Job ID = 2161565 sra ファイルのダウンロード中... Completed: 467948K bytes transferred in 7 seconds (529762K 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 19258 0 19258 0 0 24359 0 --:--:-- --:--:-- --:--:-- 32096 100 44887 0 44887 0 0 45794 0 --:--:-- --:--:-- --:--:-- 56891 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 23012193 spots for /home/okishinya/chipatlas/results/dm3/SRX030959/SRR072386.sra Written 23012193 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: 00:07:22 23012193 reads; of these: 23012193 (100.00%) were unpaired; of these: 939241 (4.08%) aligned 0 times 16849956 (73.22%) aligned exactly 1 time 5222996 (22.70%) aligned >1 times 95.92% overall alignment rate Time searching: 00:07:22 Overall time: 00:07:22 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] 3662087 / 22072952 = 0.1659 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 13:04:25: # Command line: callpeak -t SRX030959.bam -f BAM -g dm -n SRX030959.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX030959.10 # format = BAM # ChIP-seq file = ['SRX030959.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 13:04:25: # Command line: callpeak -t SRX030959.bam -f BAM -g dm -n SRX030959.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX030959.20 # format = BAM # ChIP-seq file = ['SRX030959.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 13:04:25: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:04:25: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:04:25: # Command line: callpeak -t SRX030959.bam -f BAM -g dm -n SRX030959.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX030959.05 # format = BAM # ChIP-seq file = ['SRX030959.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 13:04:25: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:04:25: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:04:25: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:04:25: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:04:31: 1000000 INFO @ Tue, 21 Apr 2015 13:04:31: 1000000 INFO @ Tue, 21 Apr 2015 13:04:31: 1000000 INFO @ Tue, 21 Apr 2015 13:04:37: 2000000 INFO @ Tue, 21 Apr 2015 13:04:38: 2000000 INFO @ Tue, 21 Apr 2015 13:04:38: 2000000 INFO @ Tue, 21 Apr 2015 13:04:44: 3000000 INFO @ Tue, 21 Apr 2015 13:04:45: 3000000 INFO @ Tue, 21 Apr 2015 13:04:45: 3000000 INFO @ Tue, 21 Apr 2015 13:04:50: 4000000 INFO @ Tue, 21 Apr 2015 13:04:52: 4000000 INFO @ Tue, 21 Apr 2015 13:04:52: 4000000 INFO @ Tue, 21 Apr 2015 13:04:56: 5000000 INFO @ Tue, 21 Apr 2015 13:04:59: 5000000 INFO @ Tue, 21 Apr 2015 13:04:59: 5000000 INFO @ Tue, 21 Apr 2015 13:05:02: 6000000 INFO @ Tue, 21 Apr 2015 13:05:06: 6000000 INFO @ Tue, 21 Apr 2015 13:05:06: 6000000 INFO @ Tue, 21 Apr 2015 13:05:08: 7000000 INFO @ Tue, 21 Apr 2015 13:05:13: 7000000 INFO @ Tue, 21 Apr 2015 13:05:13: 7000000 INFO @ Tue, 21 Apr 2015 13:05:15: 8000000 INFO @ Tue, 21 Apr 2015 13:05:19: 8000000 INFO @ Tue, 21 Apr 2015 13:05:19: 8000000 INFO @ Tue, 21 Apr 2015 13:05:21: 9000000 INFO @ Tue, 21 Apr 2015 13:05:26: 9000000 INFO @ Tue, 21 Apr 2015 13:05:26: 9000000 INFO @ Tue, 21 Apr 2015 13:05:27: 10000000 INFO @ Tue, 21 Apr 2015 13:05:33: 10000000 INFO @ Tue, 21 Apr 2015 13:05:33: 10000000 INFO @ Tue, 21 Apr 2015 13:05:33: 11000000 INFO @ Tue, 21 Apr 2015 13:05:40: 12000000 INFO @ Tue, 21 Apr 2015 13:05:40: 11000000 INFO @ Tue, 21 Apr 2015 13:05:40: 11000000 INFO @ Tue, 21 Apr 2015 13:05:46: 13000000 INFO @ Tue, 21 Apr 2015 13:05:47: 12000000 INFO @ Tue, 21 Apr 2015 13:05:47: 12000000 INFO @ Tue, 21 Apr 2015 13:05:52: 14000000 INFO @ Tue, 21 Apr 2015 13:05:54: 13000000 INFO @ Tue, 21 Apr 2015 13:05:54: 13000000 INFO @ Tue, 21 Apr 2015 13:05:58: 15000000 INFO @ Tue, 21 Apr 2015 13:06:01: 14000000 INFO @ Tue, 21 Apr 2015 13:06:01: 14000000 INFO @ Tue, 21 Apr 2015 13:06:04: 16000000 INFO @ Tue, 21 Apr 2015 13:06:08: 15000000 INFO @ Tue, 21 Apr 2015 13:06:08: 15000000 INFO @ Tue, 21 Apr 2015 13:06:10: 17000000 INFO @ Tue, 21 Apr 2015 13:06:14: 16000000 INFO @ Tue, 21 Apr 2015 13:06:14: 16000000 INFO @ Tue, 21 Apr 2015 13:06:15: 18000000 INFO @ Tue, 21 Apr 2015 13:06:18: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:06:18: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:06:18: #1 total tags in treatment: 18410865 INFO @ Tue, 21 Apr 2015 13:06:18: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:06:18: #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 13:06:19: 17000000 INFO @ Tue, 21 Apr 2015 13:06:19: 17000000 INFO @ Tue, 21 Apr 2015 13:06:21: #1 tags after filtering in treatment: 18407150 INFO @ Tue, 21 Apr 2015 13:06:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:06:21: #1 finished! INFO @ Tue, 21 Apr 2015 13:06:21: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:06:24: #2 number of paired peaks: 103 WARNING @ Tue, 21 Apr 2015 13:06:24: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Tue, 21 Apr 2015 13:06:24: start model_add_line... INFO @ Tue, 21 Apr 2015 13:06:24: 18000000 INFO @ Tue, 21 Apr 2015 13:06:25: 18000000 INFO @ Tue, 21 Apr 2015 13:06:26: start X-correlation... INFO @ Tue, 21 Apr 2015 13:06:26: end of X-cor INFO @ Tue, 21 Apr 2015 13:06:26: #2 finished! INFO @ Tue, 21 Apr 2015 13:06:26: #2 predicted fragment length is 46 bps INFO @ Tue, 21 Apr 2015 13:06:26: #2 alternative fragment length(s) may be 46 bps INFO @ Tue, 21 Apr 2015 13:06:26: #2.2 Generate R script for model : SRX030959.05_model.r WARNING @ Tue, 21 Apr 2015 13:06:26: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:06:26: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Tue, 21 Apr 2015 13:06:26: #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 13:06:26: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:06:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:06:27: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:06:27: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:06:27: #1 total tags in treatment: 18410865 INFO @ Tue, 21 Apr 2015 13:06:27: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:06:27: #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 13:06:27: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:06:27: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:06:27: #1 total tags in treatment: 18410865 INFO @ Tue, 21 Apr 2015 13:06:27: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:06:27: #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 13:06:30: #1 tags after filtering in treatment: 18407150 INFO @ Tue, 21 Apr 2015 13:06:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:06:30: #1 finished! INFO @ Tue, 21 Apr 2015 13:06:30: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:06:30: #1 tags after filtering in treatment: 18407150 INFO @ Tue, 21 Apr 2015 13:06:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:06:30: #1 finished! INFO @ Tue, 21 Apr 2015 13:06:30: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:06:33: #2 number of paired peaks: 103 WARNING @ Tue, 21 Apr 2015 13:06:33: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Tue, 21 Apr 2015 13:06:33: start model_add_line... INFO @ Tue, 21 Apr 2015 13:06:34: #2 number of paired peaks: 103 WARNING @ Tue, 21 Apr 2015 13:06:34: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Tue, 21 Apr 2015 13:06:34: start model_add_line... INFO @ Tue, 21 Apr 2015 13:06:34: start X-correlation... INFO @ Tue, 21 Apr 2015 13:06:34: end of X-cor INFO @ Tue, 21 Apr 2015 13:06:34: #2 finished! INFO @ Tue, 21 Apr 2015 13:06:34: #2 predicted fragment length is 46 bps INFO @ Tue, 21 Apr 2015 13:06:34: #2 alternative fragment length(s) may be 46 bps INFO @ Tue, 21 Apr 2015 13:06:34: #2.2 Generate R script for model : SRX030959.10_model.r WARNING @ Tue, 21 Apr 2015 13:06:34: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:06:34: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Tue, 21 Apr 2015 13:06:34: #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 13:06:34: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:06:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:06:35: start X-correlation... INFO @ Tue, 21 Apr 2015 13:06:35: end of X-cor INFO @ Tue, 21 Apr 2015 13:06:35: #2 finished! INFO @ Tue, 21 Apr 2015 13:06:35: #2 predicted fragment length is 46 bps INFO @ Tue, 21 Apr 2015 13:06:35: #2 alternative fragment length(s) may be 46 bps INFO @ Tue, 21 Apr 2015 13:06:35: #2.2 Generate R script for model : SRX030959.20_model.r WARNING @ Tue, 21 Apr 2015 13:06:35: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:06:35: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Tue, 21 Apr 2015 13:06:35: #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 13:06:35: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:06:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:07:54: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:08:05: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:08:11: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:08:59: #4 Write output xls file... SRX030959.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:08:59: #4 Write peak in narrowPeak format file... SRX030959.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:08:59: #4 Write summits bed file... SRX030959.05_summits.bed INFO @ Tue, 21 Apr 2015 13:08:59: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2487 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:09:11: #4 Write output xls file... SRX030959.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:09:11: #4 Write peak in narrowPeak format file... SRX030959.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:09:11: #4 Write summits bed file... SRX030959.10_summits.bed INFO @ Tue, 21 Apr 2015 13:09:11: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1282 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:09:18: #4 Write output xls file... SRX030959.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:09:18: #4 Write peak in narrowPeak format file... SRX030959.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:09:18: #4 Write summits bed file... SRX030959.20_summits.bed INFO @ Tue, 21 Apr 2015 13:09:18: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (626 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。