Job ID = 10194816 sra ファイルのダウンロード中... Completed: 2416731K bytes transferred in 50 seconds (389565K 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 35664491 spots for /home/okishinya/chipatlas/results/rn6/SRX1926706/SRR3829897.sra Written 35664491 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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 02:20:22 35664491 reads; of these: 35664491 (100.00%) were unpaired; of these: 1241245 (3.48%) aligned 0 times 26193032 (73.44%) aligned exactly 1 time 8230214 (23.08%) aligned >1 times 96.52% overall alignment rate Time searching: 02:20:27 Overall time: 02:20:27 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] 13874543 / 34423246 = 0.4031 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 00:39:16: # Command line: callpeak -t SRX1926706.bam -f BAM -g 2.15e9 -n SRX1926706.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1926706.05 # format = BAM # ChIP-seq file = ['SRX1926706.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 00:39:16: # Command line: callpeak -t SRX1926706.bam -f BAM -g 2.15e9 -n SRX1926706.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1926706.20 # format = BAM # ChIP-seq file = ['SRX1926706.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 00:39:16: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:39:16: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:39:16: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:39:16: # Command line: callpeak -t SRX1926706.bam -f BAM -g 2.15e9 -n SRX1926706.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1926706.10 # format = BAM # ChIP-seq file = ['SRX1926706.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 00:39:16: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:39:16: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:39:16: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:39:27: 1000000 INFO @ Sat, 11 Nov 2017 00:39:34: 1000000 INFO @ Sat, 11 Nov 2017 00:39:36: 1000000 INFO @ Sat, 11 Nov 2017 00:39:37: 2000000 INFO @ Sat, 11 Nov 2017 00:39:46: 3000000 INFO @ Sat, 11 Nov 2017 00:39:52: 2000000 INFO @ Sat, 11 Nov 2017 00:39:55: 2000000 INFO @ Sat, 11 Nov 2017 00:39:56: 4000000 INFO @ Sat, 11 Nov 2017 00:40:06: 5000000 INFO @ Sat, 11 Nov 2017 00:40:08: 3000000 INFO @ Sat, 11 Nov 2017 00:40:14: 3000000 INFO @ Sat, 11 Nov 2017 00:40:16: 6000000 INFO @ Sat, 11 Nov 2017 00:40:25: 4000000 INFO @ Sat, 11 Nov 2017 00:40:26: 7000000 INFO @ Sat, 11 Nov 2017 00:40:34: 4000000 INFO @ Sat, 11 Nov 2017 00:40:36: 8000000 INFO @ Sat, 11 Nov 2017 00:40:41: 5000000 INFO @ Sat, 11 Nov 2017 00:40:46: 9000000 INFO @ Sat, 11 Nov 2017 00:40:53: 5000000 INFO @ Sat, 11 Nov 2017 00:40:56: 10000000 INFO @ Sat, 11 Nov 2017 00:40:57: 6000000 INFO @ Sat, 11 Nov 2017 00:41:05: 11000000 INFO @ Sat, 11 Nov 2017 00:41:12: 6000000 INFO @ Sat, 11 Nov 2017 00:41:15: 7000000 INFO @ Sat, 11 Nov 2017 00:41:15: 12000000 INFO @ Sat, 11 Nov 2017 00:41:25: 13000000 INFO @ Sat, 11 Nov 2017 00:41:29: 7000000 INFO @ Sat, 11 Nov 2017 00:41:31: 8000000 INFO @ Sat, 11 Nov 2017 00:41:35: 14000000 INFO @ Sat, 11 Nov 2017 00:41:43: 8000000 INFO @ Sat, 11 Nov 2017 00:41:45: 15000000 INFO @ Sat, 11 Nov 2017 00:41:47: 9000000 INFO @ Sat, 11 Nov 2017 00:41:55: 16000000 INFO @ Sat, 11 Nov 2017 00:41:57: 9000000 INFO @ Sat, 11 Nov 2017 00:42:03: 10000000 INFO @ Sat, 11 Nov 2017 00:42:05: 17000000 INFO @ Sat, 11 Nov 2017 00:42:12: 10000000 INFO @ Sat, 11 Nov 2017 00:42:15: 18000000 INFO @ Sat, 11 Nov 2017 00:42:20: 11000000 INFO @ Sat, 11 Nov 2017 00:42:25: 19000000 INFO @ Sat, 11 Nov 2017 00:42:27: 11000000 INFO @ Sat, 11 Nov 2017 00:42:36: 20000000 INFO @ Sat, 11 Nov 2017 00:42:36: 12000000 INFO @ Sat, 11 Nov 2017 00:42:41: #1 tag size is determined as 101 bps INFO @ Sat, 11 Nov 2017 00:42:41: #1 tag size = 101 INFO @ Sat, 11 Nov 2017 00:42:41: #1 total tags in treatment: 20548703 INFO @ Sat, 11 Nov 2017 00:42:41: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:42:41: #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 00:42:42: 12000000 INFO @ Sat, 11 Nov 2017 00:42:42: #1 tags after filtering in treatment: 20548580 INFO @ Sat, 11 Nov 2017 00:42:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:42:42: #1 finished! INFO @ Sat, 11 Nov 2017 00:42:42: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:42:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:42:46: #2 number of paired peaks: 28397 INFO @ Sat, 11 Nov 2017 00:42:46: start model_add_line... INFO @ Sat, 11 Nov 2017 00:42:46: start X-correlation... INFO @ Sat, 11 Nov 2017 00:42:46: end of X-cor INFO @ Sat, 11 Nov 2017 00:42:46: #2 finished! INFO @ Sat, 11 Nov 2017 00:42:46: #2 predicted fragment length is 139 bps INFO @ Sat, 11 Nov 2017 00:42:46: #2 alternative fragment length(s) may be 139 bps INFO @ Sat, 11 Nov 2017 00:42:46: #2.2 Generate R script for model : SRX1926706.05_model.r WARNING @ Sat, 11 Nov 2017 00:42:47: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:42:47: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Sat, 11 Nov 2017 00:42:47: #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 00:42:47: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:42:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:42:50: 13000000 INFO @ Sat, 11 Nov 2017 00:42:56: 13000000 INFO @ Sat, 11 Nov 2017 00:43:06: 14000000 INFO @ Sat, 11 Nov 2017 00:43:09: 14000000 INFO @ Sat, 11 Nov 2017 00:43:21: 15000000 INFO @ Sat, 11 Nov 2017 00:43:23: 15000000 INFO @ Sat, 11 Nov 2017 00:43:36: 16000000 INFO @ Sat, 11 Nov 2017 00:43:36: 16000000 INFO @ Sat, 11 Nov 2017 00:43:49: 17000000 INFO @ Sat, 11 Nov 2017 00:43:50: 17000000 INFO @ Sat, 11 Nov 2017 00:43:56: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:44:03: 18000000 INFO @ Sat, 11 Nov 2017 00:44:06: 18000000 INFO @ Sat, 11 Nov 2017 00:44:17: 19000000 INFO @ Sat, 11 Nov 2017 00:44:23: 19000000 INFO @ Sat, 11 Nov 2017 00:44:31: 20000000 INFO @ Sat, 11 Nov 2017 00:44:38: #1 tag size is determined as 101 bps INFO @ Sat, 11 Nov 2017 00:44:38: #1 tag size = 101 INFO @ Sat, 11 Nov 2017 00:44:38: #1 total tags in treatment: 20548703 INFO @ Sat, 11 Nov 2017 00:44:38: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:44:38: #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 00:44:39: #1 tags after filtering in treatment: 20548580 INFO @ Sat, 11 Nov 2017 00:44:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:44:39: #1 finished! INFO @ Sat, 11 Nov 2017 00:44:39: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:44:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:44:40: 20000000 INFO @ Sat, 11 Nov 2017 00:44:43: #2 number of paired peaks: 28397 INFO @ Sat, 11 Nov 2017 00:44:43: start model_add_line... INFO @ Sat, 11 Nov 2017 00:44:43: #4 Write output xls file... SRX1926706.05_peaks.xls INFO @ Sat, 11 Nov 2017 00:44:43: #4 Write peak in narrowPeak format file... SRX1926706.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:44:43: #4 Write summits bed file... SRX1926706.05_summits.bed INFO @ Sat, 11 Nov 2017 00:44:43: Done! INFO @ Sat, 11 Nov 2017 00:44:43: start X-correlation... INFO @ Sat, 11 Nov 2017 00:44:43: end of X-cor INFO @ Sat, 11 Nov 2017 00:44:43: #2 finished! INFO @ Sat, 11 Nov 2017 00:44:43: #2 predicted fragment length is 139 bps INFO @ Sat, 11 Nov 2017 00:44:43: #2 alternative fragment length(s) may be 139 bps INFO @ Sat, 11 Nov 2017 00:44:43: #2.2 Generate R script for model : SRX1926706.20_model.r WARNING @ Sat, 11 Nov 2017 00:44:43: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:44:43: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Sat, 11 Nov 2017 00:44:43: #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 00:44:43: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:44:43: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (68 chroms): 2 millis pass2 - checking and writing primary data (1500 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:44:51: #1 tag size is determined as 101 bps INFO @ Sat, 11 Nov 2017 00:44:51: #1 tag size = 101 INFO @ Sat, 11 Nov 2017 00:44:51: #1 total tags in treatment: 20548703 INFO @ Sat, 11 Nov 2017 00:44:51: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:44:51: #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 00:44:52: #1 tags after filtering in treatment: 20548580 INFO @ Sat, 11 Nov 2017 00:44:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:44:52: #1 finished! INFO @ Sat, 11 Nov 2017 00:44:52: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:44:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:44:56: #2 number of paired peaks: 28397 INFO @ Sat, 11 Nov 2017 00:44:56: start model_add_line... INFO @ Sat, 11 Nov 2017 00:44:57: start X-correlation... INFO @ Sat, 11 Nov 2017 00:44:57: end of X-cor INFO @ Sat, 11 Nov 2017 00:44:57: #2 finished! INFO @ Sat, 11 Nov 2017 00:44:57: #2 predicted fragment length is 139 bps INFO @ Sat, 11 Nov 2017 00:44:57: #2 alternative fragment length(s) may be 139 bps INFO @ Sat, 11 Nov 2017 00:44:57: #2.2 Generate R script for model : SRX1926706.10_model.r WARNING @ Sat, 11 Nov 2017 00:44:57: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:44:57: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Sat, 11 Nov 2017 00:44:57: #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 00:44:57: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:44:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:45:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:46:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:46:27: #4 Write output xls file... SRX1926706.20_peaks.xls INFO @ Sat, 11 Nov 2017 00:46:27: #4 Write peak in narrowPeak format file... SRX1926706.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:46:27: #4 Write summits bed file... SRX1926706.20_summits.bed INFO @ Sat, 11 Nov 2017 00:46:27: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (413 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:46:42: #4 Write output xls file... SRX1926706.10_peaks.xls INFO @ Sat, 11 Nov 2017 00:46:42: #4 Write peak in narrowPeak format file... SRX1926706.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:46:42: #4 Write summits bed file... SRX1926706.10_summits.bed INFO @ Sat, 11 Nov 2017 00:46:42: Done! pass1 - making usageList (50 chroms): 2 millis pass2 - checking and writing primary data (804 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。