Job ID = 2162402 sra ファイルのダウンロード中... Completed: 513354K bytes transferred in 7 seconds (577047K 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 35534 0 35534 0 0 49991 0 --:--:-- --:--:-- --:--:-- 68466 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 21327048 spots for /home/okishinya/chipatlas/results/dm3/SRX085399/SRR317177.sra Written 21327048 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: 00:06:25 21327048 reads; of these: 21327048 (100.00%) were unpaired; of these: 7608099 (35.67%) aligned 0 times 11892300 (55.76%) aligned exactly 1 time 1826649 (8.56%) aligned >1 times 64.33% overall alignment rate Time searching: 00:06:25 Overall time: 00:06:25 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] 8938970 / 13718949 = 0.6516 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 13:56:18: # Command line: callpeak -t SRX085399.bam -f BAM -g dm -n SRX085399.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX085399.05 # format = BAM # ChIP-seq file = ['SRX085399.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 13:56:18: # Command line: callpeak -t SRX085399.bam -f BAM -g dm -n SRX085399.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX085399.20 # format = BAM # ChIP-seq file = ['SRX085399.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 13:56:18: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:56:18: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:56:18: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:56:18: # Command line: callpeak -t SRX085399.bam -f BAM -g dm -n SRX085399.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX085399.10 # format = BAM # ChIP-seq file = ['SRX085399.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 13:56:18: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:56:18: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:56:18: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:56:24: 1000000 INFO @ Tue, 21 Apr 2015 13:56:24: 1000000 INFO @ Tue, 21 Apr 2015 13:56:24: 1000000 INFO @ Tue, 21 Apr 2015 13:56:30: 2000000 INFO @ Tue, 21 Apr 2015 13:56:30: 2000000 INFO @ Tue, 21 Apr 2015 13:56:30: 2000000 INFO @ Tue, 21 Apr 2015 13:56:35: 3000000 INFO @ Tue, 21 Apr 2015 13:56:35: 3000000 INFO @ Tue, 21 Apr 2015 13:56:35: 3000000 INFO @ Tue, 21 Apr 2015 13:56:41: 4000000 INFO @ Tue, 21 Apr 2015 13:56:41: 4000000 INFO @ Tue, 21 Apr 2015 13:56:41: 4000000 INFO @ Tue, 21 Apr 2015 13:56:46: #1 tag size is determined as 54 bps INFO @ Tue, 21 Apr 2015 13:56:46: #1 tag size = 54 INFO @ Tue, 21 Apr 2015 13:56:46: #1 total tags in treatment: 4779979 INFO @ Tue, 21 Apr 2015 13:56:46: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:56:46: #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 13:56:46: #1 tag size is determined as 54 bps INFO @ Tue, 21 Apr 2015 13:56:46: #1 tag size = 54 INFO @ Tue, 21 Apr 2015 13:56:46: #1 total tags in treatment: 4779979 INFO @ Tue, 21 Apr 2015 13:56:46: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:56:46: #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 13:56:46: #1 tag size is determined as 54 bps INFO @ Tue, 21 Apr 2015 13:56:46: #1 tag size = 54 INFO @ Tue, 21 Apr 2015 13:56:46: #1 total tags in treatment: 4779979 INFO @ Tue, 21 Apr 2015 13:56:46: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:56:46: #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 13:56:47: #1 tags after filtering in treatment: 4698220 INFO @ Tue, 21 Apr 2015 13:56:47: #1 Redundant rate of treatment: 0.02 INFO @ Tue, 21 Apr 2015 13:56:47: #1 finished! INFO @ Tue, 21 Apr 2015 13:56:47: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:56:47: #1 tags after filtering in treatment: 4698220 INFO @ Tue, 21 Apr 2015 13:56:47: #1 Redundant rate of treatment: 0.02 INFO @ Tue, 21 Apr 2015 13:56:47: #1 finished! INFO @ Tue, 21 Apr 2015 13:56:47: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:56:47: #1 tags after filtering in treatment: 4698220 INFO @ Tue, 21 Apr 2015 13:56:47: #1 Redundant rate of treatment: 0.02 INFO @ Tue, 21 Apr 2015 13:56:47: #1 finished! INFO @ Tue, 21 Apr 2015 13:56:47: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:56:48: #2 number of paired peaks: 5266 INFO @ Tue, 21 Apr 2015 13:56:48: start model_add_line... INFO @ Tue, 21 Apr 2015 13:56:48: #2 number of paired peaks: 5266 INFO @ Tue, 21 Apr 2015 13:56:48: start model_add_line... INFO @ Tue, 21 Apr 2015 13:56:48: #2 number of paired peaks: 5266 INFO @ Tue, 21 Apr 2015 13:56:48: start model_add_line... INFO @ Tue, 21 Apr 2015 13:57:05: start X-correlation... INFO @ Tue, 21 Apr 2015 13:57:05: end of X-cor INFO @ Tue, 21 Apr 2015 13:57:05: #2 finished! INFO @ Tue, 21 Apr 2015 13:57:05: #2 predicted fragment length is 59 bps INFO @ Tue, 21 Apr 2015 13:57:05: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 21 Apr 2015 13:57:05: #2.2 Generate R script for model : SRX085399.20_model.r WARNING @ Tue, 21 Apr 2015 13:57:05: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:57:05: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 21 Apr 2015 13:57:05: #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 13:57:05: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:57:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:57:06: start X-correlation... INFO @ Tue, 21 Apr 2015 13:57:06: end of X-cor INFO @ Tue, 21 Apr 2015 13:57:06: #2 finished! INFO @ Tue, 21 Apr 2015 13:57:06: #2 predicted fragment length is 59 bps INFO @ Tue, 21 Apr 2015 13:57:06: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 21 Apr 2015 13:57:06: #2.2 Generate R script for model : SRX085399.10_model.r WARNING @ Tue, 21 Apr 2015 13:57:06: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:57:06: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 21 Apr 2015 13:57:06: #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 13:57:06: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:57:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:57:07: start X-correlation... INFO @ Tue, 21 Apr 2015 13:57:07: end of X-cor INFO @ Tue, 21 Apr 2015 13:57:07: #2 finished! INFO @ Tue, 21 Apr 2015 13:57:07: #2 predicted fragment length is 59 bps INFO @ Tue, 21 Apr 2015 13:57:07: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 21 Apr 2015 13:57:07: #2.2 Generate R script for model : SRX085399.05_model.r WARNING @ Tue, 21 Apr 2015 13:57:07: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:57:07: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 21 Apr 2015 13:57:07: #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 13:57:07: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:57:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:57:30: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:57:31: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:57:32: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:57:51: #4 Write output xls file... SRX085399.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:57:51: #4 Write peak in narrowPeak format file... SRX085399.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:57:51: #4 Write summits bed file... SRX085399.20_summits.bed INFO @ Tue, 21 Apr 2015 13:57:52: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7083 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:57:56: #4 Write output xls file... SRX085399.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:57:56: #4 Write peak in narrowPeak format file... SRX085399.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:57:56: #4 Write summits bed file... SRX085399.10_summits.bed INFO @ Tue, 21 Apr 2015 13:57:56: #4 Write output xls file... SRX085399.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:57:56: Done! INFO @ Tue, 21 Apr 2015 13:57:56: #4 Write peak in narrowPeak format file... SRX085399.05_peaks.narrowPeak pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9696 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:57:56: #4 Write summits bed file... SRX085399.05_summits.bed INFO @ Tue, 21 Apr 2015 13:57:56: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (11989 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。