Job ID = 6983654 sra ファイルのダウンロード中... Completed: 282899K bytes transferred in 7 seconds (301003K 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 35001 0 35001 0 0 46762 0 --:--:-- --:--:-- --:--:-- 61405 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 11285580 spots for /home/okishinya/chipatlas/results/dm3/SRX017462/SRR037519.sra Written 11285580 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: 00:01:46 11285580 reads; of these: 11285580 (100.00%) were unpaired; of these: 7847564 (69.54%) aligned 0 times 2525886 (22.38%) aligned exactly 1 time 912130 (8.08%) aligned >1 times 30.46% overall alignment rate Time searching: 00:01:46 Overall time: 00:01:46 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] 785280 / 3438016 = 0.2284 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 @ Sun, 05 Jun 2016 15:33:37: # Command line: callpeak -t SRX017462.bam -f BAM -g dm -n SRX017462.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX017462.20 # format = BAM # ChIP-seq file = ['SRX017462.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 @ Sun, 05 Jun 2016 15:33:37: # Command line: callpeak -t SRX017462.bam -f BAM -g dm -n SRX017462.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX017462.10 # format = BAM # ChIP-seq file = ['SRX017462.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 @ Sun, 05 Jun 2016 15:33:37: # Command line: callpeak -t SRX017462.bam -f BAM -g dm -n SRX017462.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX017462.05 # format = BAM # ChIP-seq file = ['SRX017462.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 @ Sun, 05 Jun 2016 15:33:37: #1 read tag files... INFO @ Sun, 05 Jun 2016 15:33:37: #1 read tag files... INFO @ Sun, 05 Jun 2016 15:33:37: #1 read tag files... INFO @ Sun, 05 Jun 2016 15:33:37: #1 read treatment tags... INFO @ Sun, 05 Jun 2016 15:33:37: #1 read treatment tags... INFO @ Sun, 05 Jun 2016 15:33:37: #1 read treatment tags... INFO @ Sun, 05 Jun 2016 15:33:43: 1000000 INFO @ Sun, 05 Jun 2016 15:33:43: 1000000 INFO @ Sun, 05 Jun 2016 15:33:43: 1000000 INFO @ Sun, 05 Jun 2016 15:33:48: 2000000 INFO @ Sun, 05 Jun 2016 15:33:48: 2000000 INFO @ Sun, 05 Jun 2016 15:33:48: 2000000 INFO @ Sun, 05 Jun 2016 15:33:51: #1 tag size is determined as 36 bps INFO @ Sun, 05 Jun 2016 15:33:51: #1 tag size = 36 INFO @ Sun, 05 Jun 2016 15:33:51: #1 total tags in treatment: 2652736 INFO @ Sun, 05 Jun 2016 15:33:51: #1 user defined the maximum tags... INFO @ Sun, 05 Jun 2016 15:33:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 05 Jun 2016 15:33:51: #1 tags after filtering in treatment: 2652599 INFO @ Sun, 05 Jun 2016 15:33:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 05 Jun 2016 15:33:51: #1 finished! INFO @ Sun, 05 Jun 2016 15:33:51: #2 Build Peak Model... INFO @ Sun, 05 Jun 2016 15:33:52: #1 tag size is determined as 36 bps INFO @ Sun, 05 Jun 2016 15:33:52: #1 tag size = 36 INFO @ Sun, 05 Jun 2016 15:33:52: #1 total tags in treatment: 2652736 INFO @ Sun, 05 Jun 2016 15:33:52: #1 user defined the maximum tags... INFO @ Sun, 05 Jun 2016 15:33:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 05 Jun 2016 15:33:52: #1 tag size is determined as 36 bps INFO @ Sun, 05 Jun 2016 15:33:52: #1 tag size = 36 INFO @ Sun, 05 Jun 2016 15:33:52: #1 total tags in treatment: 2652736 INFO @ Sun, 05 Jun 2016 15:33:52: #1 user defined the maximum tags... INFO @ Sun, 05 Jun 2016 15:33:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 05 Jun 2016 15:33:52: #1 tags after filtering in treatment: 2652599 INFO @ Sun, 05 Jun 2016 15:33:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 05 Jun 2016 15:33:52: #1 finished! INFO @ Sun, 05 Jun 2016 15:33:52: #2 Build Peak Model... INFO @ Sun, 05 Jun 2016 15:33:52: #2 number of paired peaks: 1223 INFO @ Sun, 05 Jun 2016 15:33:52: start model_add_line... INFO @ Sun, 05 Jun 2016 15:33:52: #1 tags after filtering in treatment: 2652599 INFO @ Sun, 05 Jun 2016 15:33:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 05 Jun 2016 15:33:52: #1 finished! INFO @ Sun, 05 Jun 2016 15:33:52: #2 Build Peak Model... INFO @ Sun, 05 Jun 2016 15:33:53: #2 number of paired peaks: 1223 INFO @ Sun, 05 Jun 2016 15:33:53: start model_add_line... INFO @ Sun, 05 Jun 2016 15:33:53: #2 number of paired peaks: 1223 INFO @ Sun, 05 Jun 2016 15:33:53: start model_add_line... INFO @ Sun, 05 Jun 2016 15:33:55: start X-correlation... INFO @ Sun, 05 Jun 2016 15:33:55: end of X-cor INFO @ Sun, 05 Jun 2016 15:33:55: #2 finished! INFO @ Sun, 05 Jun 2016 15:33:55: #2 predicted fragment length is 60 bps INFO @ Sun, 05 Jun 2016 15:33:55: #2 alternative fragment length(s) may be 60 bps INFO @ Sun, 05 Jun 2016 15:33:55: #2.2 Generate R script for model : SRX017462.10_model.r WARNING @ Sun, 05 Jun 2016 15:33:55: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 05 Jun 2016 15:33:55: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Sun, 05 Jun 2016 15:33:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 05 Jun 2016 15:33:55: #3 Call peaks... INFO @ Sun, 05 Jun 2016 15:33:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 05 Jun 2016 15:33:55: start X-correlation... INFO @ Sun, 05 Jun 2016 15:33:55: end of X-cor INFO @ Sun, 05 Jun 2016 15:33:55: #2 finished! INFO @ Sun, 05 Jun 2016 15:33:55: #2 predicted fragment length is 60 bps INFO @ Sun, 05 Jun 2016 15:33:55: #2 alternative fragment length(s) may be 60 bps INFO @ Sun, 05 Jun 2016 15:33:55: #2.2 Generate R script for model : SRX017462.20_model.r WARNING @ Sun, 05 Jun 2016 15:33:55: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 05 Jun 2016 15:33:55: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Sun, 05 Jun 2016 15:33:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 05 Jun 2016 15:33:55: #3 Call peaks... INFO @ Sun, 05 Jun 2016 15:33:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 05 Jun 2016 15:33:56: start X-correlation... INFO @ Sun, 05 Jun 2016 15:33:56: end of X-cor INFO @ Sun, 05 Jun 2016 15:33:56: #2 finished! INFO @ Sun, 05 Jun 2016 15:33:56: #2 predicted fragment length is 60 bps INFO @ Sun, 05 Jun 2016 15:33:56: #2 alternative fragment length(s) may be 60 bps INFO @ Sun, 05 Jun 2016 15:33:56: #2.2 Generate R script for model : SRX017462.05_model.r WARNING @ Sun, 05 Jun 2016 15:33:56: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 05 Jun 2016 15:33:56: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Sun, 05 Jun 2016 15:33:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 05 Jun 2016 15:33:56: #3 Call peaks... INFO @ Sun, 05 Jun 2016 15:33:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 05 Jun 2016 15:34:10: #3 Call peaks for each chromosome... INFO @ Sun, 05 Jun 2016 15:34:11: #3 Call peaks for each chromosome... INFO @ Sun, 05 Jun 2016 15:34:12: #3 Call peaks for each chromosome... INFO @ Sun, 05 Jun 2016 15:34:21: #4 Write output xls file... SRX017462.20_peaks.xls INFO @ Sun, 05 Jun 2016 15:34:21: #4 Write peak in narrowPeak format file... SRX017462.20_peaks.narrowPeak INFO @ Sun, 05 Jun 2016 15:34:21: #4 Write summits bed file... SRX017462.20_summits.bed INFO @ Sun, 05 Jun 2016 15:34:21: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (409 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 05 Jun 2016 15:34:22: #4 Write output xls file... SRX017462.10_peaks.xls INFO @ Sun, 05 Jun 2016 15:34:22: #4 Write peak in narrowPeak format file... SRX017462.10_peaks.narrowPeak INFO @ Sun, 05 Jun 2016 15:34:22: #4 Write summits bed file... SRX017462.10_summits.bed INFO @ Sun, 05 Jun 2016 15:34:22: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1520 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 05 Jun 2016 15:34:25: #4 Write output xls file... SRX017462.05_peaks.xls INFO @ Sun, 05 Jun 2016 15:34:25: #4 Write peak in narrowPeak format file... SRX017462.05_peaks.narrowPeak INFO @ Sun, 05 Jun 2016 15:34:26: #4 Write summits bed file... SRX017462.05_summits.bed INFO @ Sun, 05 Jun 2016 15:34:26: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3687 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。