Job ID = 10195044 sra ファイルのダウンロード中... Completed: 664030K bytes transferred in 10 seconds (538110K bits/sec), in 1 file. Completed: 799152K bytes transferred in 11 seconds (588399K 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 18428758 spots for /home/okishinya/chipatlas/results/rn6/SRX913513/SRR1870961.sra Written 18428758 spots total Written 25837257 spots for /home/okishinya/chipatlas/results/rn6/SRX913513/SRR1870962.sra Written 25837257 spots total 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 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: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:27:08 44266015 reads; of these: 44266015 (100.00%) were unpaired; of these: 2871883 (6.49%) aligned 0 times 29702476 (67.10%) aligned exactly 1 time 11691656 (26.41%) aligned >1 times 93.51% overall alignment rate Time searching: 00:27:10 Overall time: 00:27:10 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 20 files... [bam_rmdupse_core] 23072042 / 41394132 = 0.5574 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 @ Sat, 11 Nov 2017 08:05:47: # Command line: callpeak -t SRX913513.bam -f BAM -g 2.15e9 -n SRX913513.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX913513.10 # format = BAM # ChIP-seq file = ['SRX913513.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 @ Sat, 11 Nov 2017 08:05:47: #1 read tag files... INFO @ Sat, 11 Nov 2017 08:05:47: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 08:05:47: # Command line: callpeak -t SRX913513.bam -f BAM -g 2.15e9 -n SRX913513.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX913513.05 # format = BAM # ChIP-seq file = ['SRX913513.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 @ Sat, 11 Nov 2017 08:05:47: #1 read tag files... INFO @ Sat, 11 Nov 2017 08:05:47: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 08:05:47: # Command line: callpeak -t SRX913513.bam -f BAM -g 2.15e9 -n SRX913513.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX913513.20 # format = BAM # ChIP-seq file = ['SRX913513.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 @ Sat, 11 Nov 2017 08:05:47: #1 read tag files... INFO @ Sat, 11 Nov 2017 08:05:47: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 08:05:54: 1000000 INFO @ Sat, 11 Nov 2017 08:05:54: 1000000 INFO @ Sat, 11 Nov 2017 08:05:54: 1000000 INFO @ Sat, 11 Nov 2017 08:06:00: 2000000 INFO @ Sat, 11 Nov 2017 08:06:01: 2000000 INFO @ Sat, 11 Nov 2017 08:06:01: 2000000 INFO @ Sat, 11 Nov 2017 08:06:07: 3000000 INFO @ Sat, 11 Nov 2017 08:06:08: 3000000 INFO @ Sat, 11 Nov 2017 08:06:08: 3000000 INFO @ Sat, 11 Nov 2017 08:06:15: 4000000 INFO @ Sat, 11 Nov 2017 08:06:15: 4000000 INFO @ Sat, 11 Nov 2017 08:06:16: 4000000 INFO @ Sat, 11 Nov 2017 08:06:22: 5000000 INFO @ Sat, 11 Nov 2017 08:06:23: 5000000 INFO @ Sat, 11 Nov 2017 08:06:24: 5000000 INFO @ Sat, 11 Nov 2017 08:06:29: 6000000 INFO @ Sat, 11 Nov 2017 08:06:31: 6000000 INFO @ Sat, 11 Nov 2017 08:06:32: 6000000 INFO @ Sat, 11 Nov 2017 08:06:36: 7000000 INFO @ Sat, 11 Nov 2017 08:06:38: 7000000 INFO @ Sat, 11 Nov 2017 08:06:40: 7000000 INFO @ Sat, 11 Nov 2017 08:06:44: 8000000 INFO @ Sat, 11 Nov 2017 08:06:46: 8000000 INFO @ Sat, 11 Nov 2017 08:06:48: 8000000 INFO @ Sat, 11 Nov 2017 08:06:51: 9000000 INFO @ Sat, 11 Nov 2017 08:06:53: 9000000 INFO @ Sat, 11 Nov 2017 08:06:56: 9000000 INFO @ Sat, 11 Nov 2017 08:06:58: 10000000 INFO @ Sat, 11 Nov 2017 08:07:01: 10000000 INFO @ Sat, 11 Nov 2017 08:07:04: 10000000 INFO @ Sat, 11 Nov 2017 08:07:05: 11000000 INFO @ Sat, 11 Nov 2017 08:07:08: 11000000 INFO @ Sat, 11 Nov 2017 08:07:12: 11000000 INFO @ Sat, 11 Nov 2017 08:07:12: 12000000 INFO @ Sat, 11 Nov 2017 08:07:16: 12000000 INFO @ Sat, 11 Nov 2017 08:07:19: 13000000 INFO @ Sat, 11 Nov 2017 08:07:20: 12000000 INFO @ Sat, 11 Nov 2017 08:07:23: 13000000 INFO @ Sat, 11 Nov 2017 08:07:27: 14000000 INFO @ Sat, 11 Nov 2017 08:07:28: 13000000 INFO @ Sat, 11 Nov 2017 08:07:31: 14000000 INFO @ Sat, 11 Nov 2017 08:07:34: 15000000 INFO @ Sat, 11 Nov 2017 08:07:36: 14000000 INFO @ Sat, 11 Nov 2017 08:07:38: 15000000 INFO @ Sat, 11 Nov 2017 08:07:41: 16000000 INFO @ Sat, 11 Nov 2017 08:07:43: 15000000 INFO @ Sat, 11 Nov 2017 08:07:46: 16000000 INFO @ Sat, 11 Nov 2017 08:07:48: 17000000 INFO @ Sat, 11 Nov 2017 08:07:51: 16000000 INFO @ Sat, 11 Nov 2017 08:07:53: 17000000 INFO @ Sat, 11 Nov 2017 08:07:56: 18000000 INFO @ Sat, 11 Nov 2017 08:07:58: #1 tag size is determined as 46 bps INFO @ Sat, 11 Nov 2017 08:07:58: #1 tag size = 46 INFO @ Sat, 11 Nov 2017 08:07:58: #1 total tags in treatment: 18322090 INFO @ Sat, 11 Nov 2017 08:07:58: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 08:07:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 08:07:59: #1 tags after filtering in treatment: 18321972 INFO @ Sat, 11 Nov 2017 08:07:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 08:07:59: #1 finished! INFO @ Sat, 11 Nov 2017 08:07:59: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 08:07:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 08:07:59: 17000000 INFO @ Sat, 11 Nov 2017 08:08:01: 18000000 INFO @ Sat, 11 Nov 2017 08:08:01: #2 number of paired peaks: 10018 INFO @ Sat, 11 Nov 2017 08:08:01: start model_add_line... INFO @ Sat, 11 Nov 2017 08:08:01: start X-correlation... INFO @ Sat, 11 Nov 2017 08:08:01: end of X-cor INFO @ Sat, 11 Nov 2017 08:08:01: #2 finished! INFO @ Sat, 11 Nov 2017 08:08:01: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Nov 2017 08:08:01: #2 alternative fragment length(s) may be 48 bps INFO @ Sat, 11 Nov 2017 08:08:01: #2.2 Generate R script for model : SRX913513.05_model.r WARNING @ Sat, 11 Nov 2017 08:08:01: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 08:08:01: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sat, 11 Nov 2017 08:08:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 08:08:01: #3 Call peaks... INFO @ Sat, 11 Nov 2017 08:08:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 08:08:03: #1 tag size is determined as 46 bps INFO @ Sat, 11 Nov 2017 08:08:03: #1 tag size = 46 INFO @ Sat, 11 Nov 2017 08:08:03: #1 total tags in treatment: 18322090 INFO @ Sat, 11 Nov 2017 08:08:03: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 08:08:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 08:08:04: #1 tags after filtering in treatment: 18321972 INFO @ Sat, 11 Nov 2017 08:08:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 08:08:04: #1 finished! INFO @ Sat, 11 Nov 2017 08:08:04: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 08:08:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 08:08:06: #2 number of paired peaks: 10018 INFO @ Sat, 11 Nov 2017 08:08:06: start model_add_line... INFO @ Sat, 11 Nov 2017 08:08:06: 18000000 INFO @ Sat, 11 Nov 2017 08:08:06: start X-correlation... INFO @ Sat, 11 Nov 2017 08:08:06: end of X-cor INFO @ Sat, 11 Nov 2017 08:08:06: #2 finished! INFO @ Sat, 11 Nov 2017 08:08:06: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Nov 2017 08:08:06: #2 alternative fragment length(s) may be 48 bps INFO @ Sat, 11 Nov 2017 08:08:06: #2.2 Generate R script for model : SRX913513.10_model.r WARNING @ Sat, 11 Nov 2017 08:08:06: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 08:08:06: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sat, 11 Nov 2017 08:08:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 08:08:06: #3 Call peaks... INFO @ Sat, 11 Nov 2017 08:08:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 08:08:08: #1 tag size is determined as 46 bps INFO @ Sat, 11 Nov 2017 08:08:08: #1 tag size = 46 INFO @ Sat, 11 Nov 2017 08:08:08: #1 total tags in treatment: 18322090 INFO @ Sat, 11 Nov 2017 08:08:08: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 08:08:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 08:08:09: #1 tags after filtering in treatment: 18321972 INFO @ Sat, 11 Nov 2017 08:08:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 08:08:09: #1 finished! INFO @ Sat, 11 Nov 2017 08:08:09: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 08:08:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 08:08:11: #2 number of paired peaks: 10018 INFO @ Sat, 11 Nov 2017 08:08:11: start model_add_line... INFO @ Sat, 11 Nov 2017 08:08:11: start X-correlation... INFO @ Sat, 11 Nov 2017 08:08:11: end of X-cor INFO @ Sat, 11 Nov 2017 08:08:11: #2 finished! INFO @ Sat, 11 Nov 2017 08:08:11: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Nov 2017 08:08:11: #2 alternative fragment length(s) may be 48 bps INFO @ Sat, 11 Nov 2017 08:08:11: #2.2 Generate R script for model : SRX913513.20_model.r WARNING @ Sat, 11 Nov 2017 08:08:11: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 08:08:11: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sat, 11 Nov 2017 08:08:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 08:08:11: #3 Call peaks... INFO @ Sat, 11 Nov 2017 08:08:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 08:08:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 08:08:48: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 08:08:57: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 08:09:07: #4 Write output xls file... SRX913513.05_peaks.xls INFO @ Sat, 11 Nov 2017 08:09:07: #4 Write peak in narrowPeak format file... SRX913513.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 08:09:07: #4 Write summits bed file... SRX913513.05_summits.bed INFO @ Sat, 11 Nov 2017 08:09:07: Done! pass1 - making usageList (65 chroms): 8 millis pass2 - checking and writing primary data (1462 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 08:09:12: #4 Write output xls file... SRX913513.10_peaks.xls INFO @ Sat, 11 Nov 2017 08:09:12: #4 Write peak in narrowPeak format file... SRX913513.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 08:09:12: #4 Write summits bed file... SRX913513.10_summits.bed INFO @ Sat, 11 Nov 2017 08:09:12: Done! pass1 - making usageList (47 chroms): 1 millis pass2 - checking and writing primary data (746 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 08:09:24: #4 Write output xls file... SRX913513.20_peaks.xls INFO @ Sat, 11 Nov 2017 08:09:24: #4 Write peak in narrowPeak format file... SRX913513.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 08:09:25: #4 Write summits bed file... SRX913513.20_summits.bed INFO @ Sat, 11 Nov 2017 08:09:25: Done! pass1 - making usageList (33 chroms): 1 millis pass2 - checking and writing primary data (316 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。