Job ID = 11632728 sra ファイルのダウンロード中... Completed: 650552K bytes transferred in 9 seconds (567833K 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 34756625 spots for /home/okishinya/chipatlas/results/rn6/SRX4497198/SRR7633468.sra Written 34756625 spots for /home/okishinya/chipatlas/results/rn6/SRX4497198/SRR7633468.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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:27:09 34756625 reads; of these: 34756625 (100.00%) were unpaired; of these: 1471990 (4.24%) aligned 0 times 23641455 (68.02%) aligned exactly 1 time 9643180 (27.74%) aligned >1 times 95.76% overall alignment rate Time searching: 00:27:14 Overall time: 00:27:14 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] 3624572 / 33284635 = 0.1089 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 07:37:23: # Command line: callpeak -t SRX4497198.bam -f BAM -g 2.15e9 -n SRX4497198.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4497198.10 # format = BAM # ChIP-seq file = ['SRX4497198.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 07:37:23: # Command line: callpeak -t SRX4497198.bam -f BAM -g 2.15e9 -n SRX4497198.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4497198.20 # format = BAM # ChIP-seq file = ['SRX4497198.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 07:37:23: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:37:23: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:37:23: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:37:23: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:37:23: # Command line: callpeak -t SRX4497198.bam -f BAM -g 2.15e9 -n SRX4497198.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4497198.05 # format = BAM # ChIP-seq file = ['SRX4497198.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 07:37:23: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:37:23: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:37:29: 1000000 INFO @ Fri, 15 Feb 2019 07:37:30: 1000000 INFO @ Fri, 15 Feb 2019 07:37:30: 1000000 INFO @ Fri, 15 Feb 2019 07:37:36: 2000000 INFO @ Fri, 15 Feb 2019 07:37:36: 2000000 INFO @ Fri, 15 Feb 2019 07:37:36: 2000000 INFO @ Fri, 15 Feb 2019 07:37:42: 3000000 INFO @ Fri, 15 Feb 2019 07:37:42: 3000000 INFO @ Fri, 15 Feb 2019 07:37:42: 3000000 INFO @ Fri, 15 Feb 2019 07:37:48: 4000000 INFO @ Fri, 15 Feb 2019 07:37:48: 4000000 INFO @ Fri, 15 Feb 2019 07:37:49: 4000000 INFO @ Fri, 15 Feb 2019 07:37:55: 5000000 INFO @ Fri, 15 Feb 2019 07:37:55: 5000000 INFO @ Fri, 15 Feb 2019 07:37:55: 5000000 INFO @ Fri, 15 Feb 2019 07:38:01: 6000000 INFO @ Fri, 15 Feb 2019 07:38:01: 6000000 INFO @ Fri, 15 Feb 2019 07:38:01: 6000000 INFO @ Fri, 15 Feb 2019 07:38:07: 7000000 INFO @ Fri, 15 Feb 2019 07:38:08: 7000000 INFO @ Fri, 15 Feb 2019 07:38:08: 7000000 INFO @ Fri, 15 Feb 2019 07:38:13: 8000000 INFO @ Fri, 15 Feb 2019 07:38:14: 8000000 INFO @ Fri, 15 Feb 2019 07:38:14: 8000000 INFO @ Fri, 15 Feb 2019 07:38:20: 9000000 INFO @ Fri, 15 Feb 2019 07:38:20: 9000000 INFO @ Fri, 15 Feb 2019 07:38:21: 9000000 INFO @ Fri, 15 Feb 2019 07:38:26: 10000000 INFO @ Fri, 15 Feb 2019 07:38:27: 10000000 INFO @ Fri, 15 Feb 2019 07:38:27: 10000000 INFO @ Fri, 15 Feb 2019 07:38:32: 11000000 INFO @ Fri, 15 Feb 2019 07:38:33: 11000000 INFO @ Fri, 15 Feb 2019 07:38:33: 11000000 INFO @ Fri, 15 Feb 2019 07:38:39: 12000000 INFO @ Fri, 15 Feb 2019 07:38:39: 12000000 INFO @ Fri, 15 Feb 2019 07:38:40: 12000000 INFO @ Fri, 15 Feb 2019 07:38:45: 13000000 INFO @ Fri, 15 Feb 2019 07:38:46: 13000000 INFO @ Fri, 15 Feb 2019 07:38:46: 13000000 INFO @ Fri, 15 Feb 2019 07:38:51: 14000000 INFO @ Fri, 15 Feb 2019 07:38:52: 14000000 INFO @ Fri, 15 Feb 2019 07:38:53: 14000000 INFO @ Fri, 15 Feb 2019 07:38:58: 15000000 INFO @ Fri, 15 Feb 2019 07:38:58: 15000000 INFO @ Fri, 15 Feb 2019 07:38:59: 15000000 INFO @ Fri, 15 Feb 2019 07:39:04: 16000000 INFO @ Fri, 15 Feb 2019 07:39:04: 16000000 INFO @ Fri, 15 Feb 2019 07:39:05: 16000000 INFO @ Fri, 15 Feb 2019 07:39:10: 17000000 INFO @ Fri, 15 Feb 2019 07:39:11: 17000000 INFO @ Fri, 15 Feb 2019 07:39:12: 17000000 INFO @ Fri, 15 Feb 2019 07:39:17: 18000000 INFO @ Fri, 15 Feb 2019 07:39:17: 18000000 INFO @ Fri, 15 Feb 2019 07:39:18: 18000000 INFO @ Fri, 15 Feb 2019 07:39:23: 19000000 INFO @ Fri, 15 Feb 2019 07:39:23: 19000000 INFO @ Fri, 15 Feb 2019 07:39:25: 19000000 INFO @ Fri, 15 Feb 2019 07:39:30: 20000000 INFO @ Fri, 15 Feb 2019 07:39:30: 20000000 INFO @ Fri, 15 Feb 2019 07:39:31: 20000000 INFO @ Fri, 15 Feb 2019 07:39:36: 21000000 INFO @ Fri, 15 Feb 2019 07:39:36: 21000000 INFO @ Fri, 15 Feb 2019 07:39:37: 21000000 INFO @ Fri, 15 Feb 2019 07:39:42: 22000000 INFO @ Fri, 15 Feb 2019 07:39:43: 22000000 INFO @ Fri, 15 Feb 2019 07:39:44: 22000000 INFO @ Fri, 15 Feb 2019 07:39:49: 23000000 INFO @ Fri, 15 Feb 2019 07:39:49: 23000000 INFO @ Fri, 15 Feb 2019 07:39:50: 23000000 INFO @ Fri, 15 Feb 2019 07:39:55: 24000000 INFO @ Fri, 15 Feb 2019 07:39:55: 24000000 INFO @ Fri, 15 Feb 2019 07:39:57: 24000000 INFO @ Fri, 15 Feb 2019 07:40:01: 25000000 INFO @ Fri, 15 Feb 2019 07:40:02: 25000000 INFO @ Fri, 15 Feb 2019 07:40:03: 25000000 INFO @ Fri, 15 Feb 2019 07:40:07: 26000000 INFO @ Fri, 15 Feb 2019 07:40:08: 26000000 INFO @ Fri, 15 Feb 2019 07:40:09: 26000000 INFO @ Fri, 15 Feb 2019 07:40:14: 27000000 INFO @ Fri, 15 Feb 2019 07:40:14: 27000000 INFO @ Fri, 15 Feb 2019 07:40:16: 27000000 INFO @ Fri, 15 Feb 2019 07:40:20: 28000000 INFO @ Fri, 15 Feb 2019 07:40:20: 28000000 INFO @ Fri, 15 Feb 2019 07:40:22: 28000000 INFO @ Fri, 15 Feb 2019 07:40:26: 29000000 INFO @ Fri, 15 Feb 2019 07:40:27: 29000000 INFO @ Fri, 15 Feb 2019 07:40:29: 29000000 INFO @ Fri, 15 Feb 2019 07:40:31: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:40:31: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:40:31: #1 total tags in treatment: 29660063 INFO @ Fri, 15 Feb 2019 07:40:31: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:40:31: #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 07:40:31: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:40:31: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:40:31: #1 total tags in treatment: 29660063 INFO @ Fri, 15 Feb 2019 07:40:31: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:40:31: #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 07:40:32: #1 tags after filtering in treatment: 29659962 INFO @ Fri, 15 Feb 2019 07:40:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:40:32: #1 finished! INFO @ Fri, 15 Feb 2019 07:40:32: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:40:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:40:32: #1 tags after filtering in treatment: 29659962 INFO @ Fri, 15 Feb 2019 07:40:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:40:32: #1 finished! INFO @ Fri, 15 Feb 2019 07:40:32: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:40:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:40:34: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:40:34: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:40:34: #1 total tags in treatment: 29660063 INFO @ Fri, 15 Feb 2019 07:40:34: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:40:34: #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 07:40:34: #1 tags after filtering in treatment: 29659962 INFO @ Fri, 15 Feb 2019 07:40:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:40:34: #1 finished! INFO @ Fri, 15 Feb 2019 07:40:34: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:40:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:40:35: #2 number of paired peaks: 9949 INFO @ Fri, 15 Feb 2019 07:40:35: start model_add_line... INFO @ Fri, 15 Feb 2019 07:40:35: #2 number of paired peaks: 9949 INFO @ Fri, 15 Feb 2019 07:40:35: start model_add_line... INFO @ Fri, 15 Feb 2019 07:40:35: start X-correlation... INFO @ Fri, 15 Feb 2019 07:40:35: end of X-cor INFO @ Fri, 15 Feb 2019 07:40:35: #2 finished! INFO @ Fri, 15 Feb 2019 07:40:35: #2 predicted fragment length is 51 bps INFO @ Fri, 15 Feb 2019 07:40:35: #2 alternative fragment length(s) may be 51,141 bps INFO @ Fri, 15 Feb 2019 07:40:35: #2.2 Generate R script for model : SRX4497198.10_model.r WARNING @ Fri, 15 Feb 2019 07:40:35: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 07:40:35: #2 You may need to consider one of the other alternative d(s): 51,141 WARNING @ Fri, 15 Feb 2019 07:40:35: #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 07:40:35: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:40:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:40:36: start X-correlation... INFO @ Fri, 15 Feb 2019 07:40:36: end of X-cor INFO @ Fri, 15 Feb 2019 07:40:36: #2 finished! INFO @ Fri, 15 Feb 2019 07:40:36: #2 predicted fragment length is 51 bps INFO @ Fri, 15 Feb 2019 07:40:36: #2 alternative fragment length(s) may be 51,141 bps INFO @ Fri, 15 Feb 2019 07:40:36: #2.2 Generate R script for model : SRX4497198.05_model.r WARNING @ Fri, 15 Feb 2019 07:40:36: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 07:40:36: #2 You may need to consider one of the other alternative d(s): 51,141 WARNING @ Fri, 15 Feb 2019 07:40:36: #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 07:40:36: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:40:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:40:38: #2 number of paired peaks: 9949 INFO @ Fri, 15 Feb 2019 07:40:38: start model_add_line... INFO @ Fri, 15 Feb 2019 07:40:38: start X-correlation... INFO @ Fri, 15 Feb 2019 07:40:38: end of X-cor INFO @ Fri, 15 Feb 2019 07:40:38: #2 finished! INFO @ Fri, 15 Feb 2019 07:40:38: #2 predicted fragment length is 51 bps INFO @ Fri, 15 Feb 2019 07:40:38: #2 alternative fragment length(s) may be 51,141 bps INFO @ Fri, 15 Feb 2019 07:40:38: #2.2 Generate R script for model : SRX4497198.20_model.r WARNING @ Fri, 15 Feb 2019 07:40:38: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 07:40:38: #2 You may need to consider one of the other alternative d(s): 51,141 WARNING @ Fri, 15 Feb 2019 07:40:38: #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 07:40:38: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:40:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:41:49: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:41:49: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:41:49: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:42:27: #4 Write output xls file... SRX4497198.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:42:27: #4 Write peak in narrowPeak format file... SRX4497198.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:42:27: #4 Write summits bed file... SRX4497198.10_summits.bed INFO @ Fri, 15 Feb 2019 07:42:27: Done! pass1 - making usageList (47 chroms): 2 millis pass2 - checking and writing primary data (975 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:42:28: #4 Write output xls file... SRX4497198.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:42:28: #4 Write peak in narrowPeak format file... SRX4497198.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:42:28: #4 Write summits bed file... SRX4497198.20_summits.bed INFO @ Fri, 15 Feb 2019 07:42:28: Done! pass1 - making usageList (36 chroms): 2 millis pass2 - checking and writing primary data (411 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:42:28: #4 Write output xls file... SRX4497198.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:42:28: #4 Write peak in narrowPeak format file... SRX4497198.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:42:28: #4 Write summits bed file... SRX4497198.05_summits.bed INFO @ Fri, 15 Feb 2019 07:42:28: Done! pass1 - making usageList (65 chroms): 3 millis pass2 - checking and writing primary data (1809 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。