Job ID = 10194723 sra ファイルのダウンロード中... Completed: 3893160K bytes transferred in 51 seconds (617107K bits/sec), in 1 file. 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 65994592 spots for /home/okishinya/chipatlas/results/rn6/SRX1037558/SRR2039162.sra Written 65994592 spots total rm: cannot remove `[DSE]RX*': No such file or directory rm: cannot remove `[DSE]RR*.fastq': No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 03:44:21 65994592 reads; of these: 65994592 (100.00%) were unpaired; of these: 4808694 (7.29%) aligned 0 times 45159243 (68.43%) aligned exactly 1 time 16026655 (24.28%) aligned >1 times 92.71% overall alignment rate Time searching: 03:44:25 Overall time: 03:44:25 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 28 files... [bam_rmdupse_core] 57625864 / 61185898 = 0.9418 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 @ Fri, 10 Nov 2017 23:22:55: # Command line: callpeak -t SRX1037558.bam -f BAM -g 2.15e9 -n SRX1037558.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1037558.20 # format = BAM # ChIP-seq file = ['SRX1037558.bam'] # control file = None # effective genome size = 2.15e+09 # 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 # Paired-End mode is off INFO @ Fri, 10 Nov 2017 23:22:55: # Command line: callpeak -t SRX1037558.bam -f BAM -g 2.15e9 -n SRX1037558.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1037558.10 # format = BAM # ChIP-seq file = ['SRX1037558.bam'] # control file = None # effective genome size = 2.15e+09 # 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 # Paired-End mode is off INFO @ Fri, 10 Nov 2017 23:22:55: # Command line: callpeak -t SRX1037558.bam -f BAM -g 2.15e9 -n SRX1037558.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1037558.05 # format = BAM # ChIP-seq file = ['SRX1037558.bam'] # control file = None # effective genome size = 2.15e+09 # 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 # Paired-End mode is off INFO @ Fri, 10 Nov 2017 23:22:55: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:22:55: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:22:55: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:22:55: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:22:55: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:22:55: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:23:12: 1000000 INFO @ Fri, 10 Nov 2017 23:23:13: 1000000 INFO @ Fri, 10 Nov 2017 23:23:16: 1000000 INFO @ Fri, 10 Nov 2017 23:23:29: 2000000 INFO @ Fri, 10 Nov 2017 23:23:34: 2000000 INFO @ Fri, 10 Nov 2017 23:23:37: 2000000 INFO @ Fri, 10 Nov 2017 23:23:47: 3000000 INFO @ Fri, 10 Nov 2017 23:23:54: 3000000 INFO @ Fri, 10 Nov 2017 23:23:55: 3000000 INFO @ Fri, 10 Nov 2017 23:23:56: #1 tag size is determined as 100 bps INFO @ Fri, 10 Nov 2017 23:23:56: #1 tag size = 100 INFO @ Fri, 10 Nov 2017 23:23:56: #1 total tags in treatment: 3560034 INFO @ Fri, 10 Nov 2017 23:23:56: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:23:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:23:56: #1 tags after filtering in treatment: 3559713 INFO @ Fri, 10 Nov 2017 23:23:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:23:56: #1 finished! INFO @ Fri, 10 Nov 2017 23:23:56: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:23:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:24:01: #2 number of paired peaks: 74555 INFO @ Fri, 10 Nov 2017 23:24:01: start model_add_line... INFO @ Fri, 10 Nov 2017 23:24:01: start X-correlation... INFO @ Fri, 10 Nov 2017 23:24:01: end of X-cor INFO @ Fri, 10 Nov 2017 23:24:01: #2 finished! INFO @ Fri, 10 Nov 2017 23:24:01: #2 predicted fragment length is 120 bps INFO @ Fri, 10 Nov 2017 23:24:01: #2 alternative fragment length(s) may be 120 bps INFO @ Fri, 10 Nov 2017 23:24:01: #2.2 Generate R script for model : SRX1037558.10_model.r WARNING @ Fri, 10 Nov 2017 23:24:01: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:24:01: #2 You may need to consider one of the other alternative d(s): 120 WARNING @ Fri, 10 Nov 2017 23:24:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 23:24:01: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:24:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:24:02: #1 tag size is determined as 100 bps INFO @ Fri, 10 Nov 2017 23:24:02: #1 tag size = 100 INFO @ Fri, 10 Nov 2017 23:24:02: #1 total tags in treatment: 3560034 INFO @ Fri, 10 Nov 2017 23:24:02: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:24:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:24:02: #1 tags after filtering in treatment: 3559713 INFO @ Fri, 10 Nov 2017 23:24:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:24:02: #1 finished! INFO @ Fri, 10 Nov 2017 23:24:02: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:24:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:24:06: #1 tag size is determined as 100 bps INFO @ Fri, 10 Nov 2017 23:24:06: #1 tag size = 100 INFO @ Fri, 10 Nov 2017 23:24:06: #1 total tags in treatment: 3560034 INFO @ Fri, 10 Nov 2017 23:24:06: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:24:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:24:06: #1 tags after filtering in treatment: 3559713 INFO @ Fri, 10 Nov 2017 23:24:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:24:06: #1 finished! INFO @ Fri, 10 Nov 2017 23:24:06: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:24:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:24:07: #2 number of paired peaks: 74555 INFO @ Fri, 10 Nov 2017 23:24:07: start model_add_line... INFO @ Fri, 10 Nov 2017 23:24:07: start X-correlation... INFO @ Fri, 10 Nov 2017 23:24:07: end of X-cor INFO @ Fri, 10 Nov 2017 23:24:07: #2 finished! INFO @ Fri, 10 Nov 2017 23:24:07: #2 predicted fragment length is 120 bps INFO @ Fri, 10 Nov 2017 23:24:07: #2 alternative fragment length(s) may be 120 bps INFO @ Fri, 10 Nov 2017 23:24:07: #2.2 Generate R script for model : SRX1037558.20_model.r WARNING @ Fri, 10 Nov 2017 23:24:07: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:24:07: #2 You may need to consider one of the other alternative d(s): 120 WARNING @ Fri, 10 Nov 2017 23:24:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 23:24:07: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:24:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:24:10: #2 number of paired peaks: 74555 INFO @ Fri, 10 Nov 2017 23:24:10: start model_add_line... INFO @ Fri, 10 Nov 2017 23:24:10: start X-correlation... INFO @ Fri, 10 Nov 2017 23:24:10: end of X-cor INFO @ Fri, 10 Nov 2017 23:24:10: #2 finished! INFO @ Fri, 10 Nov 2017 23:24:10: #2 predicted fragment length is 120 bps INFO @ Fri, 10 Nov 2017 23:24:10: #2 alternative fragment length(s) may be 120 bps INFO @ Fri, 10 Nov 2017 23:24:10: #2.2 Generate R script for model : SRX1037558.05_model.r WARNING @ Fri, 10 Nov 2017 23:24:10: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:24:10: #2 You may need to consider one of the other alternative d(s): 120 WARNING @ Fri, 10 Nov 2017 23:24:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 23:24:10: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:24:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:24:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:24:18: #4 Write output xls file... SRX1037558.10_peaks.xls INFO @ Fri, 10 Nov 2017 23:24:18: #4 Write peak in narrowPeak format file... SRX1037558.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:24:18: #4 Write summits bed file... SRX1037558.10_summits.bed INFO @ Fri, 10 Nov 2017 23:24:18: Done! pass1 - making usageList (38 chroms): 2 millis pass2 - checking and writing primary data (558 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:24:18: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:24:21: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:24:25: #4 Write output xls file... SRX1037558.20_peaks.xls INFO @ Fri, 10 Nov 2017 23:24:25: #4 Write peak in narrowPeak format file... SRX1037558.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:24:25: #4 Write summits bed file... SRX1037558.20_summits.bed INFO @ Fri, 10 Nov 2017 23:24:25: Done! pass1 - making usageList (25 chroms): 2 millis pass2 - checking and writing primary data (172 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:24:27: #4 Write output xls file... SRX1037558.05_peaks.xls INFO @ Fri, 10 Nov 2017 23:24:28: #4 Write peak in narrowPeak format file... SRX1037558.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:24:28: #4 Write summits bed file... SRX1037558.05_summits.bed INFO @ Fri, 10 Nov 2017 23:24:28: Done! pass1 - making usageList (66 chroms): 3 millis pass2 - checking and writing primary data (5003 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。