Job ID = 2162424 sra ファイルのダウンロード中... Completed: 674606K bytes transferred in 8 seconds (688562K 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 36867 0 36867 0 0 49420 0 --:--:-- --:--:-- --:--:-- 66546 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 30067888 spots for /home/okishinya/chipatlas/results/dm3/SRX097616/SRR345567.sra Written 30067888 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: 00:09:26 30067888 reads; of these: 30067888 (100.00%) were unpaired; of these: 3393974 (11.29%) aligned 0 times 20041514 (66.65%) aligned exactly 1 time 6632400 (22.06%) aligned >1 times 88.71% overall alignment rate Time searching: 00:09:26 Overall time: 00:09:26 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] 16064874 / 26673914 = 0.6023 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 14:08:54: # Command line: callpeak -t SRX097616.bam -f BAM -g dm -n SRX097616.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX097616.10 # format = BAM # ChIP-seq file = ['SRX097616.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 14:08:54: # Command line: callpeak -t SRX097616.bam -f BAM -g dm -n SRX097616.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX097616.20 # format = BAM # ChIP-seq file = ['SRX097616.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 14:08:54: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:08:54: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:08:54: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:08:54: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:08:54: # Command line: callpeak -t SRX097616.bam -f BAM -g dm -n SRX097616.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX097616.05 # format = BAM # ChIP-seq file = ['SRX097616.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 14:08:54: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:08:54: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:09:00: 1000000 INFO @ Tue, 21 Apr 2015 14:09:01: 1000000 INFO @ Tue, 21 Apr 2015 14:09:01: 1000000 INFO @ Tue, 21 Apr 2015 14:09:06: 2000000 INFO @ Tue, 21 Apr 2015 14:09:07: 2000000 INFO @ Tue, 21 Apr 2015 14:09:07: 2000000 INFO @ Tue, 21 Apr 2015 14:09:12: 3000000 INFO @ Tue, 21 Apr 2015 14:09:13: 3000000 INFO @ Tue, 21 Apr 2015 14:09:13: 3000000 INFO @ Tue, 21 Apr 2015 14:09:18: 4000000 INFO @ Tue, 21 Apr 2015 14:09:19: 4000000 INFO @ Tue, 21 Apr 2015 14:09:20: 4000000 INFO @ Tue, 21 Apr 2015 14:09:24: 5000000 INFO @ Tue, 21 Apr 2015 14:09:25: 5000000 INFO @ Tue, 21 Apr 2015 14:09:27: 5000000 INFO @ Tue, 21 Apr 2015 14:09:30: 6000000 INFO @ Tue, 21 Apr 2015 14:09:32: 6000000 INFO @ Tue, 21 Apr 2015 14:09:33: 6000000 INFO @ Tue, 21 Apr 2015 14:09:37: 7000000 INFO @ Tue, 21 Apr 2015 14:09:39: 7000000 INFO @ Tue, 21 Apr 2015 14:09:41: 7000000 INFO @ Tue, 21 Apr 2015 14:09:46: 8000000 INFO @ Tue, 21 Apr 2015 14:09:46: 8000000 INFO @ Tue, 21 Apr 2015 14:09:48: 8000000 INFO @ Tue, 21 Apr 2015 14:09:53: 9000000 INFO @ Tue, 21 Apr 2015 14:09:53: 9000000 INFO @ Tue, 21 Apr 2015 14:09:56: 9000000 INFO @ Tue, 21 Apr 2015 14:10:00: 10000000 INFO @ Tue, 21 Apr 2015 14:10:01: 10000000 INFO @ Tue, 21 Apr 2015 14:10:03: 10000000 INFO @ Tue, 21 Apr 2015 14:10:05: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 14:10:05: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 14:10:05: #1 total tags in treatment: 10609040 INFO @ Tue, 21 Apr 2015 14:10:05: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:10:05: #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 14:10:06: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 14:10:06: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 14:10:06: #1 total tags in treatment: 10609040 INFO @ Tue, 21 Apr 2015 14:10:06: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:10:06: #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 14:10:07: #1 tags after filtering in treatment: 10607570 INFO @ Tue, 21 Apr 2015 14:10:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:10:07: #1 finished! INFO @ Tue, 21 Apr 2015 14:10:07: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:10:07: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 14:10:07: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 14:10:07: #1 total tags in treatment: 10609040 INFO @ Tue, 21 Apr 2015 14:10:07: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:10:07: #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 14:10:08: #1 tags after filtering in treatment: 10607570 INFO @ Tue, 21 Apr 2015 14:10:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:10:08: #1 finished! INFO @ Tue, 21 Apr 2015 14:10:08: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:10:09: #2 number of paired peaks: 1681 INFO @ Tue, 21 Apr 2015 14:10:09: start model_add_line... INFO @ Tue, 21 Apr 2015 14:10:09: #1 tags after filtering in treatment: 10607570 INFO @ Tue, 21 Apr 2015 14:10:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:10:09: #1 finished! INFO @ Tue, 21 Apr 2015 14:10:09: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:10:10: #2 number of paired peaks: 1681 INFO @ Tue, 21 Apr 2015 14:10:10: start model_add_line... INFO @ Tue, 21 Apr 2015 14:10:11: #2 number of paired peaks: 1681 INFO @ Tue, 21 Apr 2015 14:10:11: start model_add_line... INFO @ Tue, 21 Apr 2015 14:10:21: start X-correlation... INFO @ Tue, 21 Apr 2015 14:10:21: end of X-cor INFO @ Tue, 21 Apr 2015 14:10:21: #2 finished! INFO @ Tue, 21 Apr 2015 14:10:21: #2 predicted fragment length is 80 bps INFO @ Tue, 21 Apr 2015 14:10:21: #2 alternative fragment length(s) may be 80 bps INFO @ Tue, 21 Apr 2015 14:10:21: #2.2 Generate R script for model : SRX097616.10_model.r WARNING @ Tue, 21 Apr 2015 14:10:21: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 14:10:21: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Tue, 21 Apr 2015 14:10:21: #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 14:10:21: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:10:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:10:22: start X-correlation... INFO @ Tue, 21 Apr 2015 14:10:22: end of X-cor INFO @ Tue, 21 Apr 2015 14:10:22: #2 finished! INFO @ Tue, 21 Apr 2015 14:10:22: #2 predicted fragment length is 80 bps INFO @ Tue, 21 Apr 2015 14:10:22: #2 alternative fragment length(s) may be 80 bps INFO @ Tue, 21 Apr 2015 14:10:22: #2.2 Generate R script for model : SRX097616.05_model.r WARNING @ Tue, 21 Apr 2015 14:10:22: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 14:10:22: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Tue, 21 Apr 2015 14:10:22: #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 14:10:22: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:10:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:10:23: start X-correlation... INFO @ Tue, 21 Apr 2015 14:10:23: end of X-cor INFO @ Tue, 21 Apr 2015 14:10:23: #2 finished! INFO @ Tue, 21 Apr 2015 14:10:23: #2 predicted fragment length is 80 bps INFO @ Tue, 21 Apr 2015 14:10:23: #2 alternative fragment length(s) may be 80 bps INFO @ Tue, 21 Apr 2015 14:10:23: #2.2 Generate R script for model : SRX097616.20_model.r WARNING @ Tue, 21 Apr 2015 14:10:23: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 14:10:23: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Tue, 21 Apr 2015 14:10:23: #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 14:10:23: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:10:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:11:20: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:11:21: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:11:21: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:12:04: #4 Write output xls file... SRX097616.10_peaks.xls INFO @ Tue, 21 Apr 2015 14:12:05: #4 Write peak in narrowPeak format file... SRX097616.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:12:05: #4 Write summits bed file... SRX097616.10_summits.bed INFO @ Tue, 21 Apr 2015 14:12:05: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4410 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:12:05: #4 Write output xls file... SRX097616.20_peaks.xls INFO @ Tue, 21 Apr 2015 14:12:05: #4 Write peak in narrowPeak format file... SRX097616.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:12:05: #4 Write summits bed file... SRX097616.20_summits.bed INFO @ Tue, 21 Apr 2015 14:12:05: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2365 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:12:08: #4 Write output xls file... SRX097616.05_peaks.xls INFO @ Tue, 21 Apr 2015 14:12:08: #4 Write peak in narrowPeak format file... SRX097616.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:12:08: #4 Write summits bed file... SRX097616.05_summits.bed INFO @ Tue, 21 Apr 2015 14:12:08: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6909 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。