Job ID = 2161432 sra ファイルのダウンロード中... Completed: 586498K bytes transferred in 7 seconds (612367K 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 45324 0 45324 0 0 48909 0 --:--:-- --:--:-- --:--:-- 61665 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 24680990 spots for /home/okishinya/chipatlas/results/dm3/SRX026862/SRR065762.sra Written 24680990 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: 00:11:30 24680990 reads; of these: 24680990 (100.00%) were unpaired; of these: 906769 (3.67%) aligned 0 times 14551252 (58.96%) aligned exactly 1 time 9222969 (37.37%) aligned >1 times 96.33% overall alignment rate Time searching: 00:11:30 Overall time: 00:11:30 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] 4830979 / 23774221 = 0.2032 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 12:58:20: # Command line: callpeak -t SRX026862.bam -f BAM -g dm -n SRX026862.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX026862.20 # format = BAM # ChIP-seq file = ['SRX026862.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 12:58:20: # Command line: callpeak -t SRX026862.bam -f BAM -g dm -n SRX026862.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX026862.05 # format = BAM # ChIP-seq file = ['SRX026862.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 12:58:20: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:58:20: # Command line: callpeak -t SRX026862.bam -f BAM -g dm -n SRX026862.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX026862.10 # format = BAM # ChIP-seq file = ['SRX026862.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 12:58:20: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:58:20: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:58:20: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:58:20: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:58:20: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:58:25: 1000000 INFO @ Tue, 21 Apr 2015 12:58:25: 1000000 INFO @ Tue, 21 Apr 2015 12:58:25: 1000000 INFO @ Tue, 21 Apr 2015 12:58:31: 2000000 INFO @ Tue, 21 Apr 2015 12:58:31: 2000000 INFO @ Tue, 21 Apr 2015 12:58:31: 2000000 INFO @ Tue, 21 Apr 2015 12:58:36: 3000000 INFO @ Tue, 21 Apr 2015 12:58:37: 3000000 INFO @ Tue, 21 Apr 2015 12:58:37: 3000000 INFO @ Tue, 21 Apr 2015 12:58:41: 4000000 INFO @ Tue, 21 Apr 2015 12:58:42: 4000000 INFO @ Tue, 21 Apr 2015 12:58:42: 4000000 INFO @ Tue, 21 Apr 2015 12:58:47: 5000000 INFO @ Tue, 21 Apr 2015 12:58:48: 5000000 INFO @ Tue, 21 Apr 2015 12:58:48: 5000000 INFO @ Tue, 21 Apr 2015 12:58:52: 6000000 INFO @ Tue, 21 Apr 2015 12:58:54: 6000000 INFO @ Tue, 21 Apr 2015 12:58:54: 6000000 INFO @ Tue, 21 Apr 2015 12:58:58: 7000000 INFO @ Tue, 21 Apr 2015 12:58:59: 7000000 INFO @ Tue, 21 Apr 2015 12:58:59: 7000000 INFO @ Tue, 21 Apr 2015 12:59:03: 8000000 INFO @ Tue, 21 Apr 2015 12:59:05: 8000000 INFO @ Tue, 21 Apr 2015 12:59:05: 8000000 INFO @ Tue, 21 Apr 2015 12:59:08: 9000000 INFO @ Tue, 21 Apr 2015 12:59:10: 9000000 INFO @ Tue, 21 Apr 2015 12:59:10: 9000000 INFO @ Tue, 21 Apr 2015 12:59:14: 10000000 INFO @ Tue, 21 Apr 2015 12:59:16: 10000000 INFO @ Tue, 21 Apr 2015 12:59:16: 10000000 INFO @ Tue, 21 Apr 2015 12:59:19: 11000000 INFO @ Tue, 21 Apr 2015 12:59:21: 11000000 INFO @ Tue, 21 Apr 2015 12:59:21: 11000000 INFO @ Tue, 21 Apr 2015 12:59:25: 12000000 INFO @ Tue, 21 Apr 2015 12:59:27: 12000000 INFO @ Tue, 21 Apr 2015 12:59:27: 12000000 INFO @ Tue, 21 Apr 2015 12:59:30: 13000000 INFO @ Tue, 21 Apr 2015 12:59:32: 13000000 INFO @ Tue, 21 Apr 2015 12:59:32: 13000000 INFO @ Tue, 21 Apr 2015 12:59:35: 14000000 INFO @ Tue, 21 Apr 2015 12:59:38: 14000000 INFO @ Tue, 21 Apr 2015 12:59:38: 14000000 INFO @ Tue, 21 Apr 2015 12:59:41: 15000000 INFO @ Tue, 21 Apr 2015 12:59:43: 15000000 INFO @ Tue, 21 Apr 2015 12:59:43: 15000000 INFO @ Tue, 21 Apr 2015 12:59:46: 16000000 INFO @ Tue, 21 Apr 2015 12:59:49: 16000000 INFO @ Tue, 21 Apr 2015 12:59:49: 16000000 INFO @ Tue, 21 Apr 2015 12:59:52: 17000000 INFO @ Tue, 21 Apr 2015 12:59:54: 17000000 INFO @ Tue, 21 Apr 2015 12:59:54: 17000000 INFO @ Tue, 21 Apr 2015 12:59:57: 18000000 INFO @ Tue, 21 Apr 2015 13:00:00: 18000000 INFO @ Tue, 21 Apr 2015 13:00:00: 18000000 INFO @ Tue, 21 Apr 2015 13:00:02: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:00:02: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:00:02: #1 total tags in treatment: 18943242 INFO @ Tue, 21 Apr 2015 13:00:02: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:00:02: #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 13:00:05: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:00:05: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:00:05: #1 total tags in treatment: 18943242 INFO @ Tue, 21 Apr 2015 13:00:05: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:00:05: #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 13:00:06: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:00:06: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:00:06: #1 total tags in treatment: 18943242 INFO @ Tue, 21 Apr 2015 13:00:06: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:00:06: #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 13:00:06: #1 tags after filtering in treatment: 18941352 INFO @ Tue, 21 Apr 2015 13:00:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:00:06: #1 finished! INFO @ Tue, 21 Apr 2015 13:00:06: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:00:09: #1 tags after filtering in treatment: 18941352 INFO @ Tue, 21 Apr 2015 13:00:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:00:09: #1 finished! INFO @ Tue, 21 Apr 2015 13:00:09: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:00:09: #2 number of paired peaks: 408 WARNING @ Tue, 21 Apr 2015 13:00:09: Fewer paired peaks (408) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 408 pairs to build model! INFO @ Tue, 21 Apr 2015 13:00:09: start model_add_line... INFO @ Tue, 21 Apr 2015 13:00:09: #1 tags after filtering in treatment: 18941352 INFO @ Tue, 21 Apr 2015 13:00:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:00:09: #1 finished! INFO @ Tue, 21 Apr 2015 13:00:09: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:00:12: #2 number of paired peaks: 408 WARNING @ Tue, 21 Apr 2015 13:00:12: Fewer paired peaks (408) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 408 pairs to build model! INFO @ Tue, 21 Apr 2015 13:00:12: start model_add_line... INFO @ Tue, 21 Apr 2015 13:00:12: #2 number of paired peaks: 408 WARNING @ Tue, 21 Apr 2015 13:00:12: Fewer paired peaks (408) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 408 pairs to build model! INFO @ Tue, 21 Apr 2015 13:00:12: start model_add_line... INFO @ Tue, 21 Apr 2015 13:00:14: start X-correlation... INFO @ Tue, 21 Apr 2015 13:00:14: end of X-cor INFO @ Tue, 21 Apr 2015 13:00:14: #2 finished! INFO @ Tue, 21 Apr 2015 13:00:14: #2 predicted fragment length is 32 bps INFO @ Tue, 21 Apr 2015 13:00:14: #2 alternative fragment length(s) may be 32 bps INFO @ Tue, 21 Apr 2015 13:00:14: #2.2 Generate R script for model : SRX026862.20_model.r WARNING @ Tue, 21 Apr 2015 13:00:14: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:00:14: #2 You may need to consider one of the other alternative d(s): 32 WARNING @ Tue, 21 Apr 2015 13:00:14: #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 13:00:14: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:00:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:00:16: start X-correlation... INFO @ Tue, 21 Apr 2015 13:00:16: end of X-cor INFO @ Tue, 21 Apr 2015 13:00:16: #2 finished! INFO @ Tue, 21 Apr 2015 13:00:16: #2 predicted fragment length is 32 bps INFO @ Tue, 21 Apr 2015 13:00:16: #2 alternative fragment length(s) may be 32 bps INFO @ Tue, 21 Apr 2015 13:00:16: #2.2 Generate R script for model : SRX026862.10_model.r WARNING @ Tue, 21 Apr 2015 13:00:16: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:00:16: #2 You may need to consider one of the other alternative d(s): 32 WARNING @ Tue, 21 Apr 2015 13:00:16: #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 13:00:16: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:00:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:00:17: start X-correlation... INFO @ Tue, 21 Apr 2015 13:00:17: end of X-cor INFO @ Tue, 21 Apr 2015 13:00:17: #2 finished! INFO @ Tue, 21 Apr 2015 13:00:17: #2 predicted fragment length is 32 bps INFO @ Tue, 21 Apr 2015 13:00:17: #2 alternative fragment length(s) may be 32 bps INFO @ Tue, 21 Apr 2015 13:00:17: #2.2 Generate R script for model : SRX026862.05_model.r WARNING @ Tue, 21 Apr 2015 13:00:17: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:00:17: #2 You may need to consider one of the other alternative d(s): 32 WARNING @ Tue, 21 Apr 2015 13:00:17: #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 13:00:17: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:00:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:01:44: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:01:49: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:01:53: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:02:54: #4 Write output xls file... SRX026862.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:02:54: #4 Write peak in narrowPeak format file... SRX026862.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:02:54: #4 Write summits bed file... SRX026862.20_summits.bed INFO @ Tue, 21 Apr 2015 13:02:54: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1213 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:02:57: #4 Write output xls file... SRX026862.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:02:57: #4 Write peak in narrowPeak format file... SRX026862.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:02:57: #4 Write summits bed file... SRX026862.10_summits.bed INFO @ Tue, 21 Apr 2015 13:02:57: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1915 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:03:01: #4 Write output xls file... SRX026862.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:03:01: #4 Write peak in narrowPeak format file... SRX026862.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:03:01: #4 Write summits bed file... SRX026862.05_summits.bed INFO @ Tue, 21 Apr 2015 13:03:01: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (2291 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。