Job ID = 10194933 sra ファイルのダウンロード中... Completed: 682484K bytes transferred in 10 seconds (511676K 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 33471872 spots for /home/okishinya/chipatlas/results/rn6/SRX2512943/SRR5197456.sra Written 33471872 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: 00:00:00 Multiseed full-index search: 00:36:59 33471872 reads; of these: 33471872 (100.00%) were unpaired; of these: 2861958 (8.55%) aligned 0 times 19063264 (56.95%) aligned exactly 1 time 11546650 (34.50%) aligned >1 times 91.45% overall alignment rate Time searching: 00:37:02 Overall time: 00:37:02 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 8 files... [bam_rmdupse_core] 2687557 / 30609914 = 0.0878 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 00:28:58: # Command line: callpeak -t SRX2512943.bam -f BAM -g 2.15e9 -n SRX2512943.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2512943.20 # format = BAM # ChIP-seq file = ['SRX2512943.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 00:28:58: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:28:58: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:28:58: # Command line: callpeak -t SRX2512943.bam -f BAM -g 2.15e9 -n SRX2512943.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2512943.05 # format = BAM # ChIP-seq file = ['SRX2512943.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 00:28:58: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:28:58: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:28:58: # Command line: callpeak -t SRX2512943.bam -f BAM -g 2.15e9 -n SRX2512943.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2512943.10 # format = BAM # ChIP-seq file = ['SRX2512943.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 00:28:58: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:28:58: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:29:09: 1000000 INFO @ Sat, 11 Nov 2017 00:29:09: 1000000 INFO @ Sat, 11 Nov 2017 00:29:12: 1000000 INFO @ Sat, 11 Nov 2017 00:29:21: 2000000 INFO @ Sat, 11 Nov 2017 00:29:21: 2000000 INFO @ Sat, 11 Nov 2017 00:29:26: 2000000 INFO @ Sat, 11 Nov 2017 00:29:32: 3000000 INFO @ Sat, 11 Nov 2017 00:29:34: 3000000 INFO @ Sat, 11 Nov 2017 00:29:39: 3000000 INFO @ Sat, 11 Nov 2017 00:29:44: 4000000 INFO @ Sat, 11 Nov 2017 00:29:46: 4000000 INFO @ Sat, 11 Nov 2017 00:29:53: 4000000 INFO @ Sat, 11 Nov 2017 00:29:56: 5000000 INFO @ Sat, 11 Nov 2017 00:29:58: 5000000 INFO @ Sat, 11 Nov 2017 00:30:07: 5000000 INFO @ Sat, 11 Nov 2017 00:30:08: 6000000 INFO @ Sat, 11 Nov 2017 00:30:11: 6000000 INFO @ Sat, 11 Nov 2017 00:30:20: 7000000 INFO @ Sat, 11 Nov 2017 00:30:20: 6000000 INFO @ Sat, 11 Nov 2017 00:30:23: 7000000 INFO @ Sat, 11 Nov 2017 00:30:33: 8000000 INFO @ Sat, 11 Nov 2017 00:30:35: 7000000 INFO @ Sat, 11 Nov 2017 00:30:37: 8000000 INFO @ Sat, 11 Nov 2017 00:30:44: 9000000 INFO @ Sat, 11 Nov 2017 00:30:48: 9000000 INFO @ Sat, 11 Nov 2017 00:30:48: 8000000 INFO @ Sat, 11 Nov 2017 00:30:56: 10000000 INFO @ Sat, 11 Nov 2017 00:31:00: 10000000 INFO @ Sat, 11 Nov 2017 00:31:02: 9000000 INFO @ Sat, 11 Nov 2017 00:31:07: 11000000 INFO @ Sat, 11 Nov 2017 00:31:12: 11000000 INFO @ Sat, 11 Nov 2017 00:31:15: 10000000 INFO @ Sat, 11 Nov 2017 00:31:18: 12000000 INFO @ Sat, 11 Nov 2017 00:31:23: 12000000 INFO @ Sat, 11 Nov 2017 00:31:29: 13000000 INFO @ Sat, 11 Nov 2017 00:31:29: 11000000 INFO @ Sat, 11 Nov 2017 00:31:35: 13000000 INFO @ Sat, 11 Nov 2017 00:31:40: 14000000 INFO @ Sat, 11 Nov 2017 00:31:43: 12000000 INFO @ Sat, 11 Nov 2017 00:31:47: 14000000 INFO @ Sat, 11 Nov 2017 00:31:51: 15000000 INFO @ Sat, 11 Nov 2017 00:31:56: 13000000 INFO @ Sat, 11 Nov 2017 00:31:59: 15000000 INFO @ Sat, 11 Nov 2017 00:32:02: 16000000 INFO @ Sat, 11 Nov 2017 00:32:09: 14000000 INFO @ Sat, 11 Nov 2017 00:32:11: 16000000 INFO @ Sat, 11 Nov 2017 00:32:13: 17000000 INFO @ Sat, 11 Nov 2017 00:32:23: 17000000 INFO @ Sat, 11 Nov 2017 00:32:23: 15000000 INFO @ Sat, 11 Nov 2017 00:32:24: 18000000 INFO @ Sat, 11 Nov 2017 00:32:35: 18000000 INFO @ Sat, 11 Nov 2017 00:32:36: 19000000 INFO @ Sat, 11 Nov 2017 00:32:38: 16000000 INFO @ Sat, 11 Nov 2017 00:32:48: 19000000 INFO @ Sat, 11 Nov 2017 00:32:48: 20000000 INFO @ Sat, 11 Nov 2017 00:32:52: 17000000 INFO @ Sat, 11 Nov 2017 00:33:00: 20000000 INFO @ Sat, 11 Nov 2017 00:33:00: 21000000 INFO @ Sat, 11 Nov 2017 00:33:07: 18000000 INFO @ Sat, 11 Nov 2017 00:33:13: 22000000 INFO @ Sat, 11 Nov 2017 00:33:13: 21000000 INFO @ Sat, 11 Nov 2017 00:33:21: 19000000 INFO @ Sat, 11 Nov 2017 00:33:25: 23000000 INFO @ Sat, 11 Nov 2017 00:33:26: 22000000 INFO @ Sat, 11 Nov 2017 00:33:36: 20000000 INFO @ Sat, 11 Nov 2017 00:33:37: 24000000 INFO @ Sat, 11 Nov 2017 00:33:39: 23000000 INFO @ Sat, 11 Nov 2017 00:33:49: 25000000 INFO @ Sat, 11 Nov 2017 00:33:51: 21000000 INFO @ Sat, 11 Nov 2017 00:33:51: 24000000 INFO @ Sat, 11 Nov 2017 00:34:01: 26000000 INFO @ Sat, 11 Nov 2017 00:34:04: 25000000 INFO @ Sat, 11 Nov 2017 00:34:05: 22000000 INFO @ Sat, 11 Nov 2017 00:34:13: 27000000 INFO @ Sat, 11 Nov 2017 00:34:17: 26000000 INFO @ Sat, 11 Nov 2017 00:34:20: 23000000 INFO @ Sat, 11 Nov 2017 00:34:25: #1 tag size is determined as 36 bps INFO @ Sat, 11 Nov 2017 00:34:25: #1 tag size = 36 INFO @ Sat, 11 Nov 2017 00:34:25: #1 total tags in treatment: 27922357 INFO @ Sat, 11 Nov 2017 00:34:25: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:34:25: #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 00:34:26: #1 tags after filtering in treatment: 27922267 INFO @ Sat, 11 Nov 2017 00:34:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:34:26: #1 finished! INFO @ Sat, 11 Nov 2017 00:34:26: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:34:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:34:30: #2 number of paired peaks: 6431 INFO @ Sat, 11 Nov 2017 00:34:30: start model_add_line... INFO @ Sat, 11 Nov 2017 00:34:30: 27000000 INFO @ Sat, 11 Nov 2017 00:34:30: start X-correlation... INFO @ Sat, 11 Nov 2017 00:34:30: end of X-cor INFO @ Sat, 11 Nov 2017 00:34:30: #2 finished! INFO @ Sat, 11 Nov 2017 00:34:30: #2 predicted fragment length is 36 bps INFO @ Sat, 11 Nov 2017 00:34:30: #2 alternative fragment length(s) may be 36,122,212,396,576 bps INFO @ Sat, 11 Nov 2017 00:34:30: #2.2 Generate R script for model : SRX2512943.20_model.r WARNING @ Sat, 11 Nov 2017 00:34:30: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:34:30: #2 You may need to consider one of the other alternative d(s): 36,122,212,396,576 WARNING @ Sat, 11 Nov 2017 00:34:30: #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 00:34:30: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:34:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:34:34: 24000000 INFO @ Sat, 11 Nov 2017 00:34:42: #1 tag size is determined as 36 bps INFO @ Sat, 11 Nov 2017 00:34:42: #1 tag size = 36 INFO @ Sat, 11 Nov 2017 00:34:42: #1 total tags in treatment: 27922357 INFO @ Sat, 11 Nov 2017 00:34:42: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:34:42: #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 00:34:43: #1 tags after filtering in treatment: 27922267 INFO @ Sat, 11 Nov 2017 00:34:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:34:43: #1 finished! INFO @ Sat, 11 Nov 2017 00:34:43: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:34:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:34:47: #2 number of paired peaks: 6431 INFO @ Sat, 11 Nov 2017 00:34:47: start model_add_line... INFO @ Sat, 11 Nov 2017 00:34:47: start X-correlation... INFO @ Sat, 11 Nov 2017 00:34:47: end of X-cor INFO @ Sat, 11 Nov 2017 00:34:47: #2 finished! INFO @ Sat, 11 Nov 2017 00:34:47: #2 predicted fragment length is 36 bps INFO @ Sat, 11 Nov 2017 00:34:47: #2 alternative fragment length(s) may be 36,122,212,396,576 bps INFO @ Sat, 11 Nov 2017 00:34:47: #2.2 Generate R script for model : SRX2512943.05_model.r WARNING @ Sat, 11 Nov 2017 00:34:47: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:34:47: #2 You may need to consider one of the other alternative d(s): 36,122,212,396,576 WARNING @ Sat, 11 Nov 2017 00:34:47: #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 00:34:47: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:34:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:34:47: 25000000 INFO @ Sat, 11 Nov 2017 00:35:00: 26000000 INFO @ Sat, 11 Nov 2017 00:35:13: 27000000 INFO @ Sat, 11 Nov 2017 00:35:26: #1 tag size is determined as 36 bps INFO @ Sat, 11 Nov 2017 00:35:26: #1 tag size = 36 INFO @ Sat, 11 Nov 2017 00:35:26: #1 total tags in treatment: 27922357 INFO @ Sat, 11 Nov 2017 00:35:26: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:35:26: #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 00:35:27: #1 tags after filtering in treatment: 27922267 INFO @ Sat, 11 Nov 2017 00:35:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:35:27: #1 finished! INFO @ Sat, 11 Nov 2017 00:35:27: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:35:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:35:31: #2 number of paired peaks: 6431 INFO @ Sat, 11 Nov 2017 00:35:31: start model_add_line... INFO @ Sat, 11 Nov 2017 00:35:31: start X-correlation... INFO @ Sat, 11 Nov 2017 00:35:31: end of X-cor INFO @ Sat, 11 Nov 2017 00:35:31: #2 finished! INFO @ Sat, 11 Nov 2017 00:35:31: #2 predicted fragment length is 36 bps INFO @ Sat, 11 Nov 2017 00:35:31: #2 alternative fragment length(s) may be 36,122,212,396,576 bps INFO @ Sat, 11 Nov 2017 00:35:31: #2.2 Generate R script for model : SRX2512943.10_model.r WARNING @ Sat, 11 Nov 2017 00:35:31: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:35:31: #2 You may need to consider one of the other alternative d(s): 36,122,212,396,576 WARNING @ Sat, 11 Nov 2017 00:35:31: #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 00:35:31: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:35:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:35:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:36:10: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:36:44: #4 Write output xls file... SRX2512943.20_peaks.xls INFO @ Sat, 11 Nov 2017 00:36:44: #4 Write peak in narrowPeak format file... SRX2512943.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:36:45: #4 Write summits bed file... SRX2512943.20_summits.bed INFO @ Sat, 11 Nov 2017 00:36:45: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (795 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:36:54: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:37:02: #4 Write output xls file... SRX2512943.05_peaks.xls INFO @ Sat, 11 Nov 2017 00:37:02: #4 Write peak in narrowPeak format file... SRX2512943.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:37:02: #4 Write summits bed file... SRX2512943.05_summits.bed INFO @ Sat, 11 Nov 2017 00:37:02: Done! pass1 - making usageList (60 chroms): 3 millis pass2 - checking and writing primary data (2822 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:37:45: #4 Write output xls file... SRX2512943.10_peaks.xls INFO @ Sat, 11 Nov 2017 00:37:45: #4 Write peak in narrowPeak format file... SRX2512943.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:37:45: #4 Write summits bed file... SRX2512943.10_summits.bed INFO @ Sat, 11 Nov 2017 00:37:45: Done! pass1 - making usageList (45 chroms): 2 millis pass2 - checking and writing primary data (1636 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。