Job ID = 2161069 sra ファイルのダウンロード中... Completed: 122029K bytes transferred in 4 seconds (213561K 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 33847 0 33847 0 0 48804 0 --:--:-- --:--:-- --:--:-- 67424 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 5916696 spots for /home/okishinya/chipatlas/results/dm3/SRX013006/SRR030272.sra Written 5916696 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: 00:02:01 5916696 reads; of these: 5916696 (100.00%) were unpaired; of these: 1770740 (29.93%) aligned 0 times 2513002 (42.47%) aligned exactly 1 time 1632954 (27.60%) aligned >1 times 70.07% overall alignment rate Time searching: 00:02:01 Overall time: 00:02:01 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_rmdupse_core] 890690 / 4145956 = 0.2148 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 11:56:00: # Command line: callpeak -t SRX013006.bam -f BAM -g dm -n SRX013006.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013006.05 # format = BAM # ChIP-seq file = ['SRX013006.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 11:56:00: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:56:00: # Command line: callpeak -t SRX013006.bam -f BAM -g dm -n SRX013006.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013006.20 # format = BAM # ChIP-seq file = ['SRX013006.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 11:56:00: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 11:56:00: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:56:00: # Command line: callpeak -t SRX013006.bam -f BAM -g dm -n SRX013006.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013006.10 # format = BAM # ChIP-seq file = ['SRX013006.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 11:56:00: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 11:56:00: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:56:00: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 11:56:06: 1000000 INFO @ Tue, 21 Apr 2015 11:56:07: 1000000 INFO @ Tue, 21 Apr 2015 11:56:07: 1000000 INFO @ Tue, 21 Apr 2015 11:56:13: 2000000 INFO @ Tue, 21 Apr 2015 11:56:13: 2000000 INFO @ Tue, 21 Apr 2015 11:56:13: 2000000 INFO @ Tue, 21 Apr 2015 11:56:18: 3000000 INFO @ Tue, 21 Apr 2015 11:56:19: 3000000 INFO @ Tue, 21 Apr 2015 11:56:19: 3000000 INFO @ Tue, 21 Apr 2015 11:56:20: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 11:56:20: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 11:56:20: #1 total tags in treatment: 3255266 INFO @ Tue, 21 Apr 2015 11:56:20: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 11:56:20: #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 11:56:20: #1 tags after filtering in treatment: 3254231 INFO @ Tue, 21 Apr 2015 11:56:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 11:56:20: #1 finished! INFO @ Tue, 21 Apr 2015 11:56:20: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 11:56:21: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 11:56:21: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 11:56:21: #1 total tags in treatment: 3255266 INFO @ Tue, 21 Apr 2015 11:56:21: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 11:56:21: #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 11:56:21: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 11:56:21: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 11:56:21: #1 total tags in treatment: 3255266 INFO @ Tue, 21 Apr 2015 11:56:21: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 11:56:21: #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 11:56:21: #1 tags after filtering in treatment: 3254231 INFO @ Tue, 21 Apr 2015 11:56:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 11:56:21: #1 finished! INFO @ Tue, 21 Apr 2015 11:56:21: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 11:56:21: #1 tags after filtering in treatment: 3254231 INFO @ Tue, 21 Apr 2015 11:56:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 11:56:21: #1 finished! INFO @ Tue, 21 Apr 2015 11:56:21: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 11:56:21: #2 number of paired peaks: 208 WARNING @ Tue, 21 Apr 2015 11:56:21: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Tue, 21 Apr 2015 11:56:21: start model_add_line... INFO @ Tue, 21 Apr 2015 11:56:22: #2 number of paired peaks: 208 WARNING @ Tue, 21 Apr 2015 11:56:22: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Tue, 21 Apr 2015 11:56:22: start model_add_line... INFO @ Tue, 21 Apr 2015 11:56:22: #2 number of paired peaks: 208 WARNING @ Tue, 21 Apr 2015 11:56:22: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Tue, 21 Apr 2015 11:56:22: start model_add_line... INFO @ Tue, 21 Apr 2015 11:56:22: start X-correlation... INFO @ Tue, 21 Apr 2015 11:56:22: end of X-cor INFO @ Tue, 21 Apr 2015 11:56:22: #2 finished! INFO @ Tue, 21 Apr 2015 11:56:22: #2 predicted fragment length is 55 bps INFO @ Tue, 21 Apr 2015 11:56:22: #2 alternative fragment length(s) may be 55 bps INFO @ Tue, 21 Apr 2015 11:56:22: #2.2 Generate R script for model : SRX013006.10_model.r WARNING @ Tue, 21 Apr 2015 11:56:22: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 11:56:22: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Tue, 21 Apr 2015 11:56:22: #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 11:56:22: #3 Call peaks... INFO @ Tue, 21 Apr 2015 11:56:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 11:56:23: start X-correlation... INFO @ Tue, 21 Apr 2015 11:56:23: end of X-cor INFO @ Tue, 21 Apr 2015 11:56:23: #2 finished! INFO @ Tue, 21 Apr 2015 11:56:23: #2 predicted fragment length is 55 bps INFO @ Tue, 21 Apr 2015 11:56:23: #2 alternative fragment length(s) may be 55 bps INFO @ Tue, 21 Apr 2015 11:56:23: #2.2 Generate R script for model : SRX013006.20_model.r WARNING @ Tue, 21 Apr 2015 11:56:23: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 11:56:23: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Tue, 21 Apr 2015 11:56:23: #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 11:56:23: #3 Call peaks... INFO @ Tue, 21 Apr 2015 11:56:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 11:56:23: start X-correlation... INFO @ Tue, 21 Apr 2015 11:56:23: end of X-cor INFO @ Tue, 21 Apr 2015 11:56:23: #2 finished! INFO @ Tue, 21 Apr 2015 11:56:23: #2 predicted fragment length is 55 bps INFO @ Tue, 21 Apr 2015 11:56:23: #2 alternative fragment length(s) may be 55 bps INFO @ Tue, 21 Apr 2015 11:56:23: #2.2 Generate R script for model : SRX013006.05_model.r WARNING @ Tue, 21 Apr 2015 11:56:23: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 11:56:23: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Tue, 21 Apr 2015 11:56:23: #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 11:56:23: #3 Call peaks... INFO @ Tue, 21 Apr 2015 11:56:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 11:56:41: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 11:56:42: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 11:56:42: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 11:56:55: #4 Write output xls file... SRX013006.05_peaks.xls INFO @ Tue, 21 Apr 2015 11:56:55: #4 Write peak in narrowPeak format file... SRX013006.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 11:56:55: #4 Write summits bed file... SRX013006.05_summits.bed INFO @ Tue, 21 Apr 2015 11:56:55: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1672 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 11:56:55: #4 Write output xls file... SRX013006.10_peaks.xls INFO @ Tue, 21 Apr 2015 11:56:56: #4 Write peak in narrowPeak format file... SRX013006.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 11:56:56: #4 Write summits bed file... SRX013006.10_summits.bed INFO @ Tue, 21 Apr 2015 11:56:56: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (905 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 11:56:57: #4 Write output xls file... SRX013006.20_peaks.xls INFO @ Tue, 21 Apr 2015 11:56:57: #4 Write peak in narrowPeak format file... SRX013006.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 11:56:57: #4 Write summits bed file... SRX013006.20_summits.bed INFO @ Tue, 21 Apr 2015 11:56:57: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (491 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。