Job ID = 11388815 sra ファイルのダウンロード中... Completed: 252665K bytes transferred in 10 seconds (199941K bits/sec), in 1 file. Completed: 250094K bytes transferred in 8 seconds (228687K 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... Read 11433711 spots for /home/okishinya/chipatlas/results/rn6/SRX3657375/SRR6681068.sra Written 11433711 spots for /home/okishinya/chipatlas/results/rn6/SRX3657375/SRR6681068.sra Read 11514634 spots for /home/okishinya/chipatlas/results/rn6/SRX3657375/SRR6681067.sra Written 11514634 spots for /home/okishinya/chipatlas/results/rn6/SRX3657375/SRR6681067.sra 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 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: 00:42:33 22948345 reads; of these: 22948345 (100.00%) were unpaired; of these: 1970375 (8.59%) aligned 0 times 15120547 (65.89%) aligned exactly 1 time 5857423 (25.52%) aligned >1 times 91.41% overall alignment rate Time searching: 00:42:37 Overall time: 00:42:37 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] 3721826 / 20977970 = 0.1774 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 @ Wed, 12 Dec 2018 23:50:18: # Command line: callpeak -t SRX3657375.bam -f BAM -g 2.15e9 -n SRX3657375.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3657375.05 # format = BAM # ChIP-seq file = ['SRX3657375.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 @ Wed, 12 Dec 2018 23:50:18: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:50:18: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:50:18: # Command line: callpeak -t SRX3657375.bam -f BAM -g 2.15e9 -n SRX3657375.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3657375.20 # format = BAM # ChIP-seq file = ['SRX3657375.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 @ Wed, 12 Dec 2018 23:50:18: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:50:18: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:50:18: # Command line: callpeak -t SRX3657375.bam -f BAM -g 2.15e9 -n SRX3657375.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3657375.10 # format = BAM # ChIP-seq file = ['SRX3657375.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 @ Wed, 12 Dec 2018 23:50:18: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:50:18: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:50:30: 1000000 INFO @ Wed, 12 Dec 2018 23:50:38: 1000000 INFO @ Wed, 12 Dec 2018 23:50:39: 1000000 INFO @ Wed, 12 Dec 2018 23:50:40: 2000000 INFO @ Wed, 12 Dec 2018 23:50:56: 3000000 INFO @ Wed, 12 Dec 2018 23:50:58: 2000000 INFO @ Wed, 12 Dec 2018 23:50:59: 2000000 INFO @ Wed, 12 Dec 2018 23:51:11: 4000000 INFO @ Wed, 12 Dec 2018 23:51:18: 3000000 INFO @ Wed, 12 Dec 2018 23:51:20: 3000000 INFO @ Wed, 12 Dec 2018 23:51:27: 5000000 INFO @ Wed, 12 Dec 2018 23:51:37: 4000000 INFO @ Wed, 12 Dec 2018 23:51:42: 4000000 INFO @ Wed, 12 Dec 2018 23:51:43: 6000000 INFO @ Wed, 12 Dec 2018 23:51:56: 5000000 INFO @ Wed, 12 Dec 2018 23:51:57: 7000000 INFO @ Wed, 12 Dec 2018 23:52:04: 5000000 INFO @ Wed, 12 Dec 2018 23:52:13: 8000000 INFO @ Wed, 12 Dec 2018 23:52:17: 6000000 INFO @ Wed, 12 Dec 2018 23:52:23: 6000000 INFO @ Wed, 12 Dec 2018 23:52:28: 9000000 INFO @ Wed, 12 Dec 2018 23:52:39: 7000000 INFO @ Wed, 12 Dec 2018 23:52:42: 7000000 INFO @ Wed, 12 Dec 2018 23:52:45: 10000000 INFO @ Wed, 12 Dec 2018 23:53:01: 8000000 INFO @ Wed, 12 Dec 2018 23:53:02: 8000000 INFO @ Wed, 12 Dec 2018 23:53:04: 11000000 INFO @ Wed, 12 Dec 2018 23:53:22: 9000000 INFO @ Wed, 12 Dec 2018 23:53:22: 9000000 INFO @ Wed, 12 Dec 2018 23:53:23: 12000000 INFO @ Wed, 12 Dec 2018 23:53:40: 13000000 INFO @ Wed, 12 Dec 2018 23:53:41: 10000000 INFO @ Wed, 12 Dec 2018 23:53:42: 10000000 INFO @ Wed, 12 Dec 2018 23:53:57: 11000000 INFO @ Wed, 12 Dec 2018 23:53:58: 14000000 INFO @ Wed, 12 Dec 2018 23:53:59: 11000000 INFO @ Wed, 12 Dec 2018 23:54:14: 12000000 INFO @ Wed, 12 Dec 2018 23:54:16: 15000000 INFO @ Wed, 12 Dec 2018 23:54:18: 12000000 INFO @ Wed, 12 Dec 2018 23:54:30: 13000000 INFO @ Wed, 12 Dec 2018 23:54:31: 16000000 INFO @ Wed, 12 Dec 2018 23:54:37: 13000000 INFO @ Wed, 12 Dec 2018 23:54:46: 14000000 INFO @ Wed, 12 Dec 2018 23:54:48: 17000000 INFO @ Wed, 12 Dec 2018 23:54:52: #1 tag size is determined as 50 bps INFO @ Wed, 12 Dec 2018 23:54:52: #1 tag size = 50 INFO @ Wed, 12 Dec 2018 23:54:52: #1 total tags in treatment: 17256144 INFO @ Wed, 12 Dec 2018 23:54:52: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:54:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 12 Dec 2018 23:54:53: #1 tags after filtering in treatment: 17256004 INFO @ Wed, 12 Dec 2018 23:54:53: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:54:53: #1 finished! INFO @ Wed, 12 Dec 2018 23:54:53: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:54:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:54:56: #2 number of paired peaks: 5859 INFO @ Wed, 12 Dec 2018 23:54:56: start model_add_line... INFO @ Wed, 12 Dec 2018 23:54:56: start X-correlation... INFO @ Wed, 12 Dec 2018 23:54:56: end of X-cor INFO @ Wed, 12 Dec 2018 23:54:56: #2 finished! INFO @ Wed, 12 Dec 2018 23:54:56: #2 predicted fragment length is 50 bps INFO @ Wed, 12 Dec 2018 23:54:56: #2 alternative fragment length(s) may be 50,226,412,520 bps INFO @ Wed, 12 Dec 2018 23:54:56: #2.2 Generate R script for model : SRX3657375.05_model.r WARNING @ Wed, 12 Dec 2018 23:54:56: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:54:56: #2 You may need to consider one of the other alternative d(s): 50,226,412,520 WARNING @ Wed, 12 Dec 2018 23:54:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 12 Dec 2018 23:54:56: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:54:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:54:59: 14000000 INFO @ Wed, 12 Dec 2018 23:55:00: 15000000 INFO @ Wed, 12 Dec 2018 23:55:14: 16000000 INFO @ Wed, 12 Dec 2018 23:55:21: 15000000 INFO @ Wed, 12 Dec 2018 23:55:29: 17000000 INFO @ Wed, 12 Dec 2018 23:55:33: #1 tag size is determined as 50 bps INFO @ Wed, 12 Dec 2018 23:55:33: #1 tag size = 50 INFO @ Wed, 12 Dec 2018 23:55:33: #1 total tags in treatment: 17256144 INFO @ Wed, 12 Dec 2018 23:55:33: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:55:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 12 Dec 2018 23:55:33: #1 tags after filtering in treatment: 17256004 INFO @ Wed, 12 Dec 2018 23:55:33: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:55:33: #1 finished! INFO @ Wed, 12 Dec 2018 23:55:33: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:55:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:55:36: #2 number of paired peaks: 5859 INFO @ Wed, 12 Dec 2018 23:55:36: start model_add_line... INFO @ Wed, 12 Dec 2018 23:55:36: start X-correlation... INFO @ Wed, 12 Dec 2018 23:55:36: end of X-cor INFO @ Wed, 12 Dec 2018 23:55:36: #2 finished! INFO @ Wed, 12 Dec 2018 23:55:36: #2 predicted fragment length is 50 bps INFO @ Wed, 12 Dec 2018 23:55:36: #2 alternative fragment length(s) may be 50,226,412,520 bps INFO @ Wed, 12 Dec 2018 23:55:36: #2.2 Generate R script for model : SRX3657375.20_model.r WARNING @ Wed, 12 Dec 2018 23:55:36: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:55:36: #2 You may need to consider one of the other alternative d(s): 50,226,412,520 WARNING @ Wed, 12 Dec 2018 23:55:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 12 Dec 2018 23:55:36: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:55:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:55:44: 16000000 INFO @ Wed, 12 Dec 2018 23:55:49: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:56:06: 17000000 INFO @ Wed, 12 Dec 2018 23:56:11: #1 tag size is determined as 50 bps INFO @ Wed, 12 Dec 2018 23:56:11: #1 tag size = 50 INFO @ Wed, 12 Dec 2018 23:56:11: #1 total tags in treatment: 17256144 INFO @ Wed, 12 Dec 2018 23:56:11: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:56:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 12 Dec 2018 23:56:12: #1 tags after filtering in treatment: 17256004 INFO @ Wed, 12 Dec 2018 23:56:12: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:56:12: #1 finished! INFO @ Wed, 12 Dec 2018 23:56:12: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:56:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:56:14: #2 number of paired peaks: 5859 INFO @ Wed, 12 Dec 2018 23:56:14: start model_add_line... INFO @ Wed, 12 Dec 2018 23:56:15: start X-correlation... INFO @ Wed, 12 Dec 2018 23:56:15: end of X-cor INFO @ Wed, 12 Dec 2018 23:56:15: #2 finished! INFO @ Wed, 12 Dec 2018 23:56:15: #2 predicted fragment length is 50 bps INFO @ Wed, 12 Dec 2018 23:56:15: #2 alternative fragment length(s) may be 50,226,412,520 bps INFO @ Wed, 12 Dec 2018 23:56:15: #2.2 Generate R script for model : SRX3657375.10_model.r WARNING @ Wed, 12 Dec 2018 23:56:15: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:56:15: #2 You may need to consider one of the other alternative d(s): 50,226,412,520 WARNING @ Wed, 12 Dec 2018 23:56:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 12 Dec 2018 23:56:15: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:56:15: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:56:19: #4 Write output xls file... SRX3657375.05_peaks.xls INFO @ Wed, 12 Dec 2018 23:56:19: #4 Write peak in narrowPeak format file... SRX3657375.05_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:56:19: #4 Write summits bed file... SRX3657375.05_summits.bed INFO @ Wed, 12 Dec 2018 23:56:19: Done! pass1 - making usageList (63 chroms): 4 millis pass2 - checking and writing primary data (1399 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 23:56:27: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:56:56: #4 Write output xls file... SRX3657375.20_peaks.xls INFO @ Wed, 12 Dec 2018 23:56:56: #4 Write peak in narrowPeak format file... SRX3657375.20_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:56:56: #4 Write summits bed file... SRX3657375.20_summits.bed INFO @ Wed, 12 Dec 2018 23:56:56: Done! pass1 - making usageList (44 chroms): 7 millis pass2 - checking and writing primary data (383 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 23:57:07: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:57:36: #4 Write output xls file... SRX3657375.10_peaks.xls INFO @ Wed, 12 Dec 2018 23:57:36: #4 Write peak in narrowPeak format file... SRX3657375.10_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:57:36: #4 Write summits bed file... SRX3657375.10_summits.bed INFO @ Wed, 12 Dec 2018 23:57:36: Done! pass1 - making usageList (57 chroms): 5 millis pass2 - checking and writing primary data (828 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。