Job ID = 2161569 sra ファイルのダウンロード中... Completed: 427964K bytes transferred in 6 seconds (507257K 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 44896 0 44896 0 0 47718 0 --:--:-- --:--:-- --:--:-- 59941 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 21965946 spots for /home/okishinya/chipatlas/results/dm3/SRX030963/SRR072392.sra Written 21965946 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: 00:06:15 21965946 reads; of these: 21965946 (100.00%) were unpaired; of these: 2189463 (9.97%) aligned 0 times 15554613 (70.81%) aligned exactly 1 time 4221870 (19.22%) aligned >1 times 90.03% overall alignment rate Time searching: 00:06:15 Overall time: 00:06:15 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] 1878754 / 19776483 = 0.0950 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 13:04:14: # Command line: callpeak -t SRX030963.bam -f BAM -g dm -n SRX030963.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX030963.05 # format = BAM # ChIP-seq file = ['SRX030963.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 13:04:14: # Command line: callpeak -t SRX030963.bam -f BAM -g dm -n SRX030963.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX030963.10 # format = BAM # ChIP-seq file = ['SRX030963.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 13:04:14: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:04:14: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:04:14: # Command line: callpeak -t SRX030963.bam -f BAM -g dm -n SRX030963.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX030963.20 # format = BAM # ChIP-seq file = ['SRX030963.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 13:04:14: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:04:14: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:04:14: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:04:14: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:04:19: 1000000 INFO @ Tue, 21 Apr 2015 13:04:19: 1000000 INFO @ Tue, 21 Apr 2015 13:04:19: 1000000 INFO @ Tue, 21 Apr 2015 13:04:24: 2000000 INFO @ Tue, 21 Apr 2015 13:04:25: 2000000 INFO @ Tue, 21 Apr 2015 13:04:25: 2000000 INFO @ Tue, 21 Apr 2015 13:04:31: 3000000 INFO @ Tue, 21 Apr 2015 13:04:31: 3000000 INFO @ Tue, 21 Apr 2015 13:04:31: 3000000 INFO @ Tue, 21 Apr 2015 13:04:37: 4000000 INFO @ Tue, 21 Apr 2015 13:04:38: 4000000 INFO @ Tue, 21 Apr 2015 13:04:38: 4000000 INFO @ Tue, 21 Apr 2015 13:04:43: 5000000 INFO @ Tue, 21 Apr 2015 13:04:44: 5000000 INFO @ Tue, 21 Apr 2015 13:04:44: 5000000 INFO @ Tue, 21 Apr 2015 13:04:49: 6000000 INFO @ Tue, 21 Apr 2015 13:04:51: 6000000 INFO @ Tue, 21 Apr 2015 13:04:51: 6000000 INFO @ Tue, 21 Apr 2015 13:04:55: 7000000 INFO @ Tue, 21 Apr 2015 13:04:58: 7000000 INFO @ Tue, 21 Apr 2015 13:04:58: 7000000 INFO @ Tue, 21 Apr 2015 13:05:02: 8000000 INFO @ Tue, 21 Apr 2015 13:05:04: 8000000 INFO @ Tue, 21 Apr 2015 13:05:04: 8000000 INFO @ Tue, 21 Apr 2015 13:05:08: 9000000 INFO @ Tue, 21 Apr 2015 13:05:11: 9000000 INFO @ Tue, 21 Apr 2015 13:05:11: 9000000 INFO @ Tue, 21 Apr 2015 13:05:14: 10000000 INFO @ Tue, 21 Apr 2015 13:05:18: 10000000 INFO @ Tue, 21 Apr 2015 13:05:18: 10000000 INFO @ Tue, 21 Apr 2015 13:05:20: 11000000 INFO @ Tue, 21 Apr 2015 13:05:24: 11000000 INFO @ Tue, 21 Apr 2015 13:05:24: 11000000 INFO @ Tue, 21 Apr 2015 13:05:26: 12000000 INFO @ Tue, 21 Apr 2015 13:05:31: 12000000 INFO @ Tue, 21 Apr 2015 13:05:31: 12000000 INFO @ Tue, 21 Apr 2015 13:05:33: 13000000 INFO @ Tue, 21 Apr 2015 13:05:38: 13000000 INFO @ Tue, 21 Apr 2015 13:05:38: 13000000 INFO @ Tue, 21 Apr 2015 13:05:39: 14000000 INFO @ Tue, 21 Apr 2015 13:05:44: 14000000 INFO @ Tue, 21 Apr 2015 13:05:44: 14000000 INFO @ Tue, 21 Apr 2015 13:05:45: 15000000 INFO @ Tue, 21 Apr 2015 13:05:51: 15000000 INFO @ Tue, 21 Apr 2015 13:05:51: 15000000 INFO @ Tue, 21 Apr 2015 13:05:51: 16000000 INFO @ Tue, 21 Apr 2015 13:05:58: 17000000 INFO @ Tue, 21 Apr 2015 13:05:58: 16000000 INFO @ Tue, 21 Apr 2015 13:05:58: 16000000 INFO @ Tue, 21 Apr 2015 13:06:03: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:06:03: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:06:03: #1 total tags in treatment: 17897729 INFO @ Tue, 21 Apr 2015 13:06:03: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:06:03: #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 13:06:04: 17000000 INFO @ Tue, 21 Apr 2015 13:06:04: 17000000 INFO @ Tue, 21 Apr 2015 13:06:07: #1 tags after filtering in treatment: 17896245 INFO @ Tue, 21 Apr 2015 13:06:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:06:07: #1 finished! INFO @ Tue, 21 Apr 2015 13:06:07: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:06:10: #2 number of paired peaks: 133 WARNING @ Tue, 21 Apr 2015 13:06:10: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Tue, 21 Apr 2015 13:06:10: start model_add_line... INFO @ Tue, 21 Apr 2015 13:06:11: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:06:11: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:06:11: #1 total tags in treatment: 17897729 INFO @ Tue, 21 Apr 2015 13:06:11: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:06:11: #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 13:06:11: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:06:11: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:06:11: #1 total tags in treatment: 17897729 INFO @ Tue, 21 Apr 2015 13:06:11: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:06:11: #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 13:06:12: start X-correlation... INFO @ Tue, 21 Apr 2015 13:06:12: end of X-cor INFO @ Tue, 21 Apr 2015 13:06:12: #2 finished! INFO @ Tue, 21 Apr 2015 13:06:12: #2 predicted fragment length is 44 bps INFO @ Tue, 21 Apr 2015 13:06:12: #2 alternative fragment length(s) may be 44 bps INFO @ Tue, 21 Apr 2015 13:06:12: #2.2 Generate R script for model : SRX030963.05_model.r WARNING @ Tue, 21 Apr 2015 13:06:12: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:06:12: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Tue, 21 Apr 2015 13:06:12: #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 13:06:12: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:06:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:06:14: #1 tags after filtering in treatment: 17896245 INFO @ Tue, 21 Apr 2015 13:06:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:06:14: #1 finished! INFO @ Tue, 21 Apr 2015 13:06:14: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:06:14: #1 tags after filtering in treatment: 17896245 INFO @ Tue, 21 Apr 2015 13:06:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:06:14: #1 finished! INFO @ Tue, 21 Apr 2015 13:06:14: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:06:16: #2 number of paired peaks: 133 WARNING @ Tue, 21 Apr 2015 13:06:16: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Tue, 21 Apr 2015 13:06:16: start model_add_line... INFO @ Tue, 21 Apr 2015 13:06:17: #2 number of paired peaks: 133 WARNING @ Tue, 21 Apr 2015 13:06:17: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Tue, 21 Apr 2015 13:06:17: start model_add_line... INFO @ Tue, 21 Apr 2015 13:06:18: start X-correlation... INFO @ Tue, 21 Apr 2015 13:06:18: end of X-cor INFO @ Tue, 21 Apr 2015 13:06:18: #2 finished! INFO @ Tue, 21 Apr 2015 13:06:18: #2 predicted fragment length is 44 bps INFO @ Tue, 21 Apr 2015 13:06:18: #2 alternative fragment length(s) may be 44 bps INFO @ Tue, 21 Apr 2015 13:06:18: #2.2 Generate R script for model : SRX030963.10_model.r WARNING @ Tue, 21 Apr 2015 13:06:18: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:06:18: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Tue, 21 Apr 2015 13:06:18: #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 13:06:18: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:06:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:06:19: start X-correlation... INFO @ Tue, 21 Apr 2015 13:06:19: end of X-cor INFO @ Tue, 21 Apr 2015 13:06:19: #2 finished! INFO @ Tue, 21 Apr 2015 13:06:19: #2 predicted fragment length is 44 bps INFO @ Tue, 21 Apr 2015 13:06:19: #2 alternative fragment length(s) may be 44 bps INFO @ Tue, 21 Apr 2015 13:06:19: #2.2 Generate R script for model : SRX030963.20_model.r WARNING @ Tue, 21 Apr 2015 13:06:19: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:06:19: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Tue, 21 Apr 2015 13:06:19: #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 13:06:19: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:06:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:07:38: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:07:46: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:07:52: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:08:42: #4 Write output xls file... SRX030963.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:08:42: #4 Write peak in narrowPeak format file... SRX030963.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:08:42: #4 Write summits bed file... SRX030963.05_summits.bed INFO @ Tue, 21 Apr 2015 13:08:42: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1565 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:08:52: #4 Write output xls file... SRX030963.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:08:52: #4 Write peak in narrowPeak format file... SRX030963.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:08:52: #4 Write summits bed file... SRX030963.20_summits.bed INFO @ Tue, 21 Apr 2015 13:08:52: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (830 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:08:54: #4 Write output xls file... SRX030963.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:08:54: #4 Write peak in narrowPeak format file... SRX030963.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:08:54: #4 Write summits bed file... SRX030963.10_summits.bed INFO @ Tue, 21 Apr 2015 13:08:54: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1265 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。