Job ID = 10194752 sra ファイルのダウンロード中... Completed: 470317K bytes transferred in 7 seconds (532568K 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 34430728 spots for /home/okishinya/chipatlas/results/rn6/SRX1091090/SRR2095967.sra Written 34430728 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: 00:25:23 34430728 reads; of these: 34430728 (100.00%) were unpaired; of these: 2328886 (6.76%) aligned 0 times 23222423 (67.45%) aligned exactly 1 time 8879419 (25.79%) aligned >1 times 93.24% overall alignment rate Time searching: 00:25:25 Overall time: 00:25:25 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] 1323073 / 32101842 = 0.0412 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 00:52:14: # Command line: callpeak -t SRX1091090.bam -f BAM -g 2.15e9 -n SRX1091090.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1091090.05 # format = BAM # ChIP-seq file = ['SRX1091090.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 00:52:14: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:52:14: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:52:14: # Command line: callpeak -t SRX1091090.bam -f BAM -g 2.15e9 -n SRX1091090.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1091090.20 # format = BAM # ChIP-seq file = ['SRX1091090.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 00:52:14: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:52:14: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:52:14: # Command line: callpeak -t SRX1091090.bam -f BAM -g 2.15e9 -n SRX1091090.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1091090.10 # format = BAM # ChIP-seq file = ['SRX1091090.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 00:52:14: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:52:14: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:52:21: 1000000 INFO @ Sat, 11 Nov 2017 00:52:21: 1000000 INFO @ Sat, 11 Nov 2017 00:52:21: 1000000 INFO @ Sat, 11 Nov 2017 00:52:28: 2000000 INFO @ Sat, 11 Nov 2017 00:52:28: 2000000 INFO @ Sat, 11 Nov 2017 00:52:28: 2000000 INFO @ Sat, 11 Nov 2017 00:52:35: 3000000 INFO @ Sat, 11 Nov 2017 00:52:36: 3000000 INFO @ Sat, 11 Nov 2017 00:52:36: 3000000 INFO @ Sat, 11 Nov 2017 00:52:42: 4000000 INFO @ Sat, 11 Nov 2017 00:52:43: 4000000 INFO @ Sat, 11 Nov 2017 00:52:43: 4000000 INFO @ Sat, 11 Nov 2017 00:52:49: 5000000 INFO @ Sat, 11 Nov 2017 00:52:50: 5000000 INFO @ Sat, 11 Nov 2017 00:52:50: 5000000 INFO @ Sat, 11 Nov 2017 00:52:56: 6000000 INFO @ Sat, 11 Nov 2017 00:52:57: 6000000 INFO @ Sat, 11 Nov 2017 00:52:57: 6000000 INFO @ Sat, 11 Nov 2017 00:53:04: 7000000 INFO @ Sat, 11 Nov 2017 00:53:04: 7000000 INFO @ Sat, 11 Nov 2017 00:53:05: 7000000 INFO @ Sat, 11 Nov 2017 00:53:11: 8000000 INFO @ Sat, 11 Nov 2017 00:53:12: 8000000 INFO @ Sat, 11 Nov 2017 00:53:12: 8000000 INFO @ Sat, 11 Nov 2017 00:53:18: 9000000 INFO @ Sat, 11 Nov 2017 00:53:19: 9000000 INFO @ Sat, 11 Nov 2017 00:53:20: 9000000 INFO @ Sat, 11 Nov 2017 00:53:25: 10000000 INFO @ Sat, 11 Nov 2017 00:53:26: 10000000 INFO @ Sat, 11 Nov 2017 00:53:27: 10000000 INFO @ Sat, 11 Nov 2017 00:53:32: 11000000 INFO @ Sat, 11 Nov 2017 00:53:34: 11000000 INFO @ Sat, 11 Nov 2017 00:53:34: 11000000 INFO @ Sat, 11 Nov 2017 00:53:39: 12000000 INFO @ Sat, 11 Nov 2017 00:53:41: 12000000 INFO @ Sat, 11 Nov 2017 00:53:42: 12000000 INFO @ Sat, 11 Nov 2017 00:53:46: 13000000 INFO @ Sat, 11 Nov 2017 00:53:49: 13000000 INFO @ Sat, 11 Nov 2017 00:53:49: 13000000 INFO @ Sat, 11 Nov 2017 00:53:53: 14000000 INFO @ Sat, 11 Nov 2017 00:53:56: 14000000 INFO @ Sat, 11 Nov 2017 00:53:57: 14000000 INFO @ Sat, 11 Nov 2017 00:54:00: 15000000 INFO @ Sat, 11 Nov 2017 00:54:03: 15000000 INFO @ Sat, 11 Nov 2017 00:54:04: 15000000 INFO @ Sat, 11 Nov 2017 00:54:07: 16000000 INFO @ Sat, 11 Nov 2017 00:54:11: 16000000 INFO @ Sat, 11 Nov 2017 00:54:12: 16000000 INFO @ Sat, 11 Nov 2017 00:54:14: 17000000 INFO @ Sat, 11 Nov 2017 00:54:18: 17000000 INFO @ Sat, 11 Nov 2017 00:54:19: 17000000 INFO @ Sat, 11 Nov 2017 00:54:21: 18000000 INFO @ Sat, 11 Nov 2017 00:54:25: 18000000 INFO @ Sat, 11 Nov 2017 00:54:27: 18000000 INFO @ Sat, 11 Nov 2017 00:54:29: 19000000 INFO @ Sat, 11 Nov 2017 00:54:33: 19000000 INFO @ Sat, 11 Nov 2017 00:54:34: 19000000 INFO @ Sat, 11 Nov 2017 00:54:36: 20000000 INFO @ Sat, 11 Nov 2017 00:54:40: 20000000 INFO @ Sat, 11 Nov 2017 00:54:42: 20000000 INFO @ Sat, 11 Nov 2017 00:54:43: 21000000 INFO @ Sat, 11 Nov 2017 00:54:48: 21000000 INFO @ Sat, 11 Nov 2017 00:54:49: 21000000 INFO @ Sat, 11 Nov 2017 00:54:50: 22000000 INFO @ Sat, 11 Nov 2017 00:54:55: 22000000 INFO @ Sat, 11 Nov 2017 00:54:57: 23000000 INFO @ Sat, 11 Nov 2017 00:54:57: 22000000 INFO @ Sat, 11 Nov 2017 00:55:03: 23000000 INFO @ Sat, 11 Nov 2017 00:55:04: 24000000 INFO @ Sat, 11 Nov 2017 00:55:05: 23000000 INFO @ Sat, 11 Nov 2017 00:55:10: 24000000 INFO @ Sat, 11 Nov 2017 00:55:11: 25000000 INFO @ Sat, 11 Nov 2017 00:55:12: 24000000 INFO @ Sat, 11 Nov 2017 00:55:18: 25000000 INFO @ Sat, 11 Nov 2017 00:55:18: 26000000 INFO @ Sat, 11 Nov 2017 00:55:20: 25000000 INFO @ Sat, 11 Nov 2017 00:55:25: 26000000 INFO @ Sat, 11 Nov 2017 00:55:25: 27000000 INFO @ Sat, 11 Nov 2017 00:55:27: 26000000 INFO @ Sat, 11 Nov 2017 00:55:32: 28000000 INFO @ Sat, 11 Nov 2017 00:55:32: 27000000 INFO @ Sat, 11 Nov 2017 00:55:35: 27000000 INFO @ Sat, 11 Nov 2017 00:55:39: 29000000 INFO @ Sat, 11 Nov 2017 00:55:40: 28000000 INFO @ Sat, 11 Nov 2017 00:55:42: 28000000 INFO @ Sat, 11 Nov 2017 00:55:47: 30000000 INFO @ Sat, 11 Nov 2017 00:55:47: 29000000 INFO @ Sat, 11 Nov 2017 00:55:50: 29000000 INFO @ Sat, 11 Nov 2017 00:55:52: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 00:55:52: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 00:55:52: #1 total tags in treatment: 30778769 INFO @ Sat, 11 Nov 2017 00:55:52: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:55:52: #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 00:55:53: #1 tags after filtering in treatment: 30778684 INFO @ Sat, 11 Nov 2017 00:55:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:55:53: #1 finished! INFO @ Sat, 11 Nov 2017 00:55:53: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:55:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:55:55: 30000000 INFO @ Sat, 11 Nov 2017 00:55:56: #2 number of paired peaks: 5784 INFO @ Sat, 11 Nov 2017 00:55:56: start model_add_line... INFO @ Sat, 11 Nov 2017 00:55:56: start X-correlation... INFO @ Sat, 11 Nov 2017 00:55:56: end of X-cor INFO @ Sat, 11 Nov 2017 00:55:56: #2 finished! INFO @ Sat, 11 Nov 2017 00:55:56: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Nov 2017 00:55:56: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Nov 2017 00:55:56: #2.2 Generate R script for model : SRX1091090.20_model.r WARNING @ Sat, 11 Nov 2017 00:55:56: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:55:56: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Nov 2017 00:55:56: #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 00:55:56: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:55:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:55:57: 30000000 INFO @ Sat, 11 Nov 2017 00:56:01: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 00:56:01: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 00:56:01: #1 total tags in treatment: 30778769 INFO @ Sat, 11 Nov 2017 00:56:01: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:56:01: #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 00:56:02: #1 tags after filtering in treatment: 30778684 INFO @ Sat, 11 Nov 2017 00:56:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:56:02: #1 finished! INFO @ Sat, 11 Nov 2017 00:56:02: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:56:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:56:03: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 00:56:03: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 00:56:03: #1 total tags in treatment: 30778769 INFO @ Sat, 11 Nov 2017 00:56:03: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:56:03: #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 00:56:04: #1 tags after filtering in treatment: 30778684 INFO @ Sat, 11 Nov 2017 00:56:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:56:04: #1 finished! INFO @ Sat, 11 Nov 2017 00:56:04: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:56:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:56:04: #2 number of paired peaks: 5784 INFO @ Sat, 11 Nov 2017 00:56:04: start model_add_line... INFO @ Sat, 11 Nov 2017 00:56:05: start X-correlation... INFO @ Sat, 11 Nov 2017 00:56:05: end of X-cor INFO @ Sat, 11 Nov 2017 00:56:05: #2 finished! INFO @ Sat, 11 Nov 2017 00:56:05: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Nov 2017 00:56:05: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Nov 2017 00:56:05: #2.2 Generate R script for model : SRX1091090.10_model.r WARNING @ Sat, 11 Nov 2017 00:56:05: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:56:05: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Nov 2017 00:56:05: #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 00:56:05: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:56:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:56:07: #2 number of paired peaks: 5784 INFO @ Sat, 11 Nov 2017 00:56:07: start model_add_line... INFO @ Sat, 11 Nov 2017 00:56:07: start X-correlation... INFO @ Sat, 11 Nov 2017 00:56:07: end of X-cor INFO @ Sat, 11 Nov 2017 00:56:07: #2 finished! INFO @ Sat, 11 Nov 2017 00:56:07: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Nov 2017 00:56:07: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Nov 2017 00:56:07: #2.2 Generate R script for model : SRX1091090.05_model.r WARNING @ Sat, 11 Nov 2017 00:56:07: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:56:07: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Nov 2017 00:56:07: #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 00:56:07: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:56:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:57:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:57:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:57:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:57:48: #4 Write output xls file... SRX1091090.20_peaks.xls INFO @ Sat, 11 Nov 2017 00:57:48: #4 Write peak in narrowPeak format file... SRX1091090.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:57:48: #4 Write summits bed file... SRX1091090.20_summits.bed INFO @ Sat, 11 Nov 2017 00:57:48: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (556 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:58:02: #4 Write output xls file... SRX1091090.10_peaks.xls INFO @ Sat, 11 Nov 2017 00:58:02: #4 Write peak in narrowPeak format file... SRX1091090.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:58:02: #4 Write summits bed file... SRX1091090.10_summits.bed INFO @ Sat, 11 Nov 2017 00:58:02: Done! pass1 - making usageList (45 chroms): 1 millis pass2 - checking and writing primary data (1185 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:58:05: #4 Write output xls file... SRX1091090.05_peaks.xls INFO @ Sat, 11 Nov 2017 00:58:05: #4 Write peak in narrowPeak format file... SRX1091090.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:58:05: #4 Write summits bed file... SRX1091090.05_summits.bed INFO @ Sat, 11 Nov 2017 00:58:05: Done! pass1 - making usageList (54 chroms): 1 millis pass2 - checking and writing primary data (2186 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。