Job ID = 2236682 sra ファイルのダウンロード中... Completed: 153826K bytes transferred in 5 seconds (234014K bits/sec), in 2 files, 3 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 4000 0 4000 0 0 6797 0 --:--:-- --:--:-- --:--:-- 10050 100 34302 0 34302 0 0 44073 0 --:--:-- --:--:-- --:--:-- 58336 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 4196074 spots for /home/okishinya/chipatlas/results/ce10/SRX013986/SRR031092.sra Written 4196074 spots total Written 5588641 spots for /home/okishinya/chipatlas/results/ce10/SRX013986/SRR031091.sra Written 5588641 spots total 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: 00:01:44 9784715 reads; of these: 9784715 (100.00%) were unpaired; of these: 277673 (2.84%) aligned 0 times 7827973 (80.00%) aligned exactly 1 time 1679069 (17.16%) aligned >1 times 97.16% overall alignment rate Time searching: 00:01:44 Overall time: 00:01:44 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] 747062 / 9507042 = 0.0786 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 10:57:23: # Command line: callpeak -t SRX013986.bam -f BAM -g ce -n SRX013986.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013986.05 # format = BAM # ChIP-seq file = ['SRX013986.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 10:57:23: # Command line: callpeak -t SRX013986.bam -f BAM -g ce -n SRX013986.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013986.10 # format = BAM # ChIP-seq file = ['SRX013986.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 10:57:23: # Command line: callpeak -t SRX013986.bam -f BAM -g ce -n SRX013986.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013986.20 # format = BAM # ChIP-seq file = ['SRX013986.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 10:57:23: #1 read tag files... INFO @ Thu, 30 Apr 2015 10:57:23: #1 read tag files... INFO @ Thu, 30 Apr 2015 10:57:23: #1 read tag files... INFO @ Thu, 30 Apr 2015 10:57:23: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 10:57:23: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 10:57:23: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 10:57:28: 1000000 INFO @ Thu, 30 Apr 2015 10:57:28: 1000000 INFO @ Thu, 30 Apr 2015 10:57:28: 1000000 INFO @ Thu, 30 Apr 2015 10:57:34: 2000000 INFO @ Thu, 30 Apr 2015 10:57:34: 2000000 INFO @ Thu, 30 Apr 2015 10:57:34: 2000000 INFO @ Thu, 30 Apr 2015 10:57:40: 3000000 INFO @ Thu, 30 Apr 2015 10:57:40: 3000000 INFO @ Thu, 30 Apr 2015 10:57:40: 3000000 INFO @ Thu, 30 Apr 2015 10:57:46: 4000000 INFO @ Thu, 30 Apr 2015 10:57:46: 4000000 INFO @ Thu, 30 Apr 2015 10:57:46: 4000000 INFO @ Thu, 30 Apr 2015 10:57:52: 5000000 INFO @ Thu, 30 Apr 2015 10:57:52: 5000000 INFO @ Thu, 30 Apr 2015 10:57:52: 5000000 INFO @ Thu, 30 Apr 2015 10:57:57: 6000000 INFO @ Thu, 30 Apr 2015 10:57:57: 6000000 INFO @ Thu, 30 Apr 2015 10:57:58: 6000000 INFO @ Thu, 30 Apr 2015 10:58:02: 7000000 INFO @ Thu, 30 Apr 2015 10:58:02: 7000000 INFO @ Thu, 30 Apr 2015 10:58:04: 7000000 INFO @ Thu, 30 Apr 2015 10:58:08: 8000000 INFO @ Thu, 30 Apr 2015 10:58:08: 8000000 INFO @ Thu, 30 Apr 2015 10:58:10: 8000000 INFO @ Thu, 30 Apr 2015 10:58:12: #1 tag size is determined as 27 bps INFO @ Thu, 30 Apr 2015 10:58:12: #1 tag size is determined as 27 bps INFO @ Thu, 30 Apr 2015 10:58:12: #1 tag size = 27 INFO @ Thu, 30 Apr 2015 10:58:12: #1 tag size = 27 INFO @ Thu, 30 Apr 2015 10:58:12: #1 total tags in treatment: 8759980 INFO @ Thu, 30 Apr 2015 10:58:12: #1 total tags in treatment: 8759980 INFO @ Thu, 30 Apr 2015 10:58:12: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 10:58:12: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 10:58:12: #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 10:58:12: #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 10:58:13: #1 tags after filtering in treatment: 8759935 INFO @ Thu, 30 Apr 2015 10:58:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 10:58:13: #1 finished! INFO @ Thu, 30 Apr 2015 10:58:13: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 10:58:13: #1 tags after filtering in treatment: 8759935 INFO @ Thu, 30 Apr 2015 10:58:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 10:58:13: #1 finished! INFO @ Thu, 30 Apr 2015 10:58:13: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 10:58:15: #1 tag size is determined as 27 bps INFO @ Thu, 30 Apr 2015 10:58:15: #1 tag size = 27 INFO @ Thu, 30 Apr 2015 10:58:15: #1 total tags in treatment: 8759980 INFO @ Thu, 30 Apr 2015 10:58:15: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 10:58:15: #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 10:58:15: #2 number of paired peaks: 302 WARNING @ Thu, 30 Apr 2015 10:58:15: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Thu, 30 Apr 2015 10:58:15: start model_add_line... INFO @ Thu, 30 Apr 2015 10:58:15: #2 number of paired peaks: 302 WARNING @ Thu, 30 Apr 2015 10:58:15: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Thu, 30 Apr 2015 10:58:15: start model_add_line... INFO @ Thu, 30 Apr 2015 10:58:16: #1 tags after filtering in treatment: 8759935 INFO @ Thu, 30 Apr 2015 10:58:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 10:58:16: #1 finished! INFO @ Thu, 30 Apr 2015 10:58:16: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 10:58:18: #2 number of paired peaks: 302 WARNING @ Thu, 30 Apr 2015 10:58:18: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Thu, 30 Apr 2015 10:58:18: start model_add_line... INFO @ Thu, 30 Apr 2015 10:58:19: start X-correlation... INFO @ Thu, 30 Apr 2015 10:58:19: end of X-cor INFO @ Thu, 30 Apr 2015 10:58:19: #2 finished! INFO @ Thu, 30 Apr 2015 10:58:19: #2 predicted fragment length is 27 bps INFO @ Thu, 30 Apr 2015 10:58:19: #2 alternative fragment length(s) may be 1,27,554,575 bps INFO @ Thu, 30 Apr 2015 10:58:19: #2.2 Generate R script for model : SRX013986.05_model.r WARNING @ Thu, 30 Apr 2015 10:58:19: #2 Since the d (27) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 10:58:19: #2 You may need to consider one of the other alternative d(s): 1,27,554,575 WARNING @ Thu, 30 Apr 2015 10:58:19: #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 10:58:19: #3 Call peaks... INFO @ Thu, 30 Apr 2015 10:58:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 10:58:19: start X-correlation... INFO @ Thu, 30 Apr 2015 10:58:19: end of X-cor INFO @ Thu, 30 Apr 2015 10:58:19: #2 finished! INFO @ Thu, 30 Apr 2015 10:58:19: #2 predicted fragment length is 27 bps INFO @ Thu, 30 Apr 2015 10:58:19: #2 alternative fragment length(s) may be 1,27,554,575 bps INFO @ Thu, 30 Apr 2015 10:58:19: #2.2 Generate R script for model : SRX013986.10_model.r WARNING @ Thu, 30 Apr 2015 10:58:19: #2 Since the d (27) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 10:58:19: #2 You may need to consider one of the other alternative d(s): 1,27,554,575 WARNING @ Thu, 30 Apr 2015 10:58:19: #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 10:58:19: #3 Call peaks... INFO @ Thu, 30 Apr 2015 10:58:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 10:58:22: start X-correlation... INFO @ Thu, 30 Apr 2015 10:58:22: end of X-cor INFO @ Thu, 30 Apr 2015 10:58:22: #2 finished! INFO @ Thu, 30 Apr 2015 10:58:22: #2 predicted fragment length is 27 bps INFO @ Thu, 30 Apr 2015 10:58:22: #2 alternative fragment length(s) may be 1,27,554,575 bps INFO @ Thu, 30 Apr 2015 10:58:22: #2.2 Generate R script for model : SRX013986.20_model.r WARNING @ Thu, 30 Apr 2015 10:58:22: #2 Since the d (27) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 10:58:22: #2 You may need to consider one of the other alternative d(s): 1,27,554,575 WARNING @ Thu, 30 Apr 2015 10:58:22: #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 10:58:22: #3 Call peaks... INFO @ Thu, 30 Apr 2015 10:58:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 10:59:06: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 10:59:06: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 10:59:10: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 10:59:40: #4 Write output xls file... SRX013986.05_peaks.xls INFO @ Thu, 30 Apr 2015 10:59:40: #4 Write peak in narrowPeak format file... SRX013986.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 10:59:40: #4 Write summits bed file... SRX013986.05_summits.bed INFO @ Thu, 30 Apr 2015 10:59:40: Done! INFO @ Thu, 30 Apr 2015 10:59:40: #4 Write output xls file... SRX013986.10_peaks.xls INFO @ Thu, 30 Apr 2015 10:59:40: #4 Write peak in narrowPeak format file... SRX013986.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 10:59:40: #4 Write summits bed file... SRX013986.10_summits.bed INFO @ Thu, 30 Apr 2015 10:59:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (504 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (230 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 10:59:46: #4 Write output xls file... SRX013986.20_peaks.xls INFO @ Thu, 30 Apr 2015 10:59:46: #4 Write peak in narrowPeak format file... SRX013986.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 10:59:46: #4 Write summits bed file... SRX013986.20_summits.bed INFO @ Thu, 30 Apr 2015 10:59:46: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (68 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。