Job ID = 2161557 sra ファイルのダウンロード中... Completed: 9658069K bytes transferred in 112 seconds (704594K 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 11996 0 11996 0 0 23569 0 --:--:-- --:--:-- --:--:-- 37723 100 36320 0 36320 0 0 51974 0 --:--:-- --:--:-- --:--:-- 71496 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 23620125 spots for /home/okishinya/chipatlas/results/dm3/SRX027832/SRR067915.sra Written 23620125 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: 00:06:56 23620125 reads; of these: 23620125 (100.00%) were unpaired; of these: 4012009 (16.99%) aligned 0 times 13962801 (59.11%) aligned exactly 1 time 5645315 (23.90%) aligned >1 times 83.01% overall alignment rate Time searching: 00:06:56 Overall time: 00:06:56 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] 2085906 / 19608116 = 0.1064 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 13:01:56: # Command line: callpeak -t SRX027832.bam -f BAM -g dm -n SRX027832.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX027832.10 # format = BAM # ChIP-seq file = ['SRX027832.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 13:01:56: # Command line: callpeak -t SRX027832.bam -f BAM -g dm -n SRX027832.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX027832.05 # format = BAM # ChIP-seq file = ['SRX027832.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 13:01:56: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:01:56: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:01:56: # Command line: callpeak -t SRX027832.bam -f BAM -g dm -n SRX027832.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX027832.20 # format = BAM # ChIP-seq file = ['SRX027832.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 13:01:56: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:01:56: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:01:56: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:01:56: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:02:02: 1000000 INFO @ Tue, 21 Apr 2015 13:02:02: 1000000 INFO @ Tue, 21 Apr 2015 13:02:02: 1000000 INFO @ Tue, 21 Apr 2015 13:02:07: 2000000 INFO @ Tue, 21 Apr 2015 13:02:07: 2000000 INFO @ Tue, 21 Apr 2015 13:02:07: 2000000 INFO @ Tue, 21 Apr 2015 13:02:12: 3000000 INFO @ Tue, 21 Apr 2015 13:02:12: 3000000 INFO @ Tue, 21 Apr 2015 13:02:12: 3000000 INFO @ Tue, 21 Apr 2015 13:02:17: 4000000 INFO @ Tue, 21 Apr 2015 13:02:17: 4000000 INFO @ Tue, 21 Apr 2015 13:02:17: 4000000 INFO @ Tue, 21 Apr 2015 13:02:22: 5000000 INFO @ Tue, 21 Apr 2015 13:02:22: 5000000 INFO @ Tue, 21 Apr 2015 13:02:23: 5000000 INFO @ Tue, 21 Apr 2015 13:02:27: 6000000 INFO @ Tue, 21 Apr 2015 13:02:28: 6000000 INFO @ Tue, 21 Apr 2015 13:02:28: 6000000 INFO @ Tue, 21 Apr 2015 13:02:33: 7000000 INFO @ Tue, 21 Apr 2015 13:02:33: 7000000 INFO @ Tue, 21 Apr 2015 13:02:33: 7000000 INFO @ Tue, 21 Apr 2015 13:02:38: 8000000 INFO @ Tue, 21 Apr 2015 13:02:38: 8000000 INFO @ Tue, 21 Apr 2015 13:02:39: 8000000 INFO @ Tue, 21 Apr 2015 13:02:43: 9000000 INFO @ Tue, 21 Apr 2015 13:02:43: 9000000 INFO @ Tue, 21 Apr 2015 13:02:44: 9000000 INFO @ Tue, 21 Apr 2015 13:02:48: 10000000 INFO @ Tue, 21 Apr 2015 13:02:49: 10000000 INFO @ Tue, 21 Apr 2015 13:02:49: 10000000 INFO @ Tue, 21 Apr 2015 13:02:53: 11000000 INFO @ Tue, 21 Apr 2015 13:02:54: 11000000 INFO @ Tue, 21 Apr 2015 13:02:55: 11000000 INFO @ Tue, 21 Apr 2015 13:02:58: 12000000 INFO @ Tue, 21 Apr 2015 13:02:59: 12000000 INFO @ Tue, 21 Apr 2015 13:03:00: 12000000 INFO @ Tue, 21 Apr 2015 13:03:03: 13000000 INFO @ Tue, 21 Apr 2015 13:03:04: 13000000 INFO @ Tue, 21 Apr 2015 13:03:06: 13000000 INFO @ Tue, 21 Apr 2015 13:03:08: 14000000 INFO @ Tue, 21 Apr 2015 13:03:10: 14000000 INFO @ Tue, 21 Apr 2015 13:03:11: 14000000 INFO @ Tue, 21 Apr 2015 13:03:13: 15000000 INFO @ Tue, 21 Apr 2015 13:03:15: 15000000 INFO @ Tue, 21 Apr 2015 13:03:16: 15000000 INFO @ Tue, 21 Apr 2015 13:03:18: 16000000 INFO @ Tue, 21 Apr 2015 13:03:20: 16000000 INFO @ Tue, 21 Apr 2015 13:03:22: 16000000 INFO @ Tue, 21 Apr 2015 13:03:24: 17000000 INFO @ Tue, 21 Apr 2015 13:03:26: 17000000 INFO @ Tue, 21 Apr 2015 13:03:27: #1 tag size is determined as 38 bps INFO @ Tue, 21 Apr 2015 13:03:27: #1 tag size = 38 INFO @ Tue, 21 Apr 2015 13:03:27: #1 total tags in treatment: 17522210 INFO @ Tue, 21 Apr 2015 13:03:27: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:03:27: #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 13:03:27: 17000000 INFO @ Tue, 21 Apr 2015 13:03:29: #1 tag size is determined as 38 bps INFO @ Tue, 21 Apr 2015 13:03:29: #1 tag size = 38 INFO @ Tue, 21 Apr 2015 13:03:29: #1 total tags in treatment: 17522210 INFO @ Tue, 21 Apr 2015 13:03:29: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:03:29: #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 13:03:30: #1 tags after filtering in treatment: 17519876 INFO @ Tue, 21 Apr 2015 13:03:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:03:30: #1 finished! INFO @ Tue, 21 Apr 2015 13:03:30: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:03:30: #1 tag size is determined as 38 bps INFO @ Tue, 21 Apr 2015 13:03:30: #1 tag size = 38 INFO @ Tue, 21 Apr 2015 13:03:30: #1 total tags in treatment: 17522210 INFO @ Tue, 21 Apr 2015 13:03:30: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:03:30: #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 13:03:32: #1 tags after filtering in treatment: 17519876 INFO @ Tue, 21 Apr 2015 13:03:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:03:32: #1 finished! INFO @ Tue, 21 Apr 2015 13:03:32: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:03:33: #2 number of paired peaks: 510 WARNING @ Tue, 21 Apr 2015 13:03:33: Fewer paired peaks (510) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 510 pairs to build model! INFO @ Tue, 21 Apr 2015 13:03:33: start model_add_line... INFO @ Tue, 21 Apr 2015 13:03:33: #1 tags after filtering in treatment: 17519876 INFO @ Tue, 21 Apr 2015 13:03:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:03:33: #1 finished! INFO @ Tue, 21 Apr 2015 13:03:33: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:03:34: #2 number of paired peaks: 510 WARNING @ Tue, 21 Apr 2015 13:03:34: Fewer paired peaks (510) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 510 pairs to build model! INFO @ Tue, 21 Apr 2015 13:03:34: start model_add_line... INFO @ Tue, 21 Apr 2015 13:03:37: #2 number of paired peaks: 510 WARNING @ Tue, 21 Apr 2015 13:03:37: Fewer paired peaks (510) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 510 pairs to build model! INFO @ Tue, 21 Apr 2015 13:03:37: start model_add_line... INFO @ Tue, 21 Apr 2015 13:03:40: start X-correlation... INFO @ Tue, 21 Apr 2015 13:03:40: end of X-cor INFO @ Tue, 21 Apr 2015 13:03:40: #2 finished! INFO @ Tue, 21 Apr 2015 13:03:40: #2 predicted fragment length is 60 bps INFO @ Tue, 21 Apr 2015 13:03:40: #2 alternative fragment length(s) may be 4,60,529 bps INFO @ Tue, 21 Apr 2015 13:03:40: #2.2 Generate R script for model : SRX027832.20_model.r WARNING @ Tue, 21 Apr 2015 13:03:40: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:03:40: #2 You may need to consider one of the other alternative d(s): 4,60,529 WARNING @ Tue, 21 Apr 2015 13:03:40: #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 13:03:40: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:03:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:03:41: start X-correlation... INFO @ Tue, 21 Apr 2015 13:03:41: end of X-cor INFO @ Tue, 21 Apr 2015 13:03:41: #2 finished! INFO @ Tue, 21 Apr 2015 13:03:41: #2 predicted fragment length is 60 bps INFO @ Tue, 21 Apr 2015 13:03:41: #2 alternative fragment length(s) may be 4,60,529 bps INFO @ Tue, 21 Apr 2015 13:03:41: #2.2 Generate R script for model : SRX027832.05_model.r WARNING @ Tue, 21 Apr 2015 13:03:41: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:03:41: #2 You may need to consider one of the other alternative d(s): 4,60,529 WARNING @ Tue, 21 Apr 2015 13:03:41: #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 13:03:41: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:03:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:03:43: start X-correlation... INFO @ Tue, 21 Apr 2015 13:03:43: end of X-cor INFO @ Tue, 21 Apr 2015 13:03:43: #2 finished! INFO @ Tue, 21 Apr 2015 13:03:43: #2 predicted fragment length is 60 bps INFO @ Tue, 21 Apr 2015 13:03:43: #2 alternative fragment length(s) may be 4,60,529 bps INFO @ Tue, 21 Apr 2015 13:03:43: #2.2 Generate R script for model : SRX027832.10_model.r WARNING @ Tue, 21 Apr 2015 13:03:43: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:03:43: #2 You may need to consider one of the other alternative d(s): 4,60,529 WARNING @ Tue, 21 Apr 2015 13:03:43: #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 13:03:43: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:03:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:05:07: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:05:10: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:05:11: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:06:14: #4 Write output xls file... SRX027832.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:06:14: #4 Write peak in narrowPeak format file... SRX027832.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:06:14: #4 Write summits bed file... SRX027832.10_summits.bed INFO @ Tue, 21 Apr 2015 13:06:14: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2179 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:06:15: #4 Write output xls file... SRX027832.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:06:15: #4 Write peak in narrowPeak format file... SRX027832.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:06:15: #4 Write summits bed file... SRX027832.20_summits.bed INFO @ Tue, 21 Apr 2015 13:06:15: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (847 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:06:17: #4 Write output xls file... SRX027832.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:06:17: #4 Write peak in narrowPeak format file... SRX027832.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:06:17: #4 Write summits bed file... SRX027832.05_summits.bed INFO @ Tue, 21 Apr 2015 13:06:17: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4499 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。