Job ID = 2161301 sra ファイルのダウンロード中... Completed: 80203K bytes transferred in 4 seconds (158577K 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 34314 0 34314 0 0 47954 0 --:--:-- --:--:-- --:--:-- 65484 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 3321916 spots for /home/okishinya/chipatlas/results/dm3/SRX016167/SRR034735.sra Written 3321916 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: 00:01:01 3321916 reads; of these: 3321916 (100.00%) were unpaired; of these: 244604 (7.36%) aligned 0 times 2466991 (74.26%) aligned exactly 1 time 610321 (18.37%) aligned >1 times 92.64% overall alignment rate Time searching: 00:01:01 Overall time: 00:01:01 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] 447641 / 3077312 = 0.1455 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 12:16:05: # Command line: callpeak -t SRX016167.bam -f BAM -g dm -n SRX016167.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX016167.10 # format = BAM # ChIP-seq file = ['SRX016167.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 12:16:05: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:16:05: # Command line: callpeak -t SRX016167.bam -f BAM -g dm -n SRX016167.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX016167.20 # format = BAM # ChIP-seq file = ['SRX016167.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 12:16:05: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:16:05: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:16:05: # Command line: callpeak -t SRX016167.bam -f BAM -g dm -n SRX016167.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX016167.05 # format = BAM # ChIP-seq file = ['SRX016167.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 12:16:05: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:16:05: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:16:05: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:16:11: 1000000 INFO @ Tue, 21 Apr 2015 12:16:12: 1000000 INFO @ Tue, 21 Apr 2015 12:16:12: 1000000 INFO @ Tue, 21 Apr 2015 12:16:17: 2000000 INFO @ Tue, 21 Apr 2015 12:16:18: 2000000 INFO @ Tue, 21 Apr 2015 12:16:18: 2000000 INFO @ Tue, 21 Apr 2015 12:16:20: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:16:20: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:16:20: #1 total tags in treatment: 2629671 INFO @ Tue, 21 Apr 2015 12:16:20: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:16:20: #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 12:16:21: #1 tags after filtering in treatment: 2629520 INFO @ Tue, 21 Apr 2015 12:16:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:16:21: #1 finished! INFO @ Tue, 21 Apr 2015 12:16:21: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:16:21: #2 number of paired peaks: 481 WARNING @ Tue, 21 Apr 2015 12:16:21: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Tue, 21 Apr 2015 12:16:21: start model_add_line... INFO @ Tue, 21 Apr 2015 12:16:22: start X-correlation... INFO @ Tue, 21 Apr 2015 12:16:22: end of X-cor INFO @ Tue, 21 Apr 2015 12:16:22: #2 finished! INFO @ Tue, 21 Apr 2015 12:16:22: #2 predicted fragment length is 41 bps INFO @ Tue, 21 Apr 2015 12:16:22: #2 alternative fragment length(s) may be 41 bps INFO @ Tue, 21 Apr 2015 12:16:22: #2.2 Generate R script for model : SRX016167.05_model.r WARNING @ Tue, 21 Apr 2015 12:16:22: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:16:22: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Tue, 21 Apr 2015 12:16:22: #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 12:16:22: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:16:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:16:22: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:16:22: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:16:22: #1 total tags in treatment: 2629671 INFO @ Tue, 21 Apr 2015 12:16:22: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:16:22: #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 12:16:22: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:16:22: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:16:22: #1 total tags in treatment: 2629671 INFO @ Tue, 21 Apr 2015 12:16:22: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:16:22: #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 12:16:23: #1 tags after filtering in treatment: 2629520 INFO @ Tue, 21 Apr 2015 12:16:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:16:23: #1 finished! INFO @ Tue, 21 Apr 2015 12:16:23: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:16:23: #1 tags after filtering in treatment: 2629520 INFO @ Tue, 21 Apr 2015 12:16:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:16:23: #1 finished! INFO @ Tue, 21 Apr 2015 12:16:23: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:16:23: #2 number of paired peaks: 481 WARNING @ Tue, 21 Apr 2015 12:16:23: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Tue, 21 Apr 2015 12:16:23: start model_add_line... INFO @ Tue, 21 Apr 2015 12:16:23: #2 number of paired peaks: 481 WARNING @ Tue, 21 Apr 2015 12:16:23: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Tue, 21 Apr 2015 12:16:23: start model_add_line... INFO @ Tue, 21 Apr 2015 12:16:24: start X-correlation... INFO @ Tue, 21 Apr 2015 12:16:24: end of X-cor INFO @ Tue, 21 Apr 2015 12:16:24: #2 finished! INFO @ Tue, 21 Apr 2015 12:16:24: #2 predicted fragment length is 41 bps INFO @ Tue, 21 Apr 2015 12:16:24: #2 alternative fragment length(s) may be 41 bps INFO @ Tue, 21 Apr 2015 12:16:24: #2.2 Generate R script for model : SRX016167.10_model.r WARNING @ Tue, 21 Apr 2015 12:16:24: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:16:24: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Tue, 21 Apr 2015 12:16:24: #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 12:16:24: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:16:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:16:24: start X-correlation... INFO @ Tue, 21 Apr 2015 12:16:24: end of X-cor INFO @ Tue, 21 Apr 2015 12:16:24: #2 finished! INFO @ Tue, 21 Apr 2015 12:16:24: #2 predicted fragment length is 41 bps INFO @ Tue, 21 Apr 2015 12:16:24: #2 alternative fragment length(s) may be 41 bps INFO @ Tue, 21 Apr 2015 12:16:24: #2.2 Generate R script for model : SRX016167.20_model.r WARNING @ Tue, 21 Apr 2015 12:16:24: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:16:24: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Tue, 21 Apr 2015 12:16:24: #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 12:16:24: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:16:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:16:37: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:16:40: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:16:40: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:16:49: #4 Write output xls file... SRX016167.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:16:49: #4 Write peak in narrowPeak format file... SRX016167.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:16:49: #4 Write summits bed file... SRX016167.05_summits.bed INFO @ Tue, 21 Apr 2015 12:16:49: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1110 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:16:51: #4 Write output xls file... SRX016167.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:16:51: #4 Write peak in narrowPeak format file... SRX016167.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:16:51: #4 Write summits bed file... SRX016167.10_summits.bed INFO @ Tue, 21 Apr 2015 12:16:51: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (828 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:16:53: #4 Write output xls file... SRX016167.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:16:53: #4 Write peak in narrowPeak format file... SRX016167.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:16:53: #4 Write summits bed file... SRX016167.20_summits.bed INFO @ Tue, 21 Apr 2015 12:16:53: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (480 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。