Job ID = 2161430 sra ファイルのダウンロード中... Completed: 426956K bytes transferred in 6 seconds (532199K 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 --:--:-- --:--:-- --:--:-- 0 108 1088 0 1088 0 0 1831 0 --:--:-- --:--:-- --:--:-- 2693 100 44913 0 44913 0 0 46155 0 --:--:-- --:--:-- --:--:-- 57360 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 21137108 spots for /home/okishinya/chipatlas/results/dm3/SRX026860/SRR065759.sra Written 21137108 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: 00:07:31 21137108 reads; of these: 21137108 (100.00%) were unpaired; of these: 1777946 (8.41%) aligned 0 times 12212050 (57.78%) aligned exactly 1 time 7147112 (33.81%) aligned >1 times 91.59% overall alignment rate Time searching: 00:07:31 Overall time: 00:07:31 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] 3264296 / 19359162 = 0.1686 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 12:52:16: # Command line: callpeak -t SRX026860.bam -f BAM -g dm -n SRX026860.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX026860.10 # format = BAM # ChIP-seq file = ['SRX026860.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 12:52:16: # Command line: callpeak -t SRX026860.bam -f BAM -g dm -n SRX026860.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX026860.20 # format = BAM # ChIP-seq file = ['SRX026860.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 12:52:16: # Command line: callpeak -t SRX026860.bam -f BAM -g dm -n SRX026860.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX026860.05 # format = BAM # ChIP-seq file = ['SRX026860.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 12:52:16: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:52:16: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:52:16: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:52:16: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:52:16: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:52:16: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:52:21: 1000000 INFO @ Tue, 21 Apr 2015 12:52:21: 1000000 INFO @ Tue, 21 Apr 2015 12:52:21: 1000000 INFO @ Tue, 21 Apr 2015 12:52:26: 2000000 INFO @ Tue, 21 Apr 2015 12:52:26: 2000000 INFO @ Tue, 21 Apr 2015 12:52:26: 2000000 INFO @ Tue, 21 Apr 2015 12:52:31: 3000000 INFO @ Tue, 21 Apr 2015 12:52:31: 3000000 INFO @ Tue, 21 Apr 2015 12:52:32: 3000000 INFO @ Tue, 21 Apr 2015 12:52:36: 4000000 INFO @ Tue, 21 Apr 2015 12:52:37: 4000000 INFO @ Tue, 21 Apr 2015 12:52:37: 4000000 INFO @ Tue, 21 Apr 2015 12:52:41: 5000000 INFO @ Tue, 21 Apr 2015 12:52:42: 5000000 INFO @ Tue, 21 Apr 2015 12:52:42: 5000000 INFO @ Tue, 21 Apr 2015 12:52:46: 6000000 INFO @ Tue, 21 Apr 2015 12:52:47: 6000000 INFO @ Tue, 21 Apr 2015 12:52:48: 6000000 INFO @ Tue, 21 Apr 2015 12:52:51: 7000000 INFO @ Tue, 21 Apr 2015 12:52:53: 7000000 INFO @ Tue, 21 Apr 2015 12:52:53: 7000000 INFO @ Tue, 21 Apr 2015 12:52:56: 8000000 INFO @ Tue, 21 Apr 2015 12:52:58: 8000000 INFO @ Tue, 21 Apr 2015 12:52:58: 8000000 INFO @ Tue, 21 Apr 2015 12:53:01: 9000000 INFO @ Tue, 21 Apr 2015 12:53:03: 9000000 INFO @ Tue, 21 Apr 2015 12:53:03: 9000000 INFO @ Tue, 21 Apr 2015 12:53:06: 10000000 INFO @ Tue, 21 Apr 2015 12:53:07: 10000000 INFO @ Tue, 21 Apr 2015 12:53:08: 10000000 INFO @ Tue, 21 Apr 2015 12:53:10: 11000000 INFO @ Tue, 21 Apr 2015 12:53:12: 11000000 INFO @ Tue, 21 Apr 2015 12:53:13: 11000000 INFO @ Tue, 21 Apr 2015 12:53:15: 12000000 INFO @ Tue, 21 Apr 2015 12:53:17: 12000000 INFO @ Tue, 21 Apr 2015 12:53:18: 12000000 INFO @ Tue, 21 Apr 2015 12:53:20: 13000000 INFO @ Tue, 21 Apr 2015 12:53:22: 13000000 INFO @ Tue, 21 Apr 2015 12:53:23: 13000000 INFO @ Tue, 21 Apr 2015 12:53:24: 14000000 INFO @ Tue, 21 Apr 2015 12:53:27: 14000000 INFO @ Tue, 21 Apr 2015 12:53:29: 14000000 INFO @ Tue, 21 Apr 2015 12:53:29: 15000000 INFO @ Tue, 21 Apr 2015 12:53:32: 15000000 INFO @ Tue, 21 Apr 2015 12:53:34: 15000000 INFO @ Tue, 21 Apr 2015 12:53:34: 16000000 INFO @ Tue, 21 Apr 2015 12:53:35: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:53:35: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:53:35: #1 total tags in treatment: 16094866 INFO @ Tue, 21 Apr 2015 12:53:35: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:53:35: #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 12:53:37: 16000000 INFO @ Tue, 21 Apr 2015 12:53:38: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:53:38: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:53:38: #1 total tags in treatment: 16094866 INFO @ Tue, 21 Apr 2015 12:53:38: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:53:38: #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 12:53:38: #1 tags after filtering in treatment: 16093459 INFO @ Tue, 21 Apr 2015 12:53:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:53:38: #1 finished! INFO @ Tue, 21 Apr 2015 12:53:38: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:53:39: 16000000 INFO @ Tue, 21 Apr 2015 12:53:40: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:53:40: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:53:40: #1 total tags in treatment: 16094866 INFO @ Tue, 21 Apr 2015 12:53:40: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:53:40: #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 12:53:41: #1 tags after filtering in treatment: 16093459 INFO @ Tue, 21 Apr 2015 12:53:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:53:41: #1 finished! INFO @ Tue, 21 Apr 2015 12:53:41: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:53:41: #2 number of paired peaks: 209 WARNING @ Tue, 21 Apr 2015 12:53:41: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Tue, 21 Apr 2015 12:53:41: start model_add_line... INFO @ Tue, 21 Apr 2015 12:53:43: #1 tags after filtering in treatment: 16093459 INFO @ Tue, 21 Apr 2015 12:53:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:53:43: #1 finished! INFO @ Tue, 21 Apr 2015 12:53:43: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:53:44: start X-correlation... INFO @ Tue, 21 Apr 2015 12:53:44: end of X-cor INFO @ Tue, 21 Apr 2015 12:53:44: #2 finished! INFO @ Tue, 21 Apr 2015 12:53:44: #2 predicted fragment length is 34 bps INFO @ Tue, 21 Apr 2015 12:53:44: #2 alternative fragment length(s) may be 34 bps INFO @ Tue, 21 Apr 2015 12:53:44: #2.2 Generate R script for model : SRX026860.20_model.r WARNING @ Tue, 21 Apr 2015 12:53:44: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:53:44: #2 You may need to consider one of the other alternative d(s): 34 WARNING @ Tue, 21 Apr 2015 12:53:44: #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 12:53:44: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:53:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:53:44: #2 number of paired peaks: 209 WARNING @ Tue, 21 Apr 2015 12:53:44: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Tue, 21 Apr 2015 12:53:44: start model_add_line... INFO @ Tue, 21 Apr 2015 12:53:45: #2 number of paired peaks: 209 WARNING @ Tue, 21 Apr 2015 12:53:45: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Tue, 21 Apr 2015 12:53:45: start model_add_line... INFO @ Tue, 21 Apr 2015 12:53:46: start X-correlation... INFO @ Tue, 21 Apr 2015 12:53:46: end of X-cor INFO @ Tue, 21 Apr 2015 12:53:46: #2 finished! INFO @ Tue, 21 Apr 2015 12:53:46: #2 predicted fragment length is 34 bps INFO @ Tue, 21 Apr 2015 12:53:46: #2 alternative fragment length(s) may be 34 bps INFO @ Tue, 21 Apr 2015 12:53:46: #2.2 Generate R script for model : SRX026860.05_model.r WARNING @ Tue, 21 Apr 2015 12:53:46: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:53:46: #2 You may need to consider one of the other alternative d(s): 34 WARNING @ Tue, 21 Apr 2015 12:53:46: #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 12:53:46: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:53:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:53:48: start X-correlation... INFO @ Tue, 21 Apr 2015 12:53:48: end of X-cor INFO @ Tue, 21 Apr 2015 12:53:48: #2 finished! INFO @ Tue, 21 Apr 2015 12:53:48: #2 predicted fragment length is 34 bps INFO @ Tue, 21 Apr 2015 12:53:48: #2 alternative fragment length(s) may be 34 bps INFO @ Tue, 21 Apr 2015 12:53:48: #2.2 Generate R script for model : SRX026860.10_model.r WARNING @ Tue, 21 Apr 2015 12:53:48: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:53:48: #2 You may need to consider one of the other alternative d(s): 34 WARNING @ Tue, 21 Apr 2015 12:53:48: #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 12:53:48: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:53:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:55:02: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:55:07: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:55:08: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:56:01: #4 Write output xls file... SRX026860.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:56:01: #4 Write peak in narrowPeak format file... SRX026860.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:56:01: #4 Write summits bed file... SRX026860.20_summits.bed INFO @ Tue, 21 Apr 2015 12:56:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (964 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:56:09: #4 Write output xls file... SRX026860.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:56:09: #4 Write peak in narrowPeak format file... SRX026860.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:56:09: #4 Write summits bed file... SRX026860.05_summits.bed INFO @ Tue, 21 Apr 2015 12:56:09: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1893 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:56:10: #4 Write output xls file... SRX026860.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:56:10: #4 Write peak in narrowPeak format file... SRX026860.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:56:10: #4 Write summits bed file... SRX026860.10_summits.bed INFO @ Tue, 21 Apr 2015 12:56:10: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1543 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。