Job ID = 2236860 sra ファイルのダウンロード中... Completed: 475046K bytes transferred in 14 seconds (264893K 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 35013 0 35013 0 0 44653 0 --:--:-- --:--:-- --:--:-- 59043 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 19555555 spots for /home/okishinya/chipatlas/results/ce10/SRX059236/SRR190676.sra Written 19555555 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: 00:02:48 19555555 reads; of these: 19555555 (100.00%) were unpaired; of these: 8713184 (44.56%) aligned 0 times 9073552 (46.40%) aligned exactly 1 time 1768819 (9.05%) aligned >1 times 55.44% overall alignment rate Time searching: 00:02:48 Overall time: 00:02:48 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] 648671 / 10842371 = 0.0598 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 11:16:31: # Command line: callpeak -t SRX059236.bam -f BAM -g ce -n SRX059236.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX059236.10 # format = BAM # ChIP-seq file = ['SRX059236.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 11:16:31: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:16:31: # Command line: callpeak -t SRX059236.bam -f BAM -g ce -n SRX059236.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX059236.20 # format = BAM # ChIP-seq file = ['SRX059236.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 11:16:31: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:16:31: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:16:31: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:16:31: # Command line: callpeak -t SRX059236.bam -f BAM -g ce -n SRX059236.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX059236.05 # format = BAM # ChIP-seq file = ['SRX059236.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 11:16:31: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:16:31: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:16:37: 1000000 INFO @ Thu, 30 Apr 2015 11:16:37: 1000000 INFO @ Thu, 30 Apr 2015 11:16:37: 1000000 INFO @ Thu, 30 Apr 2015 11:16:43: 2000000 INFO @ Thu, 30 Apr 2015 11:16:43: 2000000 INFO @ Thu, 30 Apr 2015 11:16:43: 2000000 INFO @ Thu, 30 Apr 2015 11:16:49: 3000000 INFO @ Thu, 30 Apr 2015 11:16:49: 3000000 INFO @ Thu, 30 Apr 2015 11:16:50: 3000000 INFO @ Thu, 30 Apr 2015 11:16:55: 4000000 INFO @ Thu, 30 Apr 2015 11:16:55: 4000000 INFO @ Thu, 30 Apr 2015 11:16:55: 4000000 INFO @ Thu, 30 Apr 2015 11:17:00: 5000000 INFO @ Thu, 30 Apr 2015 11:17:00: 5000000 INFO @ Thu, 30 Apr 2015 11:17:01: 5000000 INFO @ Thu, 30 Apr 2015 11:17:06: 6000000 INFO @ Thu, 30 Apr 2015 11:17:06: 6000000 INFO @ Thu, 30 Apr 2015 11:17:06: 6000000 INFO @ Thu, 30 Apr 2015 11:17:13: 7000000 INFO @ Thu, 30 Apr 2015 11:17:13: 7000000 INFO @ Thu, 30 Apr 2015 11:17:13: 7000000 INFO @ Thu, 30 Apr 2015 11:17:19: 8000000 INFO @ Thu, 30 Apr 2015 11:17:20: 8000000 INFO @ Thu, 30 Apr 2015 11:17:20: 8000000 INFO @ Thu, 30 Apr 2015 11:17:25: 9000000 INFO @ Thu, 30 Apr 2015 11:17:27: 9000000 INFO @ Thu, 30 Apr 2015 11:17:27: 9000000 INFO @ Thu, 30 Apr 2015 11:17:31: 10000000 INFO @ Thu, 30 Apr 2015 11:17:32: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:17:32: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:17:32: #1 total tags in treatment: 10193700 INFO @ Thu, 30 Apr 2015 11:17:32: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:17:32: #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 11:17:34: 10000000 INFO @ Thu, 30 Apr 2015 11:17:34: 10000000 INFO @ Thu, 30 Apr 2015 11:17:34: #1 tags after filtering in treatment: 10192942 INFO @ Thu, 30 Apr 2015 11:17:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:17:34: #1 finished! INFO @ Thu, 30 Apr 2015 11:17:34: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:17:35: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:17:35: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:17:35: #1 total tags in treatment: 10193700 INFO @ Thu, 30 Apr 2015 11:17:35: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:17:35: #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 11:17:35: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:17:35: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:17:35: #1 total tags in treatment: 10193700 INFO @ Thu, 30 Apr 2015 11:17:35: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:17:35: #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 11:17:36: #2 number of paired peaks: 247 WARNING @ Thu, 30 Apr 2015 11:17:36: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Thu, 30 Apr 2015 11:17:36: start model_add_line... INFO @ Thu, 30 Apr 2015 11:17:37: #1 tags after filtering in treatment: 10192942 INFO @ Thu, 30 Apr 2015 11:17:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:17:37: #1 finished! INFO @ Thu, 30 Apr 2015 11:17:37: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:17:37: #1 tags after filtering in treatment: 10192942 INFO @ Thu, 30 Apr 2015 11:17:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:17:37: #1 finished! INFO @ Thu, 30 Apr 2015 11:17:37: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:17:39: #2 number of paired peaks: 247 WARNING @ Thu, 30 Apr 2015 11:17:39: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Thu, 30 Apr 2015 11:17:39: start model_add_line... INFO @ Thu, 30 Apr 2015 11:17:39: #2 number of paired peaks: 247 WARNING @ Thu, 30 Apr 2015 11:17:39: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Thu, 30 Apr 2015 11:17:39: start model_add_line... INFO @ Thu, 30 Apr 2015 11:17:39: start X-correlation... INFO @ Thu, 30 Apr 2015 11:17:39: end of X-cor INFO @ Thu, 30 Apr 2015 11:17:39: #2 finished! INFO @ Thu, 30 Apr 2015 11:17:39: #2 predicted fragment length is 30 bps INFO @ Thu, 30 Apr 2015 11:17:39: #2 alternative fragment length(s) may be 0,30,592 bps INFO @ Thu, 30 Apr 2015 11:17:39: #2.2 Generate R script for model : SRX059236.05_model.r WARNING @ Thu, 30 Apr 2015 11:17:39: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:17:39: #2 You may need to consider one of the other alternative d(s): 0,30,592 WARNING @ Thu, 30 Apr 2015 11:17:39: #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 11:17:39: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:17:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:17:42: start X-correlation... INFO @ Thu, 30 Apr 2015 11:17:42: end of X-cor INFO @ Thu, 30 Apr 2015 11:17:42: #2 finished! INFO @ Thu, 30 Apr 2015 11:17:42: #2 predicted fragment length is 30 bps INFO @ Thu, 30 Apr 2015 11:17:42: #2 alternative fragment length(s) may be 0,30,592 bps INFO @ Thu, 30 Apr 2015 11:17:42: #2.2 Generate R script for model : SRX059236.10_model.r WARNING @ Thu, 30 Apr 2015 11:17:42: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:17:42: #2 You may need to consider one of the other alternative d(s): 0,30,592 WARNING @ Thu, 30 Apr 2015 11:17:42: #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 11:17:42: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:17:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:17:43: start X-correlation... INFO @ Thu, 30 Apr 2015 11:17:43: end of X-cor INFO @ Thu, 30 Apr 2015 11:17:43: #2 finished! INFO @ Thu, 30 Apr 2015 11:17:43: #2 predicted fragment length is 30 bps INFO @ Thu, 30 Apr 2015 11:17:43: #2 alternative fragment length(s) may be 0,30,592 bps INFO @ Thu, 30 Apr 2015 11:17:43: #2.2 Generate R script for model : SRX059236.20_model.r WARNING @ Thu, 30 Apr 2015 11:17:43: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:17:43: #2 You may need to consider one of the other alternative d(s): 0,30,592 WARNING @ Thu, 30 Apr 2015 11:17:43: #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 11:17:43: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:17:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:18:32: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:18:34: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:18:34: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:19:10: #4 Write output xls file... SRX059236.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:19:10: #4 Write peak in narrowPeak format file... SRX059236.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:19:10: #4 Write summits bed file... SRX059236.05_summits.bed INFO @ Thu, 30 Apr 2015 11:19:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (583 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:19:11: #4 Write output xls file... SRX059236.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:19:11: #4 Write peak in narrowPeak format file... SRX059236.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:19:11: #4 Write summits bed file... SRX059236.10_summits.bed INFO @ Thu, 30 Apr 2015 11:19:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (244 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:19:12: #4 Write output xls file... SRX059236.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:19:12: #4 Write peak in narrowPeak format file... SRX059236.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:19:12: #4 Write summits bed file... SRX059236.20_summits.bed INFO @ Thu, 30 Apr 2015 11:19:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (50 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。