Job ID = 11632696 sra ファイルのダウンロード中... Completed: 1230955K bytes transferred in 14 seconds (714558K 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 48224159 spots for /home/okishinya/chipatlas/results/rn6/SRX3782455/SRR6826273.sra Written 48224159 spots for /home/okishinya/chipatlas/results/rn6/SRX3782455/SRR6826273.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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:23:49 48224159 reads; of these: 48224159 (100.00%) were unpaired; of these: 4380051 (9.08%) aligned 0 times 32983372 (68.40%) aligned exactly 1 time 10860736 (22.52%) aligned >1 times 90.92% overall alignment rate Time searching: 00:23:52 Overall time: 00:23:52 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 16 files... [bam_rmdupse_core] 17522918 / 43844108 = 0.3997 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, 15 Feb 2019 06:31:25: # Command line: callpeak -t SRX3782455.bam -f BAM -g 2.15e9 -n SRX3782455.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3782455.10 # format = BAM # ChIP-seq file = ['SRX3782455.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, 15 Feb 2019 06:31:25: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:31:25: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:31:25: # Command line: callpeak -t SRX3782455.bam -f BAM -g 2.15e9 -n SRX3782455.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3782455.20 # format = BAM # ChIP-seq file = ['SRX3782455.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, 15 Feb 2019 06:31:25: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:31:25: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:31:25: # Command line: callpeak -t SRX3782455.bam -f BAM -g 2.15e9 -n SRX3782455.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3782455.05 # format = BAM # ChIP-seq file = ['SRX3782455.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, 15 Feb 2019 06:31:25: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:31:25: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:31:31: 1000000 INFO @ Fri, 15 Feb 2019 06:31:31: 1000000 INFO @ Fri, 15 Feb 2019 06:31:32: 1000000 INFO @ Fri, 15 Feb 2019 06:31:38: 2000000 INFO @ Fri, 15 Feb 2019 06:31:38: 2000000 INFO @ Fri, 15 Feb 2019 06:31:38: 2000000 INFO @ Fri, 15 Feb 2019 06:31:44: 3000000 INFO @ Fri, 15 Feb 2019 06:31:44: 3000000 INFO @ Fri, 15 Feb 2019 06:31:45: 3000000 INFO @ Fri, 15 Feb 2019 06:31:51: 4000000 INFO @ Fri, 15 Feb 2019 06:31:51: 4000000 INFO @ Fri, 15 Feb 2019 06:31:52: 4000000 INFO @ Fri, 15 Feb 2019 06:31:58: 5000000 INFO @ Fri, 15 Feb 2019 06:31:58: 5000000 INFO @ Fri, 15 Feb 2019 06:31:59: 5000000 INFO @ Fri, 15 Feb 2019 06:32:05: 6000000 INFO @ Fri, 15 Feb 2019 06:32:05: 6000000 INFO @ Fri, 15 Feb 2019 06:32:06: 6000000 INFO @ Fri, 15 Feb 2019 06:32:11: 7000000 INFO @ Fri, 15 Feb 2019 06:32:11: 7000000 INFO @ Fri, 15 Feb 2019 06:32:13: 7000000 INFO @ Fri, 15 Feb 2019 06:32:17: 8000000 INFO @ Fri, 15 Feb 2019 06:32:17: 8000000 INFO @ Fri, 15 Feb 2019 06:32:20: 8000000 INFO @ Fri, 15 Feb 2019 06:32:23: 9000000 INFO @ Fri, 15 Feb 2019 06:32:24: 9000000 INFO @ Fri, 15 Feb 2019 06:32:27: 9000000 INFO @ Fri, 15 Feb 2019 06:32:30: 10000000 INFO @ Fri, 15 Feb 2019 06:32:30: 10000000 INFO @ Fri, 15 Feb 2019 06:32:33: 10000000 INFO @ Fri, 15 Feb 2019 06:32:36: 11000000 INFO @ Fri, 15 Feb 2019 06:32:36: 11000000 INFO @ Fri, 15 Feb 2019 06:32:39: 11000000 INFO @ Fri, 15 Feb 2019 06:32:42: 12000000 INFO @ Fri, 15 Feb 2019 06:32:43: 12000000 INFO @ Fri, 15 Feb 2019 06:32:46: 12000000 INFO @ Fri, 15 Feb 2019 06:32:49: 13000000 INFO @ Fri, 15 Feb 2019 06:32:49: 13000000 INFO @ Fri, 15 Feb 2019 06:32:52: 13000000 INFO @ Fri, 15 Feb 2019 06:32:55: 14000000 INFO @ Fri, 15 Feb 2019 06:32:55: 14000000 INFO @ Fri, 15 Feb 2019 06:32:58: 14000000 INFO @ Fri, 15 Feb 2019 06:33:01: 15000000 INFO @ Fri, 15 Feb 2019 06:33:02: 15000000 INFO @ Fri, 15 Feb 2019 06:33:05: 15000000 INFO @ Fri, 15 Feb 2019 06:33:08: 16000000 INFO @ Fri, 15 Feb 2019 06:33:08: 16000000 INFO @ Fri, 15 Feb 2019 06:33:11: 16000000 INFO @ Fri, 15 Feb 2019 06:33:14: 17000000 INFO @ Fri, 15 Feb 2019 06:33:14: 17000000 INFO @ Fri, 15 Feb 2019 06:33:17: 17000000 INFO @ Fri, 15 Feb 2019 06:33:20: 18000000 INFO @ Fri, 15 Feb 2019 06:33:20: 18000000 INFO @ Fri, 15 Feb 2019 06:33:23: 18000000 INFO @ Fri, 15 Feb 2019 06:33:27: 19000000 INFO @ Fri, 15 Feb 2019 06:33:27: 19000000 INFO @ Fri, 15 Feb 2019 06:33:30: 19000000 INFO @ Fri, 15 Feb 2019 06:33:33: 20000000 INFO @ Fri, 15 Feb 2019 06:33:33: 20000000 INFO @ Fri, 15 Feb 2019 06:33:36: 20000000 INFO @ Fri, 15 Feb 2019 06:33:39: 21000000 INFO @ Fri, 15 Feb 2019 06:33:40: 21000000 INFO @ Fri, 15 Feb 2019 06:33:42: 21000000 INFO @ Fri, 15 Feb 2019 06:33:46: 22000000 INFO @ Fri, 15 Feb 2019 06:33:46: 22000000 INFO @ Fri, 15 Feb 2019 06:33:49: 22000000 INFO @ Fri, 15 Feb 2019 06:33:52: 23000000 INFO @ Fri, 15 Feb 2019 06:33:52: 23000000 INFO @ Fri, 15 Feb 2019 06:33:55: 23000000 INFO @ Fri, 15 Feb 2019 06:33:58: 24000000 INFO @ Fri, 15 Feb 2019 06:33:58: 24000000 INFO @ Fri, 15 Feb 2019 06:34:01: 24000000 INFO @ Fri, 15 Feb 2019 06:34:04: 25000000 INFO @ Fri, 15 Feb 2019 06:34:05: 25000000 INFO @ Fri, 15 Feb 2019 06:34:08: 25000000 INFO @ Fri, 15 Feb 2019 06:34:11: 26000000 INFO @ Fri, 15 Feb 2019 06:34:11: 26000000 INFO @ Fri, 15 Feb 2019 06:34:13: #1 tag size is determined as 43 bps INFO @ Fri, 15 Feb 2019 06:34:13: #1 tag size = 43 INFO @ Fri, 15 Feb 2019 06:34:13: #1 total tags in treatment: 26321190 INFO @ Fri, 15 Feb 2019 06:34:13: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:34:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 06:34:14: #1 tag size is determined as 43 bps INFO @ Fri, 15 Feb 2019 06:34:14: #1 tag size = 43 INFO @ Fri, 15 Feb 2019 06:34:14: #1 total tags in treatment: 26321190 INFO @ Fri, 15 Feb 2019 06:34:14: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:34:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 06:34:14: #1 tags after filtering in treatment: 26321076 INFO @ Fri, 15 Feb 2019 06:34:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:34:14: #1 finished! INFO @ Fri, 15 Feb 2019 06:34:14: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:34:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:34:14: 26000000 INFO @ Fri, 15 Feb 2019 06:34:14: #1 tags after filtering in treatment: 26321076 INFO @ Fri, 15 Feb 2019 06:34:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:34:14: #1 finished! INFO @ Fri, 15 Feb 2019 06:34:14: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:34:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:34:16: #1 tag size is determined as 43 bps INFO @ Fri, 15 Feb 2019 06:34:16: #1 tag size = 43 INFO @ Fri, 15 Feb 2019 06:34:16: #1 total tags in treatment: 26321190 INFO @ Fri, 15 Feb 2019 06:34:16: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:34:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 06:34:16: #2 number of paired peaks: 4782 INFO @ Fri, 15 Feb 2019 06:34:16: start model_add_line... INFO @ Fri, 15 Feb 2019 06:34:17: start X-correlation... INFO @ Fri, 15 Feb 2019 06:34:17: end of X-cor INFO @ Fri, 15 Feb 2019 06:34:17: #2 finished! INFO @ Fri, 15 Feb 2019 06:34:17: #2 predicted fragment length is 42 bps INFO @ Fri, 15 Feb 2019 06:34:17: #2 alternative fragment length(s) may be 42,219,403,592 bps INFO @ Fri, 15 Feb 2019 06:34:17: #2.2 Generate R script for model : SRX3782455.10_model.r WARNING @ Fri, 15 Feb 2019 06:34:17: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 06:34:17: #2 You may need to consider one of the other alternative d(s): 42,219,403,592 WARNING @ Fri, 15 Feb 2019 06:34:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 06:34:17: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:34:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:34:17: #2 number of paired peaks: 4782 INFO @ Fri, 15 Feb 2019 06:34:17: start model_add_line... INFO @ Fri, 15 Feb 2019 06:34:17: #1 tags after filtering in treatment: 26321076 INFO @ Fri, 15 Feb 2019 06:34:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:34:17: #1 finished! INFO @ Fri, 15 Feb 2019 06:34:17: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:34:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:34:17: start X-correlation... INFO @ Fri, 15 Feb 2019 06:34:17: end of X-cor INFO @ Fri, 15 Feb 2019 06:34:17: #2 finished! INFO @ Fri, 15 Feb 2019 06:34:17: #2 predicted fragment length is 42 bps INFO @ Fri, 15 Feb 2019 06:34:17: #2 alternative fragment length(s) may be 42,219,403,592 bps INFO @ Fri, 15 Feb 2019 06:34:17: #2.2 Generate R script for model : SRX3782455.05_model.r WARNING @ Fri, 15 Feb 2019 06:34:17: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 06:34:17: #2 You may need to consider one of the other alternative d(s): 42,219,403,592 WARNING @ Fri, 15 Feb 2019 06:34:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 06:34:17: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:34:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:34:20: #2 number of paired peaks: 4782 INFO @ Fri, 15 Feb 2019 06:34:20: start model_add_line... INFO @ Fri, 15 Feb 2019 06:34:20: start X-correlation... INFO @ Fri, 15 Feb 2019 06:34:20: end of X-cor INFO @ Fri, 15 Feb 2019 06:34:20: #2 finished! INFO @ Fri, 15 Feb 2019 06:34:20: #2 predicted fragment length is 42 bps INFO @ Fri, 15 Feb 2019 06:34:20: #2 alternative fragment length(s) may be 42,219,403,592 bps INFO @ Fri, 15 Feb 2019 06:34:20: #2.2 Generate R script for model : SRX3782455.20_model.r WARNING @ Fri, 15 Feb 2019 06:34:20: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 06:34:20: #2 You may need to consider one of the other alternative d(s): 42,219,403,592 WARNING @ Fri, 15 Feb 2019 06:34:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 06:34:20: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:34:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:35:16: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:35:21: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:35:26: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:35:52: #4 Write output xls file... SRX3782455.05_peaks.xls INFO @ Fri, 15 Feb 2019 06:35:52: #4 Write peak in narrowPeak format file... SRX3782455.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:35:52: #4 Write summits bed file... SRX3782455.05_summits.bed INFO @ Fri, 15 Feb 2019 06:35:52: Done! pass1 - making usageList (48 chroms): 5 millis pass2 - checking and writing primary data (1839 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 06:35:58: #4 Write output xls file... SRX3782455.10_peaks.xls INFO @ Fri, 15 Feb 2019 06:35:59: #4 Write peak in narrowPeak format file... SRX3782455.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:35:59: #4 Write summits bed file... SRX3782455.10_summits.bed INFO @ Fri, 15 Feb 2019 06:35:59: Done! pass1 - making usageList (39 chroms): 5 millis pass2 - checking and writing primary data (1081 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 06:36:01: #4 Write output xls file... SRX3782455.20_peaks.xls INFO @ Fri, 15 Feb 2019 06:36:01: #4 Write peak in narrowPeak format file... SRX3782455.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:36:02: #4 Write summits bed file... SRX3782455.20_summits.bed INFO @ Fri, 15 Feb 2019 06:36:02: Done! pass1 - making usageList (31 chroms): 4 millis pass2 - checking and writing primary data (491 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。