Job ID = 2162385 sra ファイルのダウンロード中... Completed: 816368K bytes transferred in 10 seconds (619054K bits/sec), in 3 files, 4 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 1082 0 1082 0 0 1888 0 --:--:-- --:--:-- --:--:-- 2832 100 36203 0 36203 0 0 47470 0 --:--:-- --:--:-- --:--:-- 63291 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 6154521 spots for /home/okishinya/chipatlas/results/dm3/SRX066244/SRR222070.sra Written 6154521 spots total Written 19544210 spots for /home/okishinya/chipatlas/results/dm3/SRX066244/SRR222069.sra Written 19544210 spots total Written 21380857 spots for /home/okishinya/chipatlas/results/dm3/SRX066244/SRR222071.sra Written 21380857 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: 00:11:25 47079588 reads; of these: 47079588 (100.00%) were unpaired; of these: 19637079 (41.71%) aligned 0 times 20451924 (43.44%) aligned exactly 1 time 6990585 (14.85%) aligned >1 times 58.29% overall alignment rate Time searching: 00:11:25 Overall time: 00:11:25 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] 16971953 / 27442509 = 0.6185 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 13:56:12: # Command line: callpeak -t SRX066244.bam -f BAM -g dm -n SRX066244.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX066244.05 # format = BAM # ChIP-seq file = ['SRX066244.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 13:56:12: # Command line: callpeak -t SRX066244.bam -f BAM -g dm -n SRX066244.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX066244.20 # format = BAM # ChIP-seq file = ['SRX066244.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 13:56:12: # Command line: callpeak -t SRX066244.bam -f BAM -g dm -n SRX066244.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX066244.10 # format = BAM # ChIP-seq file = ['SRX066244.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 13:56:12: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:56:12: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:56:12: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:56:12: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:56:12: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:56:12: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:56:18: 1000000 INFO @ Tue, 21 Apr 2015 13:56:18: 1000000 INFO @ Tue, 21 Apr 2015 13:56:18: 1000000 INFO @ Tue, 21 Apr 2015 13:56:24: 2000000 INFO @ Tue, 21 Apr 2015 13:56:24: 2000000 INFO @ Tue, 21 Apr 2015 13:56:24: 2000000 INFO @ Tue, 21 Apr 2015 13:56:31: 3000000 INFO @ Tue, 21 Apr 2015 13:56:31: 3000000 INFO @ Tue, 21 Apr 2015 13:56:31: 3000000 INFO @ Tue, 21 Apr 2015 13:56:37: 4000000 INFO @ Tue, 21 Apr 2015 13:56:37: 4000000 INFO @ Tue, 21 Apr 2015 13:56:37: 4000000 INFO @ Tue, 21 Apr 2015 13:56:43: 5000000 INFO @ Tue, 21 Apr 2015 13:56:43: 5000000 INFO @ Tue, 21 Apr 2015 13:56:43: 5000000 INFO @ Tue, 21 Apr 2015 13:56:49: 6000000 INFO @ Tue, 21 Apr 2015 13:56:49: 6000000 INFO @ Tue, 21 Apr 2015 13:56:49: 6000000 INFO @ Tue, 21 Apr 2015 13:56:55: 7000000 INFO @ Tue, 21 Apr 2015 13:56:55: 7000000 INFO @ Tue, 21 Apr 2015 13:56:55: 7000000 INFO @ Tue, 21 Apr 2015 13:57:01: 8000000 INFO @ Tue, 21 Apr 2015 13:57:01: 8000000 INFO @ Tue, 21 Apr 2015 13:57:01: 8000000 INFO @ Tue, 21 Apr 2015 13:57:07: 9000000 INFO @ Tue, 21 Apr 2015 13:57:07: 9000000 INFO @ Tue, 21 Apr 2015 13:57:07: 9000000 INFO @ Tue, 21 Apr 2015 13:57:13: 10000000 INFO @ Tue, 21 Apr 2015 13:57:13: 10000000 INFO @ Tue, 21 Apr 2015 13:57:13: 10000000 INFO @ Tue, 21 Apr 2015 13:57:16: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:57:16: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:57:16: #1 total tags in treatment: 10470556 INFO @ Tue, 21 Apr 2015 13:57:16: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:57:16: #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 13:57:16: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:57:16: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:57:16: #1 total tags in treatment: 10470556 INFO @ Tue, 21 Apr 2015 13:57:16: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:57:16: #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 13:57:16: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:57:16: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:57:16: #1 total tags in treatment: 10470556 INFO @ Tue, 21 Apr 2015 13:57:16: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:57:16: #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 13:57:18: #1 tags after filtering in treatment: 10468985 INFO @ Tue, 21 Apr 2015 13:57:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:57:18: #1 finished! INFO @ Tue, 21 Apr 2015 13:57:18: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:57:18: #1 tags after filtering in treatment: 10468985 INFO @ Tue, 21 Apr 2015 13:57:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:57:18: #1 finished! INFO @ Tue, 21 Apr 2015 13:57:18: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:57:18: #1 tags after filtering in treatment: 10468985 INFO @ Tue, 21 Apr 2015 13:57:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:57:18: #1 finished! INFO @ Tue, 21 Apr 2015 13:57:18: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:57:19: #2 number of paired peaks: 509 WARNING @ Tue, 21 Apr 2015 13:57:19: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Tue, 21 Apr 2015 13:57:19: start model_add_line... INFO @ Tue, 21 Apr 2015 13:57:19: #2 number of paired peaks: 509 WARNING @ Tue, 21 Apr 2015 13:57:19: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Tue, 21 Apr 2015 13:57:19: start model_add_line... INFO @ Tue, 21 Apr 2015 13:57:20: #2 number of paired peaks: 509 WARNING @ Tue, 21 Apr 2015 13:57:20: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Tue, 21 Apr 2015 13:57:20: start model_add_line... INFO @ Tue, 21 Apr 2015 13:57:23: start X-correlation... INFO @ Tue, 21 Apr 2015 13:57:23: end of X-cor INFO @ Tue, 21 Apr 2015 13:57:23: #2 finished! INFO @ Tue, 21 Apr 2015 13:57:23: #2 predicted fragment length is 46 bps INFO @ Tue, 21 Apr 2015 13:57:23: #2 alternative fragment length(s) may be 46 bps INFO @ Tue, 21 Apr 2015 13:57:23: #2.2 Generate R script for model : SRX066244.10_model.r WARNING @ Tue, 21 Apr 2015 13:57:23: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:57:23: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Tue, 21 Apr 2015 13:57:23: #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 13:57:23: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:57:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:57:23: start X-correlation... INFO @ Tue, 21 Apr 2015 13:57:23: end of X-cor INFO @ Tue, 21 Apr 2015 13:57:23: #2 finished! INFO @ Tue, 21 Apr 2015 13:57:23: #2 predicted fragment length is 46 bps INFO @ Tue, 21 Apr 2015 13:57:23: #2 alternative fragment length(s) may be 46 bps INFO @ Tue, 21 Apr 2015 13:57:23: #2.2 Generate R script for model : SRX066244.05_model.r WARNING @ Tue, 21 Apr 2015 13:57:23: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:57:23: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Tue, 21 Apr 2015 13:57:23: #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 13:57:23: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:57:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:57:23: start X-correlation... INFO @ Tue, 21 Apr 2015 13:57:23: end of X-cor INFO @ Tue, 21 Apr 2015 13:57:23: #2 finished! INFO @ Tue, 21 Apr 2015 13:57:23: #2 predicted fragment length is 46 bps INFO @ Tue, 21 Apr 2015 13:57:23: #2 alternative fragment length(s) may be 46 bps INFO @ Tue, 21 Apr 2015 13:57:23: #2.2 Generate R script for model : SRX066244.20_model.r WARNING @ Tue, 21 Apr 2015 13:57:23: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:57:23: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Tue, 21 Apr 2015 13:57:23: #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 13:57:23: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:57:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:58:20: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:58:20: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:58:20: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:59:01: #4 Write output xls file... SRX066244.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:59:01: #4 Write peak in narrowPeak format file... SRX066244.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:59:01: #4 Write summits bed file... SRX066244.10_summits.bed INFO @ Tue, 21 Apr 2015 13:59:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2577 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:59:01: #4 Write output xls file... SRX066244.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:59:01: #4 Write peak in narrowPeak format file... SRX066244.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:59:01: #4 Write summits bed file... SRX066244.20_summits.bed INFO @ Tue, 21 Apr 2015 13:59:01: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1050 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:59:04: #4 Write output xls file... SRX066244.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:59:05: #4 Write peak in narrowPeak format file... SRX066244.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:59:05: #4 Write summits bed file... SRX066244.05_summits.bed INFO @ Tue, 21 Apr 2015 13:59:05: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6696 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。