Job ID = 2237020 sra ファイルのダウンロード中... Completed: 101419K bytes transferred in 4 seconds (182793K 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 9840 0 9840 0 0 18656 0 --:--:-- --:--:-- --:--:-- 29198 100 38210 0 38210 0 0 53255 0 --:--:-- --:--:-- --:--:-- 72504 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 5790992 spots for /home/okishinya/chipatlas/results/ce10/SRX080075/SRR298895.sra Written 5790992 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: 00:00:56 5790992 reads; of these: 5790992 (100.00%) were unpaired; of these: 1326241 (22.90%) aligned 0 times 3697610 (63.85%) aligned exactly 1 time 767141 (13.25%) aligned >1 times 77.10% overall alignment rate Time searching: 00:00:56 Overall time: 00:00:56 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 249562 / 4464751 = 0.0559 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 @ Thu, 30 Apr 2015 11:25:25: # Command line: callpeak -t SRX080075.bam -f BAM -g ce -n SRX080075.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX080075.10 # format = BAM # ChIP-seq file = ['SRX080075.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 30 Apr 2015 11:25:25: # Command line: callpeak -t SRX080075.bam -f BAM -g ce -n SRX080075.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX080075.20 # format = BAM # ChIP-seq file = ['SRX080075.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 30 Apr 2015 11:25:25: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:25: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:25: # Command line: callpeak -t SRX080075.bam -f BAM -g ce -n SRX080075.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX080075.05 # format = BAM # ChIP-seq file = ['SRX080075.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 30 Apr 2015 11:25:25: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:25: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:25: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:25: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:31: 1000000 INFO @ Thu, 30 Apr 2015 11:25:31: 1000000 INFO @ Thu, 30 Apr 2015 11:25:31: 1000000 INFO @ Thu, 30 Apr 2015 11:25:36: 2000000 INFO @ Thu, 30 Apr 2015 11:25:36: 2000000 INFO @ Thu, 30 Apr 2015 11:25:37: 2000000 INFO @ Thu, 30 Apr 2015 11:25:42: 3000000 INFO @ Thu, 30 Apr 2015 11:25:42: 3000000 INFO @ Thu, 30 Apr 2015 11:25:42: 3000000 INFO @ Thu, 30 Apr 2015 11:25:48: 4000000 INFO @ Thu, 30 Apr 2015 11:25:48: 4000000 INFO @ Thu, 30 Apr 2015 11:25:48: 4000000 INFO @ Thu, 30 Apr 2015 11:25:49: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:49: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:49: #1 total tags in treatment: 4215189 INFO @ Thu, 30 Apr 2015 11:25:49: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:25:49: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:49: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:49: #1 total tags in treatment: 4215189 INFO @ Thu, 30 Apr 2015 11:25:49: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:25:49: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:49: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:49: #1 total tags in treatment: 4215189 INFO @ Thu, 30 Apr 2015 11:25:49: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:25:49: #1 tags after filtering in treatment: 4215117 INFO @ Thu, 30 Apr 2015 11:25:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:49: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:49: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:50: #1 tags after filtering in treatment: 4215117 INFO @ Thu, 30 Apr 2015 11:25:50: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:50: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:50: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:50: #1 tags after filtering in treatment: 4215117 INFO @ Thu, 30 Apr 2015 11:25:50: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:50: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:50: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:50: #2 number of paired peaks: 415 WARNING @ Thu, 30 Apr 2015 11:25:50: Fewer paired peaks (415) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 415 pairs to build model! INFO @ Thu, 30 Apr 2015 11:25:50: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:51: #2 number of paired peaks: 415 WARNING @ Thu, 30 Apr 2015 11:25:51: Fewer paired peaks (415) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 415 pairs to build model! INFO @ Thu, 30 Apr 2015 11:25:51: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:51: #2 number of paired peaks: 415 WARNING @ Thu, 30 Apr 2015 11:25:51: Fewer paired peaks (415) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 415 pairs to build model! INFO @ Thu, 30 Apr 2015 11:25:51: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:53: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:53: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:53: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:53: #2 predicted fragment length is 34 bps INFO @ Thu, 30 Apr 2015 11:25:53: #2 alternative fragment length(s) may be 4,34,75,596 bps INFO @ Thu, 30 Apr 2015 11:25:53: #2.2 Generate R script for model : SRX080075.05_model.r WARNING @ Thu, 30 Apr 2015 11:25:53: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:25:53: #2 You may need to consider one of the other alternative d(s): 4,34,75,596 WARNING @ Thu, 30 Apr 2015 11:25:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 11:25:53: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:25:54: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:54: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:54: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:54: #2 predicted fragment length is 34 bps INFO @ Thu, 30 Apr 2015 11:25:54: #2 alternative fragment length(s) may be 4,34,75,596 bps INFO @ Thu, 30 Apr 2015 11:25:54: #2.2 Generate R script for model : SRX080075.20_model.r WARNING @ Thu, 30 Apr 2015 11:25:54: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:25:54: #2 You may need to consider one of the other alternative d(s): 4,34,75,596 WARNING @ Thu, 30 Apr 2015 11:25:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 11:25:54: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:25:54: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:54: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:54: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:54: #2 predicted fragment length is 34 bps INFO @ Thu, 30 Apr 2015 11:25:54: #2 alternative fragment length(s) may be 4,34,75,596 bps INFO @ Thu, 30 Apr 2015 11:25:54: #2.2 Generate R script for model : SRX080075.10_model.r WARNING @ Thu, 30 Apr 2015 11:25:54: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:25:54: #2 You may need to consider one of the other alternative d(s): 4,34,75,596 WARNING @ Thu, 30 Apr 2015 11:25:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 11:25:54: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:26:17: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:26:19: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:26:19: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:26:34: #4 Write output xls file... SRX080075.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:26:34: #4 Write peak in narrowPeak format file... SRX080075.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:26:34: #4 Write summits bed file... SRX080075.20_summits.bed INFO @ Thu, 30 Apr 2015 11:26:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (66 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:26:35: #4 Write output xls file... SRX080075.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:26:35: #4 Write peak in narrowPeak format file... SRX080075.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:26:35: #4 Write summits bed file... SRX080075.10_summits.bed INFO @ Thu, 30 Apr 2015 11:26:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (201 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:26:37: #4 Write output xls file... SRX080075.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:26:37: #4 Write peak in narrowPeak format file... SRX080075.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:26:37: #4 Write summits bed file... SRX080075.05_summits.bed INFO @ Thu, 30 Apr 2015 11:26:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (403 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。