015 13:55:42: start model_add_line... INFO @ Tue, 21 Apr 2015 13:55:42: #2 number of paired peaks: 4936 INFO @ Tue, 21 Apr 2015 13:55:42: start model_add_line... INFO @ Tue, 21 Apr 2015 13:55:55: start X-correlation... INFO @ Tue, 21 Apr 2015 13:55:55: end of X-cor INFO @ Tue, 21 Apr 2015 13:55:55: #2 finished! INFO @ Tue, 21 Apr 2015 13:55:55: #2 predicted fragment length is 58 bps INFO @ Tue, 21 Apr 2015 13:55:55: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 21 Apr 2015 13:55:55: #2.2 Generate R script for model : SRX085400.20_model.r WARNING @ Tue, 21 Apr 2015 13:55:55: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:55:55: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 21 Apr 2015 13:55:55: #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 13:55:55: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:55:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:55:56: start X-correlation... INFO @ Tue, 21 Apr 2015 13:55:56: start X-correlation... INFO @ Tue, 21 Apr 2015 13:55:56: end of X-cor INFO @ Tue, 21 Apr 2015 13:55:56: #2 finished! INFO @ Tue, 21 Apr 2015 13:55:56: #2 predicted fragment length is 58 bps INFO @ Tue, 21 Apr 2015 13:55:56: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 21 Apr 2015 13:55:56: #2.2 Generate R script for model : SRX085400.10_model.r INFO @ Tue, 21 Apr 2015 13:55:56: end of X-cor INFO @ Tue, 21 Apr 2015 13:55:56: #2 finished! INFO @ Tue, 21 Apr 2015 13:55:56: #2 predicted fragment length is 58 bps INFO @ Tue, 21 Apr 2015 13:55:56: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 21 Apr 2015 13:55:56: #2.2 Generate R script for model : SRX085400.05_model.r WARNING @ Tue, 21 Apr 2015 13:55:56: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:55:56: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 21 Apr 2015 13:55:56: #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 13:55:56: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:55:56: #3 Pre-compute pvalue-qvalue table... WARNING @ Tue, 21 Apr 2015 13:55:56: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:55:56: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 21 Apr 2015 13:55:56: #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 13:55:56: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:55:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:56:17: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:56:19: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:56:19: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:56:37: #4 Write output xls file... SRX085400.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:56:37: #4 Write peak in narrowPeak format file... SRX085400.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:56:37: #4 Write summits bed file... SRX085400.20_summits.bed INFO @ Tue, 21 Apr 2015 13:56:37: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (5849 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:56:38: #4 Write output xls file... SRX085400.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:56:39: #4 Write peak in narrowPeak format file... SRX085400.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:56:39: #4 Write summits bed file... SRX085400.10_summits.bed INFO @ Tue, 21 Apr 2015 13:56:39: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8661 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:56:40: #4 Write output xls file... SRX085400.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:56:40: #4 Write peak in narrowPeak format file... SRX085400.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:56:40: #4 Write summits bed file... SRX085400.05_summits.bed INFO @ Tue, 21 Apr 2015 13:56:40: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10957 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。