Job ID = 2161376 sra ファイルのダウンロード中... Completed: 126788K bytes transferred in 4 seconds (219062K 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 4007 0 4007 0 0 7305 0 --:--:-- --:--:-- --:--:-- 11192 100 44407 0 44407 0 0 47875 0 --:--:-- --:--:-- --:--:-- 60253 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 5558344 spots for /home/okishinya/chipatlas/results/dm3/SRX025465/SRR063859.sra Written 5558344 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: 00:01:26 5558344 reads; of these: 5558344 (100.00%) were unpaired; of these: 178397 (3.21%) aligned 0 times 4483630 (80.66%) aligned exactly 1 time 896317 (16.13%) aligned >1 times 96.79% overall alignment rate Time searching: 00:01:26 Overall time: 00:01:26 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] 226084 / 5379947 = 0.0420 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 12:31:36: # Command line: callpeak -t SRX025465.bam -f BAM -g dm -n SRX025465.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX025465.20 # format = BAM # ChIP-seq file = ['SRX025465.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 12:31:36: # Command line: callpeak -t SRX025465.bam -f BAM -g dm -n SRX025465.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX025465.10 # format = BAM # ChIP-seq file = ['SRX025465.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 12:31:36: # Command line: callpeak -t SRX025465.bam -f BAM -g dm -n SRX025465.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX025465.05 # format = BAM # ChIP-seq file = ['SRX025465.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 12:31:36: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:31:36: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:31:36: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:31:36: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:31:36: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:31:36: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:31:41: 1000000 INFO @ Tue, 21 Apr 2015 12:31:42: 1000000 INFO @ Tue, 21 Apr 2015 12:31:42: 1000000 INFO @ Tue, 21 Apr 2015 12:31:47: 2000000 INFO @ Tue, 21 Apr 2015 12:31:48: 2000000 INFO @ Tue, 21 Apr 2015 12:31:48: 2000000 INFO @ Tue, 21 Apr 2015 12:31:52: 3000000 INFO @ Tue, 21 Apr 2015 12:31:54: 3000000 INFO @ Tue, 21 Apr 2015 12:31:54: 3000000 INFO @ Tue, 21 Apr 2015 12:31:58: 4000000 INFO @ Tue, 21 Apr 2015 12:32:00: 4000000 INFO @ Tue, 21 Apr 2015 12:32:00: 4000000 INFO @ Tue, 21 Apr 2015 12:32:04: 5000000 INFO @ Tue, 21 Apr 2015 12:32:04: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:32:04: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:32:04: #1 total tags in treatment: 5153863 INFO @ Tue, 21 Apr 2015 12:32:04: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:32:04: #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 12:32:05: #1 tags after filtering in treatment: 5153751 INFO @ Tue, 21 Apr 2015 12:32:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:32:05: #1 finished! INFO @ Tue, 21 Apr 2015 12:32:05: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:32:06: 5000000 INFO @ Tue, 21 Apr 2015 12:32:06: 5000000 INFO @ Tue, 21 Apr 2015 12:32:06: #2 number of paired peaks: 153 WARNING @ Tue, 21 Apr 2015 12:32:06: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Tue, 21 Apr 2015 12:32:06: start model_add_line... INFO @ Tue, 21 Apr 2015 12:32:07: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:32:07: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:32:07: #1 total tags in treatment: 5153863 INFO @ Tue, 21 Apr 2015 12:32:07: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:32:07: #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 12:32:07: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:32:07: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:32:07: #1 total tags in treatment: 5153863 INFO @ Tue, 21 Apr 2015 12:32:07: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:32:07: #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 12:32:07: start X-correlation... INFO @ Tue, 21 Apr 2015 12:32:07: end of X-cor INFO @ Tue, 21 Apr 2015 12:32:07: #2 finished! INFO @ Tue, 21 Apr 2015 12:32:07: #2 predicted fragment length is 36 bps INFO @ Tue, 21 Apr 2015 12:32:07: #2 alternative fragment length(s) may be 36 bps INFO @ Tue, 21 Apr 2015 12:32:07: #2.2 Generate R script for model : SRX025465.20_model.r WARNING @ Tue, 21 Apr 2015 12:32:07: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:32:07: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Tue, 21 Apr 2015 12:32:07: #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 12:32:07: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:32:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:32:08: #1 tags after filtering in treatment: 5153751 INFO @ Tue, 21 Apr 2015 12:32:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:32:08: #1 finished! INFO @ Tue, 21 Apr 2015 12:32:08: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:32:08: #1 tags after filtering in treatment: 5153751 INFO @ Tue, 21 Apr 2015 12:32:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:32:08: #1 finished! INFO @ Tue, 21 Apr 2015 12:32:08: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:32:09: #2 number of paired peaks: 153 WARNING @ Tue, 21 Apr 2015 12:32:09: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Tue, 21 Apr 2015 12:32:09: start model_add_line... INFO @ Tue, 21 Apr 2015 12:32:09: #2 number of paired peaks: 153 WARNING @ Tue, 21 Apr 2015 12:32:09: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Tue, 21 Apr 2015 12:32:09: start model_add_line... INFO @ Tue, 21 Apr 2015 12:32:09: start X-correlation... INFO @ Tue, 21 Apr 2015 12:32:09: end of X-cor INFO @ Tue, 21 Apr 2015 12:32:09: #2 finished! INFO @ Tue, 21 Apr 2015 12:32:09: #2 predicted fragment length is 36 bps INFO @ Tue, 21 Apr 2015 12:32:09: #2 alternative fragment length(s) may be 36 bps INFO @ Tue, 21 Apr 2015 12:32:09: #2.2 Generate R script for model : SRX025465.05_model.r WARNING @ Tue, 21 Apr 2015 12:32:09: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:32:09: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Tue, 21 Apr 2015 12:32:09: #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 12:32:09: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:32:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:32:09: start X-correlation... INFO @ Tue, 21 Apr 2015 12:32:09: end of X-cor INFO @ Tue, 21 Apr 2015 12:32:09: #2 finished! INFO @ Tue, 21 Apr 2015 12:32:09: #2 predicted fragment length is 36 bps INFO @ Tue, 21 Apr 2015 12:32:09: #2 alternative fragment length(s) may be 36 bps INFO @ Tue, 21 Apr 2015 12:32:09: #2.2 Generate R script for model : SRX025465.10_model.r WARNING @ Tue, 21 Apr 2015 12:32:09: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:32:09: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Tue, 21 Apr 2015 12:32:09: #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 12:32:09: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:32:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:32:35: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:32:37: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:32:37: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:32:55: #4 Write output xls file... SRX025465.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:32:55: #4 Write peak in narrowPeak format file... SRX025465.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:32:55: #4 Write summits bed file... SRX025465.20_summits.bed INFO @ Tue, 21 Apr 2015 12:32:55: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (334 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:32:58: #4 Write output xls file... SRX025465.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:32:58: #4 Write peak in narrowPeak format file... SRX025465.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:32:58: #4 Write summits bed file... SRX025465.10_summits.bed INFO @ Tue, 21 Apr 2015 12:32:58: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (410 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:32:58: #4 Write output xls file... SRX025465.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:32:58: #4 Write peak in narrowPeak format file... SRX025465.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:32:58: #4 Write summits bed file... SRX025465.05_summits.bed INFO @ Tue, 21 Apr 2015 12:32:58: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (462 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。