Job ID = 10487613 sra ファイルのダウンロード中... Completed: 1443893K bytes transferred in 33 seconds (348129K 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 28942456 spots for /home/okishinya/chipatlas/results/rn6/SRX3358569/SRR6251628.sra Written 28942456 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:32:49 28942456 reads; of these: 28942456 (100.00%) were unpaired; of these: 1727275 (5.97%) aligned 0 times 19925095 (68.84%) aligned exactly 1 time 7290086 (25.19%) aligned >1 times 94.03% overall alignment rate Time searching: 00:32:52 Overall time: 00:32:52 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 12 files... [bam_rmdupse_core] 1908552 / 27215181 = 0.0701 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 10:55:24: # Command line: callpeak -t SRX3358569.bam -f BAM -g 2.15e9 -n SRX3358569.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3358569.20 # format = BAM # ChIP-seq file = ['SRX3358569.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 10:55:24: #1 read tag files... INFO @ Sun, 18 Mar 2018 10:55:24: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 10:55:24: # Command line: callpeak -t SRX3358569.bam -f BAM -g 2.15e9 -n SRX3358569.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3358569.05 # format = BAM # ChIP-seq file = ['SRX3358569.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 10:55:24: #1 read tag files... INFO @ Sun, 18 Mar 2018 10:55:24: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 10:55:24: # Command line: callpeak -t SRX3358569.bam -f BAM -g 2.15e9 -n SRX3358569.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3358569.10 # format = BAM # ChIP-seq file = ['SRX3358569.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 10:55:24: #1 read tag files... INFO @ Sun, 18 Mar 2018 10:55:24: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 10:55:34: 1000000 INFO @ Sun, 18 Mar 2018 10:55:34: 1000000 INFO @ Sun, 18 Mar 2018 10:55:34: 1000000 INFO @ Sun, 18 Mar 2018 10:55:42: 2000000 INFO @ Sun, 18 Mar 2018 10:55:43: 2000000 INFO @ Sun, 18 Mar 2018 10:55:43: 2000000 INFO @ Sun, 18 Mar 2018 10:55:51: 3000000 INFO @ Sun, 18 Mar 2018 10:55:51: 3000000 INFO @ Sun, 18 Mar 2018 10:55:51: 3000000 INFO @ Sun, 18 Mar 2018 10:56:00: 4000000 INFO @ Sun, 18 Mar 2018 10:56:00: 4000000 INFO @ Sun, 18 Mar 2018 10:56:00: 4000000 INFO @ Sun, 18 Mar 2018 10:56:08: 5000000 INFO @ Sun, 18 Mar 2018 10:56:08: 5000000 INFO @ Sun, 18 Mar 2018 10:56:08: 5000000 INFO @ Sun, 18 Mar 2018 10:56:18: 6000000 INFO @ Sun, 18 Mar 2018 10:56:18: 6000000 INFO @ Sun, 18 Mar 2018 10:56:18: 6000000 INFO @ Sun, 18 Mar 2018 10:56:26: 7000000 INFO @ Sun, 18 Mar 2018 10:56:28: 7000000 INFO @ Sun, 18 Mar 2018 10:56:28: 7000000 INFO @ Sun, 18 Mar 2018 10:56:36: 8000000 INFO @ Sun, 18 Mar 2018 10:56:36: 8000000 INFO @ Sun, 18 Mar 2018 10:56:37: 8000000 INFO @ Sun, 18 Mar 2018 10:56:45: 9000000 INFO @ Sun, 18 Mar 2018 10:56:46: 9000000 INFO @ Sun, 18 Mar 2018 10:56:47: 9000000 INFO @ Sun, 18 Mar 2018 10:56:53: 10000000 INFO @ Sun, 18 Mar 2018 10:56:55: 10000000 INFO @ Sun, 18 Mar 2018 10:56:56: 10000000 INFO @ Sun, 18 Mar 2018 10:57:01: 11000000 INFO @ Sun, 18 Mar 2018 10:57:04: 11000000 INFO @ Sun, 18 Mar 2018 10:57:04: 11000000 INFO @ Sun, 18 Mar 2018 10:57:10: 12000000 INFO @ Sun, 18 Mar 2018 10:57:13: 12000000 INFO @ Sun, 18 Mar 2018 10:57:13: 12000000 INFO @ Sun, 18 Mar 2018 10:57:18: 13000000 INFO @ Sun, 18 Mar 2018 10:57:22: 13000000 INFO @ Sun, 18 Mar 2018 10:57:22: 13000000 INFO @ Sun, 18 Mar 2018 10:57:27: 14000000 INFO @ Sun, 18 Mar 2018 10:57:31: 14000000 INFO @ Sun, 18 Mar 2018 10:57:31: 14000000 INFO @ Sun, 18 Mar 2018 10:57:35: 15000000 INFO @ Sun, 18 Mar 2018 10:57:39: 15000000 INFO @ Sun, 18 Mar 2018 10:57:39: 15000000 INFO @ Sun, 18 Mar 2018 10:57:45: 16000000 INFO @ Sun, 18 Mar 2018 10:57:49: 16000000 INFO @ Sun, 18 Mar 2018 10:57:49: 16000000 INFO @ Sun, 18 Mar 2018 10:57:54: 17000000 INFO @ Sun, 18 Mar 2018 10:57:59: 17000000 INFO @ Sun, 18 Mar 2018 10:58:00: 17000000 INFO @ Sun, 18 Mar 2018 10:58:04: 18000000 INFO @ Sun, 18 Mar 2018 10:58:08: 18000000 INFO @ Sun, 18 Mar 2018 10:58:10: 18000000 INFO @ Sun, 18 Mar 2018 10:58:14: 19000000 INFO @ Sun, 18 Mar 2018 10:58:18: 19000000 INFO @ Sun, 18 Mar 2018 10:58:21: 19000000 INFO @ Sun, 18 Mar 2018 10:58:24: 20000000 INFO @ Sun, 18 Mar 2018 10:58:28: 20000000 INFO @ Sun, 18 Mar 2018 10:58:30: 20000000 INFO @ Sun, 18 Mar 2018 10:58:32: 21000000 INFO @ Sun, 18 Mar 2018 10:58:36: 21000000 INFO @ Sun, 18 Mar 2018 10:58:38: 21000000 INFO @ Sun, 18 Mar 2018 10:58:41: 22000000 INFO @ Sun, 18 Mar 2018 10:58:45: 22000000 INFO @ Sun, 18 Mar 2018 10:58:47: 22000000 INFO @ Sun, 18 Mar 2018 10:58:50: 23000000 INFO @ Sun, 18 Mar 2018 10:58:53: 23000000 INFO @ Sun, 18 Mar 2018 10:58:56: 23000000 INFO @ Sun, 18 Mar 2018 10:58:58: 24000000 INFO @ Sun, 18 Mar 2018 10:59:02: 24000000 INFO @ Sun, 18 Mar 2018 10:59:04: 24000000 INFO @ Sun, 18 Mar 2018 10:59:07: 25000000 INFO @ Sun, 18 Mar 2018 10:59:10: #1 tag size is determined as 75 bps INFO @ Sun, 18 Mar 2018 10:59:10: #1 tag size = 75 INFO @ Sun, 18 Mar 2018 10:59:10: #1 total tags in treatment: 25306629 INFO @ Sun, 18 Mar 2018 10:59:10: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 10:59:10: #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 10:59:10: 25000000 INFO @ Sun, 18 Mar 2018 10:59:11: #1 tags after filtering in treatment: 25306518 INFO @ Sun, 18 Mar 2018 10:59:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 10:59:11: #1 finished! INFO @ Sun, 18 Mar 2018 10:59:11: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 10:59:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 10:59:13: #1 tag size is determined as 75 bps INFO @ Sun, 18 Mar 2018 10:59:13: #1 tag size = 75 INFO @ Sun, 18 Mar 2018 10:59:13: #1 total tags in treatment: 25306629 INFO @ Sun, 18 Mar 2018 10:59:13: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 10:59:13: #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 10:59:13: 25000000 INFO @ Sun, 18 Mar 2018 10:59:13: #2 number of paired peaks: 5233 INFO @ Sun, 18 Mar 2018 10:59:13: start model_add_line... INFO @ Sun, 18 Mar 2018 10:59:14: start X-correlation... INFO @ Sun, 18 Mar 2018 10:59:14: end of X-cor INFO @ Sun, 18 Mar 2018 10:59:14: #2 finished! INFO @ Sun, 18 Mar 2018 10:59:14: #2 predicted fragment length is 75 bps INFO @ Sun, 18 Mar 2018 10:59:14: #2 alternative fragment length(s) may be 75,524 bps INFO @ Sun, 18 Mar 2018 10:59:14: #2.2 Generate R script for model : SRX3358569.20_model.r WARNING @ Sun, 18 Mar 2018 10:59:14: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 10:59:14: #2 You may need to consider one of the other alternative d(s): 75,524 WARNING @ Sun, 18 Mar 2018 10:59:14: #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 10:59:14: #3 Call peaks... INFO @ Sun, 18 Mar 2018 10:59:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 10:59:14: #1 tags after filtering in treatment: 25306518 INFO @ Sun, 18 Mar 2018 10:59:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 10:59:14: #1 finished! INFO @ Sun, 18 Mar 2018 10:59:14: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 10:59:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 10:59:16: #1 tag size is determined as 75 bps INFO @ Sun, 18 Mar 2018 10:59:16: #1 tag size = 75 INFO @ Sun, 18 Mar 2018 10:59:16: #1 total tags in treatment: 25306629 INFO @ Sun, 18 Mar 2018 10:59:16: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 10:59:16: #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 10:59:16: #2 number of paired peaks: 5233 INFO @ Sun, 18 Mar 2018 10:59:16: start model_add_line... INFO @ Sun, 18 Mar 2018 10:59:16: start X-correlation... INFO @ Sun, 18 Mar 2018 10:59:16: end of X-cor INFO @ Sun, 18 Mar 2018 10:59:16: #2 finished! INFO @ Sun, 18 Mar 2018 10:59:16: #2 predicted fragment length is 75 bps INFO @ Sun, 18 Mar 2018 10:59:16: #2 alternative fragment length(s) may be 75,524 bps INFO @ Sun, 18 Mar 2018 10:59:16: #2.2 Generate R script for model : SRX3358569.05_model.r WARNING @ Sun, 18 Mar 2018 10:59:16: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 10:59:16: #2 You may need to consider one of the other alternative d(s): 75,524 WARNING @ Sun, 18 Mar 2018 10:59:16: #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 10:59:16: #3 Call peaks... INFO @ Sun, 18 Mar 2018 10:59:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 10:59:17: #1 tags after filtering in treatment: 25306518 INFO @ Sun, 18 Mar 2018 10:59:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 10:59:17: #1 finished! INFO @ Sun, 18 Mar 2018 10:59:17: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 10:59:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 10:59:19: #2 number of paired peaks: 5233 INFO @ Sun, 18 Mar 2018 10:59:19: start model_add_line... INFO @ Sun, 18 Mar 2018 10:59:20: start X-correlation... INFO @ Sun, 18 Mar 2018 10:59:20: end of X-cor INFO @ Sun, 18 Mar 2018 10:59:20: #2 finished! INFO @ Sun, 18 Mar 2018 10:59:20: #2 predicted fragment length is 75 bps INFO @ Sun, 18 Mar 2018 10:59:20: #2 alternative fragment length(s) may be 75,524 bps INFO @ Sun, 18 Mar 2018 10:59:20: #2.2 Generate R script for model : SRX3358569.10_model.r WARNING @ Sun, 18 Mar 2018 10:59:20: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 10:59:20: #2 You may need to consider one of the other alternative d(s): 75,524 WARNING @ Sun, 18 Mar 2018 10:59:20: #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 10:59:20: #3 Call peaks... INFO @ Sun, 18 Mar 2018 10:59:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:00:16: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:00:17: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:00:21: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:00:52: #4 Write output xls file... SRX3358569.05_peaks.xls INFO @ Sun, 18 Mar 2018 11:00:52: #4 Write peak in narrowPeak format file... SRX3358569.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:00:52: #4 Write summits bed file... SRX3358569.05_summits.bed INFO @ Sun, 18 Mar 2018 11:00:52: Done! pass1 - making usageList (54 chroms): 1 millis pass2 - checking and writing primary data (1469 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 11:00:55: #4 Write output xls file... SRX3358569.10_peaks.xls INFO @ Sun, 18 Mar 2018 11:00:55: #4 Write peak in narrowPeak format file... SRX3358569.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:00:55: #4 Write summits bed file... SRX3358569.10_summits.bed INFO @ Sun, 18 Mar 2018 11:00:55: Done! pass1 - making usageList (43 chroms): 1 millis pass2 - checking and writing primary data (842 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 11:00:56: #4 Write output xls file... SRX3358569.20_peaks.xls INFO @ Sun, 18 Mar 2018 11:00:56: #4 Write peak in narrowPeak format file... SRX3358569.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:00:56: #4 Write summits bed file... SRX3358569.20_summits.bed INFO @ Sun, 18 Mar 2018 11:00:56: Done! pass1 - making usageList (30 chroms): 1 millis pass2 - checking and writing primary data (448 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。