Job ID = 10487596 sra ファイルのダウンロード中... Completed: 4268065K bytes transferred in 87 seconds (400650K 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 63825163 spots for /home/okishinya/chipatlas/results/rn6/SRX2611118/SRR5311162.sra Written 63825163 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 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: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 03:37:08 63825163 reads; of these: 63825163 (100.00%) were unpaired; of these: 16737924 (26.22%) aligned 0 times 40799924 (63.92%) aligned exactly 1 time 6287315 (9.85%) aligned >1 times 73.78% overall alignment rate Time searching: 03:37:10 Overall time: 03:37:10 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 36 files... [bam_rmdupse_core] 13800596 / 47087239 = 0.2931 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 @ Sun, 18 Mar 2018 13:53:26: # Command line: callpeak -t SRX2611118.bam -f BAM -g 2.15e9 -n SRX2611118.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2611118.20 # format = BAM # ChIP-seq file = ['SRX2611118.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 @ Sun, 18 Mar 2018 13:53:26: # Command line: callpeak -t SRX2611118.bam -f BAM -g 2.15e9 -n SRX2611118.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2611118.05 # format = BAM # ChIP-seq file = ['SRX2611118.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 @ Sun, 18 Mar 2018 13:53:26: # Command line: callpeak -t SRX2611118.bam -f BAM -g 2.15e9 -n SRX2611118.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2611118.10 # format = BAM # ChIP-seq file = ['SRX2611118.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 @ Sun, 18 Mar 2018 13:53:26: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:53:26: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:53:26: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:53:26: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:53:26: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:53:26: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:53:37: 1000000 INFO @ Sun, 18 Mar 2018 13:53:38: 1000000 INFO @ Sun, 18 Mar 2018 13:53:38: 1000000 INFO @ Sun, 18 Mar 2018 13:53:48: 2000000 INFO @ Sun, 18 Mar 2018 13:53:50: 2000000 INFO @ Sun, 18 Mar 2018 13:53:50: 2000000 INFO @ Sun, 18 Mar 2018 13:53:59: 3000000 INFO @ Sun, 18 Mar 2018 13:54:01: 3000000 INFO @ Sun, 18 Mar 2018 13:54:02: 3000000 INFO @ Sun, 18 Mar 2018 13:54:11: 4000000 INFO @ Sun, 18 Mar 2018 13:54:13: 4000000 INFO @ Sun, 18 Mar 2018 13:54:14: 4000000 INFO @ Sun, 18 Mar 2018 13:54:22: 5000000 INFO @ Sun, 18 Mar 2018 13:54:25: 5000000 INFO @ Sun, 18 Mar 2018 13:54:26: 5000000 INFO @ Sun, 18 Mar 2018 13:54:33: 6000000 INFO @ Sun, 18 Mar 2018 13:54:37: 6000000 INFO @ Sun, 18 Mar 2018 13:54:38: 6000000 INFO @ Sun, 18 Mar 2018 13:54:44: 7000000 INFO @ Sun, 18 Mar 2018 13:54:49: 7000000 INFO @ Sun, 18 Mar 2018 13:54:50: 7000000 INFO @ Sun, 18 Mar 2018 13:54:54: 8000000 INFO @ Sun, 18 Mar 2018 13:55:01: 8000000 INFO @ Sun, 18 Mar 2018 13:55:02: 8000000 INFO @ Sun, 18 Mar 2018 13:55:06: 9000000 INFO @ Sun, 18 Mar 2018 13:55:14: 9000000 INFO @ Sun, 18 Mar 2018 13:55:15: 9000000 INFO @ Sun, 18 Mar 2018 13:55:17: 10000000 INFO @ Sun, 18 Mar 2018 13:55:26: 10000000 INFO @ Sun, 18 Mar 2018 13:55:27: 10000000 INFO @ Sun, 18 Mar 2018 13:55:28: 11000000 INFO @ Sun, 18 Mar 2018 13:55:38: 11000000 INFO @ Sun, 18 Mar 2018 13:55:39: 11000000 INFO @ Sun, 18 Mar 2018 13:55:39: 12000000 INFO @ Sun, 18 Mar 2018 13:55:50: 12000000 INFO @ Sun, 18 Mar 2018 13:55:50: 13000000 INFO @ Sun, 18 Mar 2018 13:55:50: 12000000 INFO @ Sun, 18 Mar 2018 13:56:02: 14000000 INFO @ Sun, 18 Mar 2018 13:56:02: 13000000 INFO @ Sun, 18 Mar 2018 13:56:03: 13000000 INFO @ Sun, 18 Mar 2018 13:56:14: 15000000 INFO @ Sun, 18 Mar 2018 13:56:14: 14000000 INFO @ Sun, 18 Mar 2018 13:56:15: 14000000 INFO @ Sun, 18 Mar 2018 13:56:25: 16000000 INFO @ Sun, 18 Mar 2018 13:56:26: 15000000 INFO @ Sun, 18 Mar 2018 13:56:26: 15000000 INFO @ Sun, 18 Mar 2018 13:56:36: 17000000 INFO @ Sun, 18 Mar 2018 13:56:38: 16000000 INFO @ Sun, 18 Mar 2018 13:56:38: 16000000 INFO @ Sun, 18 Mar 2018 13:56:47: 18000000 INFO @ Sun, 18 Mar 2018 13:56:49: 17000000 INFO @ Sun, 18 Mar 2018 13:56:50: 17000000 INFO @ Sun, 18 Mar 2018 13:56:58: 19000000 INFO @ Sun, 18 Mar 2018 13:57:01: 18000000 INFO @ Sun, 18 Mar 2018 13:57:01: 18000000 INFO @ Sun, 18 Mar 2018 13:57:09: 20000000 INFO @ Sun, 18 Mar 2018 13:57:13: 19000000 INFO @ Sun, 18 Mar 2018 13:57:13: 19000000 INFO @ Sun, 18 Mar 2018 13:57:20: 21000000 INFO @ Sun, 18 Mar 2018 13:57:24: 20000000 INFO @ Sun, 18 Mar 2018 13:57:24: 20000000 INFO @ Sun, 18 Mar 2018 13:57:31: 22000000 INFO @ Sun, 18 Mar 2018 13:57:36: 21000000 INFO @ Sun, 18 Mar 2018 13:57:36: 21000000 INFO @ Sun, 18 Mar 2018 13:57:42: 23000000 INFO @ Sun, 18 Mar 2018 13:57:48: 22000000 INFO @ Sun, 18 Mar 2018 13:57:48: 22000000 INFO @ Sun, 18 Mar 2018 13:57:56: 24000000 INFO @ Sun, 18 Mar 2018 13:58:01: 23000000 INFO @ Sun, 18 Mar 2018 13:58:01: 23000000 INFO @ Sun, 18 Mar 2018 13:58:10: 25000000 INFO @ Sun, 18 Mar 2018 13:58:14: 24000000 INFO @ Sun, 18 Mar 2018 13:58:14: 24000000 INFO @ Sun, 18 Mar 2018 13:58:23: 26000000 INFO @ Sun, 18 Mar 2018 13:58:27: 25000000 INFO @ Sun, 18 Mar 2018 13:58:27: 25000000 INFO @ Sun, 18 Mar 2018 13:58:37: 27000000 INFO @ Sun, 18 Mar 2018 13:58:40: 26000000 INFO @ Sun, 18 Mar 2018 13:58:40: 26000000 INFO @ Sun, 18 Mar 2018 13:58:50: 28000000 INFO @ Sun, 18 Mar 2018 13:58:53: 27000000 INFO @ Sun, 18 Mar 2018 13:58:53: 27000000 INFO @ Sun, 18 Mar 2018 13:59:03: 29000000 INFO @ Sun, 18 Mar 2018 13:59:06: 28000000 INFO @ Sun, 18 Mar 2018 13:59:06: 28000000 INFO @ Sun, 18 Mar 2018 13:59:16: 30000000 INFO @ Sun, 18 Mar 2018 13:59:18: 29000000 INFO @ Sun, 18 Mar 2018 13:59:18: 29000000 INFO @ Sun, 18 Mar 2018 13:59:30: 31000000 INFO @ Sun, 18 Mar 2018 13:59:31: 30000000 INFO @ Sun, 18 Mar 2018 13:59:31: 30000000 INFO @ Sun, 18 Mar 2018 13:59:43: 32000000 INFO @ Sun, 18 Mar 2018 13:59:44: 31000000 INFO @ Sun, 18 Mar 2018 13:59:44: 31000000 INFO @ Sun, 18 Mar 2018 13:59:57: 32000000 INFO @ Sun, 18 Mar 2018 13:59:57: 32000000 INFO @ Sun, 18 Mar 2018 13:59:57: 33000000 INFO @ Sun, 18 Mar 2018 14:00:01: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 14:00:01: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 14:00:01: #1 total tags in treatment: 33286643 INFO @ Sun, 18 Mar 2018 14:00:01: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 14:00:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 14:00:02: #1 tags after filtering in treatment: 33286534 INFO @ Sun, 18 Mar 2018 14:00:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 14:00:02: #1 finished! INFO @ Sun, 18 Mar 2018 14:00:02: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 14:00:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 14:00:06: #2 number of paired peaks: 15421 INFO @ Sun, 18 Mar 2018 14:00:06: start model_add_line... INFO @ Sun, 18 Mar 2018 14:00:06: start X-correlation... INFO @ Sun, 18 Mar 2018 14:00:06: end of X-cor INFO @ Sun, 18 Mar 2018 14:00:06: #2 finished! INFO @ Sun, 18 Mar 2018 14:00:06: #2 predicted fragment length is 161 bps INFO @ Sun, 18 Mar 2018 14:00:06: #2 alternative fragment length(s) may be 161 bps INFO @ Sun, 18 Mar 2018 14:00:06: #2.2 Generate R script for model : SRX2611118.10_model.r WARNING @ Sun, 18 Mar 2018 14:00:06: #2 Since the d (161) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 14:00:06: #2 You may need to consider one of the other alternative d(s): 161 WARNING @ Sun, 18 Mar 2018 14:00:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 14:00:06: #3 Call peaks... INFO @ Sun, 18 Mar 2018 14:00:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 14:00:09: 33000000 INFO @ Sun, 18 Mar 2018 14:00:09: 33000000 INFO @ Sun, 18 Mar 2018 14:00:12: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 14:00:12: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 14:00:12: #1 total tags in treatment: 33286643 INFO @ Sun, 18 Mar 2018 14:00:12: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 14:00:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 14:00:13: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 14:00:13: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 14:00:13: #1 total tags in treatment: 33286643 INFO @ Sun, 18 Mar 2018 14:00:13: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 14:00:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 14:00:13: #1 tags after filtering in treatment: 33286534 INFO @ Sun, 18 Mar 2018 14:00:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 14:00:13: #1 finished! INFO @ Sun, 18 Mar 2018 14:00:13: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 14:00:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 14:00:14: #1 tags after filtering in treatment: 33286534 INFO @ Sun, 18 Mar 2018 14:00:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 14:00:14: #1 finished! INFO @ Sun, 18 Mar 2018 14:00:14: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 14:00:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 14:00:17: #2 number of paired peaks: 15421 INFO @ Sun, 18 Mar 2018 14:00:17: start model_add_line... INFO @ Sun, 18 Mar 2018 14:00:17: #2 number of paired peaks: 15421 INFO @ Sun, 18 Mar 2018 14:00:17: start model_add_line... INFO @ Sun, 18 Mar 2018 14:00:17: start X-correlation... INFO @ Sun, 18 Mar 2018 14:00:17: end of X-cor INFO @ Sun, 18 Mar 2018 14:00:17: #2 finished! INFO @ Sun, 18 Mar 2018 14:00:17: #2 predicted fragment length is 161 bps INFO @ Sun, 18 Mar 2018 14:00:17: #2 alternative fragment length(s) may be 161 bps INFO @ Sun, 18 Mar 2018 14:00:17: #2.2 Generate R script for model : SRX2611118.05_model.r WARNING @ Sun, 18 Mar 2018 14:00:17: #2 Since the d (161) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 14:00:17: #2 You may need to consider one of the other alternative d(s): 161 WARNING @ Sun, 18 Mar 2018 14:00:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 14:00:17: #3 Call peaks... INFO @ Sun, 18 Mar 2018 14:00:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 14:00:18: start X-correlation... INFO @ Sun, 18 Mar 2018 14:00:18: end of X-cor INFO @ Sun, 18 Mar 2018 14:00:18: #2 finished! INFO @ Sun, 18 Mar 2018 14:00:18: #2 predicted fragment length is 161 bps INFO @ Sun, 18 Mar 2018 14:00:18: #2 alternative fragment length(s) may be 161 bps INFO @ Sun, 18 Mar 2018 14:00:18: #2.2 Generate R script for model : SRX2611118.20_model.r WARNING @ Sun, 18 Mar 2018 14:00:18: #2 Since the d (161) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 14:00:18: #2 You may need to consider one of the other alternative d(s): 161 WARNING @ Sun, 18 Mar 2018 14:00:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 14:00:18: #3 Call peaks... INFO @ Sun, 18 Mar 2018 14:00:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 14:01:35: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 14:01:40: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 14:01:42: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 14:02:28: #4 Write output xls file... SRX2611118.10_peaks.xls INFO @ Sun, 18 Mar 2018 14:02:28: #4 Write peak in narrowPeak format file... SRX2611118.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 14:02:28: #4 Write summits bed file... SRX2611118.10_summits.bed INFO @ Sun, 18 Mar 2018 14:02:28: Done! pass1 - making usageList (41 chroms): 1 millis pass2 - checking and writing primary data (1384 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 14:02:29: #4 Write output xls file... SRX2611118.05_peaks.xls INFO @ Sun, 18 Mar 2018 14:02:29: #4 Write peak in narrowPeak format file... SRX2611118.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 14:02:29: #4 Write summits bed file... SRX2611118.05_summits.bed INFO @ Sun, 18 Mar 2018 14:02:29: Done! pass1 - making usageList (66 chroms): 2 millis pass2 - checking and writing primary data (5775 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 14:02:31: #4 Write output xls file... SRX2611118.20_peaks.xls INFO @ Sun, 18 Mar 2018 14:02:31: #4 Write peak in narrowPeak format file... SRX2611118.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 14:02:31: #4 Write summits bed file... SRX2611118.20_summits.bed INFO @ Sun, 18 Mar 2018 14:02:32: Done! pass1 - making usageList (32 chroms): 0 millis pass2 - checking and writing primary data (475 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。