Job ID = 2237034 sra ファイルのダウンロード中... Completed: 56247K bytes transferred in 4 seconds (106912K 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 16374 0 16374 0 0 22980 0 --:--:-- --:--:-- --:--:-- 31367 100 37986 0 37986 0 0 53240 0 --:--:-- --:--:-- --:--:-- 72630 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 3503602 spots for /home/okishinya/chipatlas/results/ce10/SRX080089/SRR298909.sra Written 3503602 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: 00:00:29 3503602 reads; of these: 3503602 (100.00%) were unpaired; of these: 1454593 (41.52%) aligned 0 times 1734850 (49.52%) aligned exactly 1 time 314159 (8.97%) aligned >1 times 58.48% overall alignment rate Time searching: 00:00:29 Overall time: 00:00:29 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] 606344 / 2049009 = 0.2959 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 11:25:02: # Command line: callpeak -t SRX080089.bam -f BAM -g ce -n SRX080089.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX080089.20 # format = BAM # ChIP-seq file = ['SRX080089.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 11:25:02: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:02: # Command line: callpeak -t SRX080089.bam -f BAM -g ce -n SRX080089.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX080089.05 # format = BAM # ChIP-seq file = ['SRX080089.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 11:25:02: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:02: # Command line: callpeak -t SRX080089.bam -f BAM -g ce -n SRX080089.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX080089.10 # format = BAM # ChIP-seq file = ['SRX080089.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 11:25:02: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:02: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:02: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:02: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:06: 1000000 INFO @ Thu, 30 Apr 2015 11:25:06: 1000000 INFO @ Thu, 30 Apr 2015 11:25:06: 1000000 INFO @ Thu, 30 Apr 2015 11:25:08: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:08: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:08: #1 total tags in treatment: 1442665 INFO @ Thu, 30 Apr 2015 11:25:08: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:08: #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 11:25:08: #1 tags after filtering in treatment: 1442632 INFO @ Thu, 30 Apr 2015 11:25:08: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:08: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:08: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:09: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:09: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:09: #1 total tags in treatment: 1442665 INFO @ Thu, 30 Apr 2015 11:25:09: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:09: #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 11:25:09: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:09: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:09: #1 total tags in treatment: 1442665 INFO @ Thu, 30 Apr 2015 11:25:09: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:09: #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 11:25:09: #2 number of paired peaks: 238 WARNING @ Thu, 30 Apr 2015 11:25:09: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Thu, 30 Apr 2015 11:25:09: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:09: #1 tags after filtering in treatment: 1442632 INFO @ Thu, 30 Apr 2015 11:25:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:09: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:09: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:09: #1 tags after filtering in treatment: 1442632 INFO @ Thu, 30 Apr 2015 11:25:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:09: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:09: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:09: #2 number of paired peaks: 238 WARNING @ Thu, 30 Apr 2015 11:25:09: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Thu, 30 Apr 2015 11:25:09: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:09: #2 number of paired peaks: 238 WARNING @ Thu, 30 Apr 2015 11:25:09: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Thu, 30 Apr 2015 11:25:09: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:09: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:09: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:09: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:09: #2 predicted fragment length is 38 bps INFO @ Thu, 30 Apr 2015 11:25:09: #2 alternative fragment length(s) may be 38,105,166,241,305,363,410,459,506,539,582,590 bps INFO @ Thu, 30 Apr 2015 11:25:09: #2.2 Generate R script for model : SRX080089.05_model.r WARNING @ Thu, 30 Apr 2015 11:25:09: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:25:09: #2 You may need to consider one of the other alternative d(s): 38,105,166,241,305,363,410,459,506,539,582,590 WARNING @ Thu, 30 Apr 2015 11:25:09: #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 11:25:09: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:25:10: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:10: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:10: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:10: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:10: #2 predicted fragment length is 38 bps INFO @ Thu, 30 Apr 2015 11:25:10: #2 alternative fragment length(s) may be 38,105,166,241,305,363,410,459,506,539,582,590 bps INFO @ Thu, 30 Apr 2015 11:25:10: #2.2 Generate R script for model : SRX080089.10_model.r INFO @ Thu, 30 Apr 2015 11:25:10: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:10: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:10: #2 predicted fragment length is 38 bps INFO @ Thu, 30 Apr 2015 11:25:10: #2 alternative fragment length(s) may be 38,105,166,241,305,363,410,459,506,539,582,590 bps INFO @ Thu, 30 Apr 2015 11:25:10: #2.2 Generate R script for model : SRX080089.20_model.r WARNING @ Thu, 30 Apr 2015 11:25:10: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:25:10: #2 You may need to consider one of the other alternative d(s): 38,105,166,241,305,363,410,459,506,539,582,590 WARNING @ Thu, 30 Apr 2015 11:25:10: #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 11:25:10: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:10: #3 Pre-compute pvalue-qvalue table... WARNING @ Thu, 30 Apr 2015 11:25:10: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:25:10: #2 You may need to consider one of the other alternative d(s): 38,105,166,241,305,363,410,459,506,539,582,590 WARNING @ Thu, 30 Apr 2015 11:25:10: #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 11:25:10: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:25:18: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:25:18: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:25:19: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:25:23: #4 Write output xls file... SRX080089.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:25:23: #4 Write peak in narrowPeak format file... SRX080089.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:25:23: #4 Write summits bed file... SRX080089.05_summits.bed INFO @ Thu, 30 Apr 2015 11:25:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (109 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:25:25: #4 Write output xls file... SRX080089.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:25:25: #4 Write peak in narrowPeak format file... SRX080089.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:25:25: #4 Write summits bed file... SRX080089.20_summits.bed INFO @ Thu, 30 Apr 2015 11:25:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (21 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:25:25: #4 Write output xls file... SRX080089.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:25:25: #4 Write peak in narrowPeak format file... SRX080089.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:25:25: #4 Write summits bed file... SRX080089.10_summits.bed INFO @ Thu, 30 Apr 2015 11:25:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (45 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。