Job ID = 2161938 sra ファイルのダウンロード中... Completed: 677487K bytes transferred in 10 seconds (531507K 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 45244 0 --:--:-- --:--:-- --:--:-- 59831 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 28664264 spots for /home/okishinya/chipatlas/results/dm3/SRX041410/SRR099153.sra Written 28664264 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: 00:11:00 28664264 reads; of these: 28664264 (100.00%) were unpaired; of these: 1717333 (5.99%) aligned 0 times 16675458 (58.18%) aligned exactly 1 time 10271473 (35.83%) aligned >1 times 94.01% overall alignment rate Time searching: 00:11:00 Overall time: 00:11:00 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] 9674670 / 26946931 = 0.3590 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 13:38:29: # Command line: callpeak -t SRX041410.bam -f BAM -g dm -n SRX041410.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX041410.10 # format = BAM # ChIP-seq file = ['SRX041410.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 13:38:29: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:38:29: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:38:29: # Command line: callpeak -t SRX041410.bam -f BAM -g dm -n SRX041410.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX041410.05 # format = BAM # ChIP-seq file = ['SRX041410.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 13:38:29: # Command line: callpeak -t SRX041410.bam -f BAM -g dm -n SRX041410.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX041410.20 # format = BAM # ChIP-seq file = ['SRX041410.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 13:38:29: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:38:29: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:38:29: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:38:29: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:38:35: 1000000 INFO @ Tue, 21 Apr 2015 13:38:35: 1000000 INFO @ Tue, 21 Apr 2015 13:38:35: 1000000 INFO @ Tue, 21 Apr 2015 13:38:41: 2000000 INFO @ Tue, 21 Apr 2015 13:38:41: 2000000 INFO @ Tue, 21 Apr 2015 13:38:41: 2000000 INFO @ Tue, 21 Apr 2015 13:38:46: 3000000 INFO @ Tue, 21 Apr 2015 13:38:47: 3000000 INFO @ Tue, 21 Apr 2015 13:38:48: 3000000 INFO @ Tue, 21 Apr 2015 13:38:53: 4000000 INFO @ Tue, 21 Apr 2015 13:38:53: 4000000 INFO @ Tue, 21 Apr 2015 13:38:55: 4000000 INFO @ Tue, 21 Apr 2015 13:38:59: 5000000 INFO @ Tue, 21 Apr 2015 13:38:59: 5000000 INFO @ Tue, 21 Apr 2015 13:39:02: 5000000 INFO @ Tue, 21 Apr 2015 13:39:06: 6000000 INFO @ Tue, 21 Apr 2015 13:39:06: 6000000 INFO @ Tue, 21 Apr 2015 13:39:10: 6000000 INFO @ Tue, 21 Apr 2015 13:39:13: 7000000 INFO @ Tue, 21 Apr 2015 13:39:14: 7000000 INFO @ Tue, 21 Apr 2015 13:39:18: 7000000 INFO @ Tue, 21 Apr 2015 13:39:20: 8000000 INFO @ Tue, 21 Apr 2015 13:39:22: 8000000 INFO @ Tue, 21 Apr 2015 13:39:26: 8000000 INFO @ Tue, 21 Apr 2015 13:39:27: 9000000 INFO @ Tue, 21 Apr 2015 13:39:30: 9000000 INFO @ Tue, 21 Apr 2015 13:39:34: 9000000 INFO @ Tue, 21 Apr 2015 13:39:34: 10000000 INFO @ Tue, 21 Apr 2015 13:39:37: 10000000 INFO @ Tue, 21 Apr 2015 13:39:41: 11000000 INFO @ Tue, 21 Apr 2015 13:39:42: 10000000 INFO @ Tue, 21 Apr 2015 13:39:45: 11000000 INFO @ Tue, 21 Apr 2015 13:39:49: 12000000 INFO @ Tue, 21 Apr 2015 13:39:50: 11000000 INFO @ Tue, 21 Apr 2015 13:39:53: 12000000 INFO @ Tue, 21 Apr 2015 13:39:56: 13000000 INFO @ Tue, 21 Apr 2015 13:39:58: 12000000 INFO @ Tue, 21 Apr 2015 13:40:01: 13000000 INFO @ Tue, 21 Apr 2015 13:40:03: 14000000 INFO @ Tue, 21 Apr 2015 13:40:06: 13000000 INFO @ Tue, 21 Apr 2015 13:40:09: 14000000 INFO @ Tue, 21 Apr 2015 13:40:10: 15000000 INFO @ Tue, 21 Apr 2015 13:40:14: 14000000 INFO @ Tue, 21 Apr 2015 13:40:17: 15000000 INFO @ Tue, 21 Apr 2015 13:40:17: 16000000 INFO @ Tue, 21 Apr 2015 13:40:22: 15000000 INFO @ Tue, 21 Apr 2015 13:40:25: 17000000 INFO @ Tue, 21 Apr 2015 13:40:25: 16000000 INFO @ Tue, 21 Apr 2015 13:40:27: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:40:27: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:40:27: #1 total tags in treatment: 17272261 INFO @ Tue, 21 Apr 2015 13:40:27: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:40:27: #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 13:40:29: 16000000 INFO @ Tue, 21 Apr 2015 13:40:30: #1 tags after filtering in treatment: 17265800 INFO @ Tue, 21 Apr 2015 13:40:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:40:30: #1 finished! INFO @ Tue, 21 Apr 2015 13:40:30: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:40:32: 17000000 INFO @ Tue, 21 Apr 2015 13:40:33: #2 number of paired peaks: 1137 INFO @ Tue, 21 Apr 2015 13:40:33: start model_add_line... INFO @ Tue, 21 Apr 2015 13:40:34: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:40:34: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:40:34: #1 total tags in treatment: 17272261 INFO @ Tue, 21 Apr 2015 13:40:34: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:40:34: #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 13:40:36: 17000000 INFO @ Tue, 21 Apr 2015 13:40:37: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:40:37: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:40:37: #1 total tags in treatment: 17272261 INFO @ Tue, 21 Apr 2015 13:40:37: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:40:37: #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 13:40:39: #1 tags after filtering in treatment: 17265800 INFO @ Tue, 21 Apr 2015 13:40:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:40:39: #1 finished! INFO @ Tue, 21 Apr 2015 13:40:39: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:40:41: #1 tags after filtering in treatment: 17265800 INFO @ Tue, 21 Apr 2015 13:40:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:40:41: #1 finished! INFO @ Tue, 21 Apr 2015 13:40:41: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:40:42: #2 number of paired peaks: 1137 INFO @ Tue, 21 Apr 2015 13:40:42: start model_add_line... INFO @ Tue, 21 Apr 2015 13:40:44: #2 number of paired peaks: 1137 INFO @ Tue, 21 Apr 2015 13:40:44: start model_add_line... INFO @ Tue, 21 Apr 2015 13:40:45: start X-correlation... INFO @ Tue, 21 Apr 2015 13:40:45: end of X-cor INFO @ Tue, 21 Apr 2015 13:40:45: #2 finished! INFO @ Tue, 21 Apr 2015 13:40:45: #2 predicted fragment length is 66 bps INFO @ Tue, 21 Apr 2015 13:40:45: #2 alternative fragment length(s) may be 4,62,66 bps INFO @ Tue, 21 Apr 2015 13:40:45: #2.2 Generate R script for model : SRX041410.10_model.r WARNING @ Tue, 21 Apr 2015 13:40:45: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:40:45: #2 You may need to consider one of the other alternative d(s): 4,62,66 WARNING @ Tue, 21 Apr 2015 13:40:45: #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 13:40:45: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:40:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:40:54: start X-correlation... INFO @ Tue, 21 Apr 2015 13:40:54: end of X-cor INFO @ Tue, 21 Apr 2015 13:40:54: #2 finished! INFO @ Tue, 21 Apr 2015 13:40:54: #2 predicted fragment length is 66 bps INFO @ Tue, 21 Apr 2015 13:40:54: #2 alternative fragment length(s) may be 4,62,66 bps INFO @ Tue, 21 Apr 2015 13:40:54: #2.2 Generate R script for model : SRX041410.05_model.r WARNING @ Tue, 21 Apr 2015 13:40:54: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:40:54: #2 You may need to consider one of the other alternative d(s): 4,62,66 WARNING @ Tue, 21 Apr 2015 13:40:54: #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 13:40:54: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:40:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:40:55: start X-correlation... INFO @ Tue, 21 Apr 2015 13:40:55: end of X-cor INFO @ Tue, 21 Apr 2015 13:40:55: #2 finished! INFO @ Tue, 21 Apr 2015 13:40:55: #2 predicted fragment length is 66 bps INFO @ Tue, 21 Apr 2015 13:40:55: #2 alternative fragment length(s) may be 4,62,66 bps INFO @ Tue, 21 Apr 2015 13:40:55: #2.2 Generate R script for model : SRX041410.20_model.r WARNING @ Tue, 21 Apr 2015 13:40:55: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:40:55: #2 You may need to consider one of the other alternative d(s): 4,62,66 WARNING @ Tue, 21 Apr 2015 13:40:55: #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 13:40:55: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:40:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:42:10: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:42:15: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:42:20: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:43:20: #4 Write output xls file... SRX041410.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:43:20: #4 Write peak in narrowPeak format file... SRX041410.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:43:21: #4 Write summits bed file... SRX041410.10_summits.bed INFO @ Tue, 21 Apr 2015 13:43:21: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (11181 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:43:21: #4 Write output xls file... SRX041410.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:43:21: #4 Write peak in narrowPeak format file... SRX041410.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:43:21: #4 Write summits bed file... SRX041410.20_summits.bed INFO @ Tue, 21 Apr 2015 13:43:21: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3066 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:43:32: #4 Write output xls file... SRX041410.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:43:33: #4 Write peak in narrowPeak format file... SRX041410.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:43:33: #4 Write summits bed file... SRX041410.05_summits.bed INFO @ Tue, 21 Apr 2015 13:43:33: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (19918 records, 4 fields): 24 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。