Job ID = 2161385 sra ファイルのダウンロード中... Completed: 460323K bytes transferred in 7 seconds (525240K bits/sec), in 2 files, 3 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 44448 0 44448 0 0 47458 0 --:--:-- --:--:-- --:--:-- 59581 100 44448 0 44448 0 0 47418 0 --:--:-- --:--:-- --:--:-- 59502 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 4441203 spots for /home/okishinya/chipatlas/results/dm3/SRX025474/SRR063872.sra Written 4441203 spots total Written 14214811 spots for /home/okishinya/chipatlas/results/dm3/SRX025474/SRR063871.sra Written 14214811 spots total 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: 00:05:24 18656014 reads; of these: 18656014 (100.00%) were unpaired; of these: 1310592 (7.03%) aligned 0 times 13673518 (73.29%) aligned exactly 1 time 3671904 (19.68%) aligned >1 times 92.97% overall alignment rate Time searching: 00:05:24 Overall time: 00:05:24 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] 5212810 / 17345422 = 0.3005 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 12:40:48: # Command line: callpeak -t SRX025474.bam -f BAM -g dm -n SRX025474.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX025474.20 # format = BAM # ChIP-seq file = ['SRX025474.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 12:40:48: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:40:48: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:40:48: # Command line: callpeak -t SRX025474.bam -f BAM -g dm -n SRX025474.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX025474.05 # format = BAM # ChIP-seq file = ['SRX025474.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 12:40:48: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:40:48: # Command line: callpeak -t SRX025474.bam -f BAM -g dm -n SRX025474.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX025474.10 # format = BAM # ChIP-seq file = ['SRX025474.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 12:40:48: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:40:48: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:40:48: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:40:54: 1000000 INFO @ Tue, 21 Apr 2015 12:40:54: 1000000 INFO @ Tue, 21 Apr 2015 12:40:54: 1000000 INFO @ Tue, 21 Apr 2015 12:41:01: 2000000 INFO @ Tue, 21 Apr 2015 12:41:01: 2000000 INFO @ Tue, 21 Apr 2015 12:41:01: 2000000 INFO @ Tue, 21 Apr 2015 12:41:06: 3000000 INFO @ Tue, 21 Apr 2015 12:41:06: 3000000 INFO @ Tue, 21 Apr 2015 12:41:07: 3000000 INFO @ Tue, 21 Apr 2015 12:41:12: 4000000 INFO @ Tue, 21 Apr 2015 12:41:12: 4000000 INFO @ Tue, 21 Apr 2015 12:41:13: 4000000 INFO @ Tue, 21 Apr 2015 12:41:18: 5000000 INFO @ Tue, 21 Apr 2015 12:41:18: 5000000 INFO @ Tue, 21 Apr 2015 12:41:18: 5000000 INFO @ Tue, 21 Apr 2015 12:41:24: 6000000 INFO @ Tue, 21 Apr 2015 12:41:24: 6000000 INFO @ Tue, 21 Apr 2015 12:41:24: 6000000 INFO @ Tue, 21 Apr 2015 12:41:30: 7000000 INFO @ Tue, 21 Apr 2015 12:41:30: 7000000 INFO @ Tue, 21 Apr 2015 12:41:30: 7000000 INFO @ Tue, 21 Apr 2015 12:41:36: 8000000 INFO @ Tue, 21 Apr 2015 12:41:36: 8000000 INFO @ Tue, 21 Apr 2015 12:41:36: 8000000 INFO @ Tue, 21 Apr 2015 12:41:42: 9000000 INFO @ Tue, 21 Apr 2015 12:41:42: 9000000 INFO @ Tue, 21 Apr 2015 12:41:42: 9000000 INFO @ Tue, 21 Apr 2015 12:41:48: 10000000 INFO @ Tue, 21 Apr 2015 12:41:48: 10000000 INFO @ Tue, 21 Apr 2015 12:41:48: 10000000 INFO @ Tue, 21 Apr 2015 12:41:54: 11000000 INFO @ Tue, 21 Apr 2015 12:41:54: 11000000 INFO @ Tue, 21 Apr 2015 12:41:55: 11000000 INFO @ Tue, 21 Apr 2015 12:42:00: 12000000 INFO @ Tue, 21 Apr 2015 12:42:01: 12000000 INFO @ Tue, 21 Apr 2015 12:42:01: 12000000 INFO @ Tue, 21 Apr 2015 12:42:01: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:42:01: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:42:01: #1 total tags in treatment: 12132612 INFO @ Tue, 21 Apr 2015 12:42:01: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:42:01: #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 12:42:02: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:42:02: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:42:02: #1 total tags in treatment: 12132612 INFO @ Tue, 21 Apr 2015 12:42:02: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:42:02: #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 12:42:02: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:42:02: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:42:02: #1 total tags in treatment: 12132612 INFO @ Tue, 21 Apr 2015 12:42:02: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:42:02: #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 12:42:04: #1 tags after filtering in treatment: 12131845 INFO @ Tue, 21 Apr 2015 12:42:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:42:04: #1 finished! INFO @ Tue, 21 Apr 2015 12:42:04: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:42:05: #1 tags after filtering in treatment: 12131845 INFO @ Tue, 21 Apr 2015 12:42:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:42:05: #1 finished! INFO @ Tue, 21 Apr 2015 12:42:05: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:42:05: #1 tags after filtering in treatment: 12131845 INFO @ Tue, 21 Apr 2015 12:42:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:42:05: #1 finished! INFO @ Tue, 21 Apr 2015 12:42:05: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:42:06: #2 number of paired peaks: 165 WARNING @ Tue, 21 Apr 2015 12:42:06: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Tue, 21 Apr 2015 12:42:06: start model_add_line... INFO @ Tue, 21 Apr 2015 12:42:07: #2 number of paired peaks: 165 WARNING @ Tue, 21 Apr 2015 12:42:07: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Tue, 21 Apr 2015 12:42:07: start model_add_line... INFO @ Tue, 21 Apr 2015 12:42:07: #2 number of paired peaks: 165 WARNING @ Tue, 21 Apr 2015 12:42:07: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Tue, 21 Apr 2015 12:42:07: start model_add_line... INFO @ Tue, 21 Apr 2015 12:42:07: start X-correlation... INFO @ Tue, 21 Apr 2015 12:42:07: end of X-cor INFO @ Tue, 21 Apr 2015 12:42:07: #2 finished! INFO @ Tue, 21 Apr 2015 12:42:07: #2 predicted fragment length is 38 bps INFO @ Tue, 21 Apr 2015 12:42:07: #2 alternative fragment length(s) may be 38 bps INFO @ Tue, 21 Apr 2015 12:42:07: #2.2 Generate R script for model : SRX025474.10_model.r WARNING @ Tue, 21 Apr 2015 12:42:07: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:42:07: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Tue, 21 Apr 2015 12:42:07: #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 12:42:07: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:42:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:42:08: start X-correlation... INFO @ Tue, 21 Apr 2015 12:42:08: end of X-cor INFO @ Tue, 21 Apr 2015 12:42:08: #2 finished! INFO @ Tue, 21 Apr 2015 12:42:08: #2 predicted fragment length is 38 bps INFO @ Tue, 21 Apr 2015 12:42:08: #2 alternative fragment length(s) may be 38 bps INFO @ Tue, 21 Apr 2015 12:42:08: #2.2 Generate R script for model : SRX025474.05_model.r WARNING @ Tue, 21 Apr 2015 12:42:08: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:42:08: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Tue, 21 Apr 2015 12:42:08: #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 12:42:08: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:42:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:42:08: start X-correlation... INFO @ Tue, 21 Apr 2015 12:42:08: end of X-cor INFO @ Tue, 21 Apr 2015 12:42:08: #2 finished! INFO @ Tue, 21 Apr 2015 12:42:08: #2 predicted fragment length is 38 bps INFO @ Tue, 21 Apr 2015 12:42:08: #2 alternative fragment length(s) may be 38 bps INFO @ Tue, 21 Apr 2015 12:42:08: #2.2 Generate R script for model : SRX025474.20_model.r WARNING @ Tue, 21 Apr 2015 12:42:08: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:42:08: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Tue, 21 Apr 2015 12:42:08: #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 12:42:08: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:42:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:43:07: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:43:10: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:43:14: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:43:52: #4 Write output xls file... SRX025474.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:43:52: #4 Write peak in narrowPeak format file... SRX025474.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:43:52: #4 Write summits bed file... SRX025474.20_summits.bed INFO @ Tue, 21 Apr 2015 12:43:52: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (431 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:43:56: #4 Write output xls file... SRX025474.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:43:56: #4 Write peak in narrowPeak format file... SRX025474.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:43:56: #4 Write summits bed file... SRX025474.05_summits.bed INFO @ Tue, 21 Apr 2015 12:43:56: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (998 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:43:59: #4 Write output xls file... SRX025474.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:43:59: #4 Write peak in narrowPeak format file... SRX025474.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:43:59: #4 Write summits bed file... SRX025474.10_summits.bed INFO @ Tue, 21 Apr 2015 12:43:59: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (667 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。