Job ID = 10851041 sra ファイルのダウンロード中... Completed: 681676K bytes transferred in 14 seconds (394854K 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... Read 15664537 spots for /home/okishinya/chipatlas/results/rn6/SRX3461657/SRR6366135.sra Written 15664537 spots for /home/okishinya/chipatlas/results/rn6/SRX3461657/SRR6366135.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:00:02 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:27:44 15664537 reads; of these: 15664537 (100.00%) were unpaired; of these: 618976 (3.95%) aligned 0 times 11360624 (72.52%) aligned exactly 1 time 3684937 (23.52%) aligned >1 times 96.05% overall alignment rate Time searching: 00:27:52 Overall time: 00:27:52 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 8 files... [bam_rmdupse_core] 289430 / 15045561 = 0.0192 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, 05 Jul 2018 22:39:06: # Command line: callpeak -t SRX3461657.bam -f BAM -g 2.15e9 -n SRX3461657.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3461657.05 # format = BAM # ChIP-seq file = ['SRX3461657.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 @ Thu, 05 Jul 2018 22:39:06: # Command line: callpeak -t SRX3461657.bam -f BAM -g 2.15e9 -n SRX3461657.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3461657.20 # format = BAM # ChIP-seq file = ['SRX3461657.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 @ Thu, 05 Jul 2018 22:39:06: # Command line: callpeak -t SRX3461657.bam -f BAM -g 2.15e9 -n SRX3461657.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3461657.10 # format = BAM # ChIP-seq file = ['SRX3461657.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 @ Thu, 05 Jul 2018 22:39:06: #1 read tag files... INFO @ Thu, 05 Jul 2018 22:39:06: #1 read tag files... INFO @ Thu, 05 Jul 2018 22:39:06: #1 read treatment tags... INFO @ Thu, 05 Jul 2018 22:39:06: #1 read tag files... INFO @ Thu, 05 Jul 2018 22:39:06: #1 read treatment tags... INFO @ Thu, 05 Jul 2018 22:39:06: #1 read treatment tags... INFO @ Thu, 05 Jul 2018 22:39:20: 1000000 INFO @ Thu, 05 Jul 2018 22:39:24: 1000000 INFO @ Thu, 05 Jul 2018 22:39:24: 1000000 INFO @ Thu, 05 Jul 2018 22:39:34: 2000000 INFO @ Thu, 05 Jul 2018 22:39:40: 2000000 INFO @ Thu, 05 Jul 2018 22:39:42: 2000000 INFO @ Thu, 05 Jul 2018 22:39:48: 3000000 INFO @ Thu, 05 Jul 2018 22:39:54: 3000000 INFO @ Thu, 05 Jul 2018 22:40:00: 3000000 INFO @ Thu, 05 Jul 2018 22:40:03: 4000000 INFO @ Thu, 05 Jul 2018 22:40:08: 4000000 INFO @ Thu, 05 Jul 2018 22:40:17: 5000000 INFO @ Thu, 05 Jul 2018 22:40:18: 4000000 INFO @ Thu, 05 Jul 2018 22:40:22: 5000000 INFO @ Thu, 05 Jul 2018 22:40:31: 6000000 INFO @ Thu, 05 Jul 2018 22:40:36: 5000000 INFO @ Thu, 05 Jul 2018 22:40:36: 6000000 INFO @ Thu, 05 Jul 2018 22:40:45: 7000000 INFO @ Thu, 05 Jul 2018 22:40:50: 7000000 INFO @ Thu, 05 Jul 2018 22:40:53: 6000000 INFO @ Thu, 05 Jul 2018 22:40:59: 8000000 INFO @ Thu, 05 Jul 2018 22:41:04: 8000000 INFO @ Thu, 05 Jul 2018 22:41:11: 7000000 INFO @ Thu, 05 Jul 2018 22:41:13: 9000000 INFO @ Thu, 05 Jul 2018 22:41:18: 9000000 INFO @ Thu, 05 Jul 2018 22:41:27: 10000000 INFO @ Thu, 05 Jul 2018 22:41:29: 8000000 INFO @ Thu, 05 Jul 2018 22:41:32: 10000000 INFO @ Thu, 05 Jul 2018 22:41:41: 11000000 INFO @ Thu, 05 Jul 2018 22:41:46: 9000000 INFO @ Thu, 05 Jul 2018 22:41:46: 11000000 INFO @ Thu, 05 Jul 2018 22:41:56: 12000000 INFO @ Thu, 05 Jul 2018 22:42:01: 12000000 INFO @ Thu, 05 Jul 2018 22:42:02: 10000000 INFO @ Thu, 05 Jul 2018 22:42:11: 13000000 INFO @ Thu, 05 Jul 2018 22:42:16: 13000000 INFO @ Thu, 05 Jul 2018 22:42:19: 11000000 INFO @ Thu, 05 Jul 2018 22:42:28: 14000000 INFO @ Thu, 05 Jul 2018 22:42:30: 14000000 INFO @ Thu, 05 Jul 2018 22:42:34: 12000000 INFO @ Thu, 05 Jul 2018 22:42:41: #1 tag size is determined as 75 bps INFO @ Thu, 05 Jul 2018 22:42:41: #1 tag size = 75 INFO @ Thu, 05 Jul 2018 22:42:41: #1 total tags in treatment: 14756131 INFO @ Thu, 05 Jul 2018 22:42:41: #1 user defined the maximum tags... INFO @ Thu, 05 Jul 2018 22:42:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Jul 2018 22:42:42: #1 tags after filtering in treatment: 14755955 INFO @ Thu, 05 Jul 2018 22:42:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Jul 2018 22:42:42: #1 finished! INFO @ Thu, 05 Jul 2018 22:42:42: #2 Build Peak Model... INFO @ Thu, 05 Jul 2018 22:42:42: #1 tag size is determined as 75 bps INFO @ Thu, 05 Jul 2018 22:42:42: #1 tag size = 75 INFO @ Thu, 05 Jul 2018 22:42:42: #1 total tags in treatment: 14756131 INFO @ Thu, 05 Jul 2018 22:42:42: #1 user defined the maximum tags... INFO @ Thu, 05 Jul 2018 22:42:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Jul 2018 22:42:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Jul 2018 22:42:43: #1 tags after filtering in treatment: 14755955 INFO @ Thu, 05 Jul 2018 22:42:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Jul 2018 22:42:43: #1 finished! INFO @ Thu, 05 Jul 2018 22:42:43: #2 Build Peak Model... INFO @ Thu, 05 Jul 2018 22:42:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Jul 2018 22:42:44: #2 number of paired peaks: 11343 INFO @ Thu, 05 Jul 2018 22:42:44: start model_add_line... INFO @ Thu, 05 Jul 2018 22:42:44: start X-correlation... INFO @ Thu, 05 Jul 2018 22:42:45: #2 number of paired peaks: 11343 INFO @ Thu, 05 Jul 2018 22:42:45: start model_add_line... INFO @ Thu, 05 Jul 2018 22:42:45: end of X-cor INFO @ Thu, 05 Jul 2018 22:42:45: #2 finished! INFO @ Thu, 05 Jul 2018 22:42:45: #2 predicted fragment length is 132 bps INFO @ Thu, 05 Jul 2018 22:42:45: #2 alternative fragment length(s) may be 132 bps INFO @ Thu, 05 Jul 2018 22:42:45: #2.2 Generate R script for model : SRX3461657.05_model.r WARNING @ Thu, 05 Jul 2018 22:42:45: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Jul 2018 22:42:45: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Thu, 05 Jul 2018 22:42:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Jul 2018 22:42:45: #3 Call peaks... INFO @ Thu, 05 Jul 2018 22:42:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Jul 2018 22:42:45: start X-correlation... INFO @ Thu, 05 Jul 2018 22:42:45: end of X-cor INFO @ Thu, 05 Jul 2018 22:42:45: #2 finished! INFO @ Thu, 05 Jul 2018 22:42:45: #2 predicted fragment length is 132 bps INFO @ Thu, 05 Jul 2018 22:42:45: #2 alternative fragment length(s) may be 132 bps INFO @ Thu, 05 Jul 2018 22:42:45: #2.2 Generate R script for model : SRX3461657.20_model.r WARNING @ Thu, 05 Jul 2018 22:42:45: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Jul 2018 22:42:45: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Thu, 05 Jul 2018 22:42:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Jul 2018 22:42:45: #3 Call peaks... INFO @ Thu, 05 Jul 2018 22:42:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Jul 2018 22:42:51: 13000000 INFO @ Thu, 05 Jul 2018 22:43:08: 14000000 INFO @ Thu, 05 Jul 2018 22:43:20: #1 tag size is determined as 75 bps INFO @ Thu, 05 Jul 2018 22:43:21: #1 tag size = 75 INFO @ Thu, 05 Jul 2018 22:43:21: #1 total tags in treatment: 14756131 INFO @ Thu, 05 Jul 2018 22:43:21: #1 user defined the maximum tags... INFO @ Thu, 05 Jul 2018 22:43:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Jul 2018 22:43:21: #1 tags after filtering in treatment: 14755955 INFO @ Thu, 05 Jul 2018 22:43:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Jul 2018 22:43:21: #1 finished! INFO @ Thu, 05 Jul 2018 22:43:21: #2 Build Peak Model... INFO @ Thu, 05 Jul 2018 22:43:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Jul 2018 22:43:24: #2 number of paired peaks: 11343 INFO @ Thu, 05 Jul 2018 22:43:24: start model_add_line... INFO @ Thu, 05 Jul 2018 22:43:24: start X-correlation... INFO @ Thu, 05 Jul 2018 22:43:25: #3 Call peaks for each chromosome... INFO @ Thu, 05 Jul 2018 22:43:26: #3 Call peaks for each chromosome... INFO @ Thu, 05 Jul 2018 22:43:30: end of X-cor INFO @ Thu, 05 Jul 2018 22:43:30: #2 finished! INFO @ Thu, 05 Jul 2018 22:43:30: #2 predicted fragment length is 132 bps INFO @ Thu, 05 Jul 2018 22:43:30: #2 alternative fragment length(s) may be 132 bps INFO @ Thu, 05 Jul 2018 22:43:30: #2.2 Generate R script for model : SRX3461657.10_model.r WARNING @ Thu, 05 Jul 2018 22:43:30: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Jul 2018 22:43:30: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Thu, 05 Jul 2018 22:43:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Jul 2018 22:43:30: #3 Call peaks... INFO @ Thu, 05 Jul 2018 22:43:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Jul 2018 22:43:48: #4 Write output xls file... SRX3461657.05_peaks.xls INFO @ Thu, 05 Jul 2018 22:43:48: #4 Write peak in narrowPeak format file... SRX3461657.05_peaks.narrowPeak INFO @ Thu, 05 Jul 2018 22:43:48: #4 Write summits bed file... SRX3461657.05_summits.bed INFO @ Thu, 05 Jul 2018 22:43:48: Done! INFO @ Thu, 05 Jul 2018 22:43:49: #4 Write output xls file... SRX3461657.20_peaks.xls INFO @ Thu, 05 Jul 2018 22:43:49: #4 Write peak in narrowPeak format file... SRX3461657.20_peaks.narrowPeak INFO @ Thu, 05 Jul 2018 22:43:49: #4 Write summits bed file... SRX3461657.20_summits.bed INFO @ Thu, 05 Jul 2018 22:43:49: Done! pass1 - making usageList (27 chroms): 1 millis pass1 - making usageList (49 chroms): 2 millis pass2 - checking and writing primary data (331 records, 4 fields): 7 millis pass2 - checking and writing primary data (2677 records, 4 fields): 10 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Thu, 05 Jul 2018 22:44:11: #3 Call peaks for each chromosome... INFO @ Thu, 05 Jul 2018 22:44:32: #4 Write output xls file... SRX3461657.10_peaks.xls INFO @ Thu, 05 Jul 2018 22:44:32: #4 Write peak in narrowPeak format file... SRX3461657.10_peaks.narrowPeak INFO @ Thu, 05 Jul 2018 22:44:32: #4 Write summits bed file... SRX3461657.10_summits.bed INFO @ Thu, 05 Jul 2018 22:44:32: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (1059 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。