Job ID = 2162161 sra ファイルのダウンロード中... Completed: 75967K bytes transferred in 4 seconds (150284K 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 --:--:-- --:--:-- --:--:-- 0 108 1088 0 1088 0 0 1831 0 --:--:-- --:--:-- --:--:-- 2699 100 35430 0 35430 0 0 45183 0 --:--:-- --:--:-- --:--:-- 59747 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 3973515 spots for /home/okishinya/chipatlas/results/dm3/SRX050598/SRR139080.sra Written 3973515 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:02 3973515 reads; of these: 3973515 (100.00%) were unpaired; of these: 179402 (4.51%) aligned 0 times 2970261 (74.75%) aligned exactly 1 time 823852 (20.73%) aligned >1 times 95.49% overall alignment rate Time searching: 00:01:03 Overall time: 00:01:03 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] 96601 / 3794113 = 0.0255 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 13:32:09: # Command line: callpeak -t SRX050598.bam -f BAM -g dm -n SRX050598.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX050598.20 # format = BAM # ChIP-seq file = ['SRX050598.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 13:32:09: # Command line: callpeak -t SRX050598.bam -f BAM -g dm -n SRX050598.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX050598.05 # format = BAM # ChIP-seq file = ['SRX050598.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 13:32:09: # Command line: callpeak -t SRX050598.bam -f BAM -g dm -n SRX050598.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX050598.10 # format = BAM # ChIP-seq file = ['SRX050598.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 13:32:09: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:32:09: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:32:09: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:32:09: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:32:09: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:32:09: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:32:14: 1000000 INFO @ Tue, 21 Apr 2015 13:32:15: 1000000 INFO @ Tue, 21 Apr 2015 13:32:15: 1000000 INFO @ Tue, 21 Apr 2015 13:32:20: 2000000 INFO @ Tue, 21 Apr 2015 13:32:21: 2000000 INFO @ Tue, 21 Apr 2015 13:32:21: 2000000 INFO @ Tue, 21 Apr 2015 13:32:25: 3000000 INFO @ Tue, 21 Apr 2015 13:32:27: 3000000 INFO @ Tue, 21 Apr 2015 13:32:27: 3000000 INFO @ Tue, 21 Apr 2015 13:32:29: #1 tag size is determined as 30 bps INFO @ Tue, 21 Apr 2015 13:32:29: #1 tag size = 30 INFO @ Tue, 21 Apr 2015 13:32:29: #1 total tags in treatment: 3697512 INFO @ Tue, 21 Apr 2015 13:32:29: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:32:29: #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 13:32:30: #1 tags after filtering in treatment: 3697429 INFO @ Tue, 21 Apr 2015 13:32:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:32:30: #1 finished! INFO @ Tue, 21 Apr 2015 13:32:30: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:32:30: #2 number of paired peaks: 309 WARNING @ Tue, 21 Apr 2015 13:32:30: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Tue, 21 Apr 2015 13:32:30: start model_add_line... INFO @ Tue, 21 Apr 2015 13:32:31: start X-correlation... INFO @ Tue, 21 Apr 2015 13:32:31: end of X-cor INFO @ Tue, 21 Apr 2015 13:32:31: #2 finished! INFO @ Tue, 21 Apr 2015 13:32:31: #2 predicted fragment length is 42 bps INFO @ Tue, 21 Apr 2015 13:32:31: #2 alternative fragment length(s) may be 42 bps INFO @ Tue, 21 Apr 2015 13:32:31: #2.2 Generate R script for model : SRX050598.20_model.r WARNING @ Tue, 21 Apr 2015 13:32:31: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:32:31: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Tue, 21 Apr 2015 13:32:31: #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 13:32:31: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:32:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:32:31: #1 tag size is determined as 30 bps INFO @ Tue, 21 Apr 2015 13:32:31: #1 tag size = 30 INFO @ Tue, 21 Apr 2015 13:32:31: #1 total tags in treatment: 3697512 INFO @ Tue, 21 Apr 2015 13:32:31: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:32:31: #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 13:32:31: #1 tag size is determined as 30 bps INFO @ Tue, 21 Apr 2015 13:32:31: #1 tag size = 30 INFO @ Tue, 21 Apr 2015 13:32:31: #1 total tags in treatment: 3697512 INFO @ Tue, 21 Apr 2015 13:32:31: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:32:31: #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 13:32:32: #1 tags after filtering in treatment: 3697429 INFO @ Tue, 21 Apr 2015 13:32:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:32:32: #1 finished! INFO @ Tue, 21 Apr 2015 13:32:32: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:32:32: #1 tags after filtering in treatment: 3697429 INFO @ Tue, 21 Apr 2015 13:32:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:32:32: #1 finished! INFO @ Tue, 21 Apr 2015 13:32:32: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:32:33: #2 number of paired peaks: 309 WARNING @ Tue, 21 Apr 2015 13:32:33: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Tue, 21 Apr 2015 13:32:33: start model_add_line... INFO @ Tue, 21 Apr 2015 13:32:33: #2 number of paired peaks: 309 WARNING @ Tue, 21 Apr 2015 13:32:33: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Tue, 21 Apr 2015 13:32:33: start model_add_line... INFO @ Tue, 21 Apr 2015 13:32:34: start X-correlation... INFO @ Tue, 21 Apr 2015 13:32:34: end of X-cor INFO @ Tue, 21 Apr 2015 13:32:34: #2 finished! INFO @ Tue, 21 Apr 2015 13:32:34: #2 predicted fragment length is 42 bps INFO @ Tue, 21 Apr 2015 13:32:34: #2 alternative fragment length(s) may be 42 bps INFO @ Tue, 21 Apr 2015 13:32:34: #2.2 Generate R script for model : SRX050598.05_model.r WARNING @ Tue, 21 Apr 2015 13:32:34: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:32:34: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Tue, 21 Apr 2015 13:32:34: #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 13:32:34: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:32:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:32:34: start X-correlation... INFO @ Tue, 21 Apr 2015 13:32:34: end of X-cor INFO @ Tue, 21 Apr 2015 13:32:34: #2 finished! INFO @ Tue, 21 Apr 2015 13:32:34: #2 predicted fragment length is 42 bps INFO @ Tue, 21 Apr 2015 13:32:34: #2 alternative fragment length(s) may be 42 bps INFO @ Tue, 21 Apr 2015 13:32:34: #2.2 Generate R script for model : SRX050598.10_model.r WARNING @ Tue, 21 Apr 2015 13:32:34: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:32:34: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Tue, 21 Apr 2015 13:32:34: #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 13:32:34: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:32:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:32:53: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:32:55: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:32:56: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:33:07: #4 Write output xls file... SRX050598.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:33:07: #4 Write peak in narrowPeak format file... SRX050598.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:33:07: #4 Write summits bed file... SRX050598.20_summits.bed INFO @ Tue, 21 Apr 2015 13:33:07: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (304 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:33:11: #4 Write output xls file... SRX050598.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:33:11: #4 Write peak in narrowPeak format file... SRX050598.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:33:11: #4 Write summits bed file... SRX050598.10_summits.bed INFO @ Tue, 21 Apr 2015 13:33:11: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (477 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:33:12: #4 Write output xls file... SRX050598.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:33:12: #4 Write peak in narrowPeak format file... SRX050598.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:33:12: #4 Write summits bed file... SRX050598.05_summits.bed INFO @ Tue, 21 Apr 2015 13:33:12: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (988 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。