Job ID = 2236681 sra ファイルのダウンロード中... Completed: 2269134K bytes transferred in 25 seconds (733305K 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 16381 0 16381 0 0 22812 0 --:--:-- --:--:-- --:--:-- 31083 100 37025 0 37025 0 0 51497 0 --:--:-- --:--:-- --:--:-- 70123 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 13402463 spots for /home/okishinya/chipatlas/results/ce10/SRX012300/SRR029219.sra Written 13402463 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: 00:02:08 13402463 reads; of these: 13402463 (100.00%) were unpaired; of these: 5030869 (37.54%) aligned 0 times 6643425 (49.57%) aligned exactly 1 time 1728169 (12.89%) aligned >1 times 62.46% overall alignment rate Time searching: 00:02:08 Overall time: 00:02:08 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] 1470136 / 8371594 = 0.1756 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 10:58:27: # Command line: callpeak -t SRX012300.bam -f BAM -g ce -n SRX012300.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX012300.20 # format = BAM # ChIP-seq file = ['SRX012300.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 10:58:27: #1 read tag files... INFO @ Thu, 30 Apr 2015 10:58:27: # Command line: callpeak -t SRX012300.bam -f BAM -g ce -n SRX012300.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX012300.05 # format = BAM # ChIP-seq file = ['SRX012300.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 10:58:27: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 10:58:27: #1 read tag files... INFO @ Thu, 30 Apr 2015 10:58:27: # Command line: callpeak -t SRX012300.bam -f BAM -g ce -n SRX012300.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX012300.10 # format = BAM # ChIP-seq file = ['SRX012300.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 10:58:27: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 10:58:27: #1 read tag files... INFO @ Thu, 30 Apr 2015 10:58:27: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 10:58:32: 1000000 INFO @ Thu, 30 Apr 2015 10:58:33: 1000000 INFO @ Thu, 30 Apr 2015 10:58:33: 1000000 INFO @ Thu, 30 Apr 2015 10:58:38: 2000000 INFO @ Thu, 30 Apr 2015 10:58:38: 2000000 INFO @ Thu, 30 Apr 2015 10:58:38: 2000000 INFO @ Thu, 30 Apr 2015 10:58:44: 3000000 INFO @ Thu, 30 Apr 2015 10:58:44: 3000000 INFO @ Thu, 30 Apr 2015 10:58:44: 3000000 INFO @ Thu, 30 Apr 2015 10:58:49: 4000000 INFO @ Thu, 30 Apr 2015 10:58:50: 4000000 INFO @ Thu, 30 Apr 2015 10:58:50: 4000000 INFO @ Thu, 30 Apr 2015 10:58:55: 5000000 INFO @ Thu, 30 Apr 2015 10:58:55: 5000000 INFO @ Thu, 30 Apr 2015 10:58:56: 5000000 INFO @ Thu, 30 Apr 2015 10:59:01: 6000000 INFO @ Thu, 30 Apr 2015 10:59:01: 6000000 INFO @ Thu, 30 Apr 2015 10:59:01: 6000000 INFO @ Thu, 30 Apr 2015 10:59:06: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 10:59:06: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 10:59:06: #1 total tags in treatment: 6901458 INFO @ Thu, 30 Apr 2015 10:59:06: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 10:59:06: #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 10:59:07: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 10:59:07: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 10:59:07: #1 total tags in treatment: 6901458 INFO @ Thu, 30 Apr 2015 10:59:07: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 10:59:07: #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 10:59:07: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 10:59:07: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 10:59:07: #1 total tags in treatment: 6901458 INFO @ Thu, 30 Apr 2015 10:59:07: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 10:59:07: #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 10:59:07: #1 tags after filtering in treatment: 6900944 INFO @ Thu, 30 Apr 2015 10:59:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 10:59:07: #1 finished! INFO @ Thu, 30 Apr 2015 10:59:07: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 10:59:08: #1 tags after filtering in treatment: 6900944 INFO @ Thu, 30 Apr 2015 10:59:08: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 10:59:08: #1 finished! INFO @ Thu, 30 Apr 2015 10:59:08: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 10:59:08: #1 tags after filtering in treatment: 6900944 INFO @ Thu, 30 Apr 2015 10:59:08: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 10:59:08: #1 finished! INFO @ Thu, 30 Apr 2015 10:59:08: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 10:59:08: #2 number of paired peaks: 320 WARNING @ Thu, 30 Apr 2015 10:59:08: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Thu, 30 Apr 2015 10:59:08: start model_add_line... INFO @ Thu, 30 Apr 2015 10:59:09: #2 number of paired peaks: 320 WARNING @ Thu, 30 Apr 2015 10:59:09: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Thu, 30 Apr 2015 10:59:09: start model_add_line... INFO @ Thu, 30 Apr 2015 10:59:09: #2 number of paired peaks: 320 WARNING @ Thu, 30 Apr 2015 10:59:09: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Thu, 30 Apr 2015 10:59:09: start model_add_line... INFO @ Thu, 30 Apr 2015 10:59:11: start X-correlation... INFO @ Thu, 30 Apr 2015 10:59:11: end of X-cor INFO @ Thu, 30 Apr 2015 10:59:11: #2 finished! INFO @ Thu, 30 Apr 2015 10:59:11: #2 predicted fragment length is 35 bps INFO @ Thu, 30 Apr 2015 10:59:11: #2 alternative fragment length(s) may be 2,35,81,483,510,524,526,552,589 bps INFO @ Thu, 30 Apr 2015 10:59:11: #2.2 Generate R script for model : SRX012300.20_model.r WARNING @ Thu, 30 Apr 2015 10:59:11: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 10:59:11: #2 You may need to consider one of the other alternative d(s): 2,35,81,483,510,524,526,552,589 WARNING @ Thu, 30 Apr 2015 10:59:11: #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 10:59:11: #3 Call peaks... INFO @ Thu, 30 Apr 2015 10:59:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 10:59:12: start X-correlation... INFO @ Thu, 30 Apr 2015 10:59:12: end of X-cor INFO @ Thu, 30 Apr 2015 10:59:12: #2 finished! INFO @ Thu, 30 Apr 2015 10:59:12: #2 predicted fragment length is 35 bps INFO @ Thu, 30 Apr 2015 10:59:12: #2 alternative fragment length(s) may be 2,35,81,483,510,524,526,552,589 bps INFO @ Thu, 30 Apr 2015 10:59:12: #2.2 Generate R script for model : SRX012300.10_model.r WARNING @ Thu, 30 Apr 2015 10:59:12: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 10:59:12: #2 You may need to consider one of the other alternative d(s): 2,35,81,483,510,524,526,552,589 WARNING @ Thu, 30 Apr 2015 10:59:12: #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 10:59:12: #3 Call peaks... INFO @ Thu, 30 Apr 2015 10:59:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 10:59:12: start X-correlation... INFO @ Thu, 30 Apr 2015 10:59:12: end of X-cor INFO @ Thu, 30 Apr 2015 10:59:12: #2 finished! INFO @ Thu, 30 Apr 2015 10:59:12: #2 predicted fragment length is 35 bps INFO @ Thu, 30 Apr 2015 10:59:12: #2 alternative fragment length(s) may be 2,35,81,483,510,524,526,552,589 bps INFO @ Thu, 30 Apr 2015 10:59:12: #2.2 Generate R script for model : SRX012300.05_model.r WARNING @ Thu, 30 Apr 2015 10:59:12: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 10:59:12: #2 You may need to consider one of the other alternative d(s): 2,35,81,483,510,524,526,552,589 WARNING @ Thu, 30 Apr 2015 10:59:12: #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 10:59:12: #3 Call peaks... INFO @ Thu, 30 Apr 2015 10:59:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 10:59:49: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 10:59:52: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 10:59:52: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:00:16: #4 Write output xls file... SRX012300.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:00:16: #4 Write peak in narrowPeak format file... SRX012300.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:00:16: #4 Write summits bed file... SRX012300.20_summits.bed INFO @ Thu, 30 Apr 2015 11:00:16: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:00:18: #4 Write output xls file... SRX012300.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:00:18: #4 Write peak in narrowPeak format file... SRX012300.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:00:18: #4 Write summits bed file... SRX012300.05_summits.bed INFO @ Thu, 30 Apr 2015 11:00:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (202 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:00:23: #4 Write output xls file... SRX012300.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:00:23: #4 Write peak in narrowPeak format file... SRX012300.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:00:23: #4 Write summits bed file... SRX012300.10_summits.bed INFO @ Thu, 30 Apr 2015 11:00:23: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (64 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。