Job ID = 11388804 sra ファイルのダウンロード中... Completed: 245156K bytes transferred in 8 seconds (243613K bits/sec), in 1 file. Completed: 255734K bytes transferred in 10 seconds (193220K 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 11279698 spots for /home/okishinya/chipatlas/results/rn6/SRX3657371/SRR6681059.sra Written 11279698 spots for /home/okishinya/chipatlas/results/rn6/SRX3657371/SRR6681059.sra Read 11641929 spots for /home/okishinya/chipatlas/results/rn6/SRX3657371/SRR6681060.sra Written 11641929 spots for /home/okishinya/chipatlas/results/rn6/SRX3657371/SRR6681060.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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:43:28 22921627 reads; of these: 22921627 (100.00%) were unpaired; of these: 894955 (3.90%) aligned 0 times 15860910 (69.20%) aligned exactly 1 time 6165762 (26.90%) aligned >1 times 96.10% overall alignment rate Time searching: 00:43:32 Overall time: 00:43:32 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] 1715140 / 22026672 = 0.0779 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 23:47:03: # Command line: callpeak -t SRX3657371.bam -f BAM -g 2.15e9 -n SRX3657371.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3657371.10 # format = BAM # ChIP-seq file = ['SRX3657371.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 23:47:03: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:47:03: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:47:03: # Command line: callpeak -t SRX3657371.bam -f BAM -g 2.15e9 -n SRX3657371.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3657371.05 # format = BAM # ChIP-seq file = ['SRX3657371.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 23:47:03: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:47:03: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:47:03: # Command line: callpeak -t SRX3657371.bam -f BAM -g 2.15e9 -n SRX3657371.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3657371.20 # format = BAM # ChIP-seq file = ['SRX3657371.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 23:47:03: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:47:03: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:47:12: 1000000 INFO @ Wed, 12 Dec 2018 23:47:12: 1000000 INFO @ Wed, 12 Dec 2018 23:47:13: 1000000 INFO @ Wed, 12 Dec 2018 23:47:21: 2000000 INFO @ Wed, 12 Dec 2018 23:47:22: 2000000 INFO @ Wed, 12 Dec 2018 23:47:23: 2000000 INFO @ Wed, 12 Dec 2018 23:47:30: 3000000 INFO @ Wed, 12 Dec 2018 23:47:32: 3000000 INFO @ Wed, 12 Dec 2018 23:47:33: 3000000 INFO @ Wed, 12 Dec 2018 23:47:40: 4000000 INFO @ Wed, 12 Dec 2018 23:47:42: 4000000 INFO @ Wed, 12 Dec 2018 23:47:42: 4000000 INFO @ Wed, 12 Dec 2018 23:47:48: 5000000 INFO @ Wed, 12 Dec 2018 23:47:52: 5000000 INFO @ Wed, 12 Dec 2018 23:47:54: 5000000 INFO @ Wed, 12 Dec 2018 23:47:58: 6000000 INFO @ Wed, 12 Dec 2018 23:48:04: 6000000 INFO @ Wed, 12 Dec 2018 23:48:05: 6000000 INFO @ Wed, 12 Dec 2018 23:48:09: 7000000 INFO @ Wed, 12 Dec 2018 23:48:16: 7000000 INFO @ Wed, 12 Dec 2018 23:48:16: 7000000 INFO @ Wed, 12 Dec 2018 23:48:21: 8000000 INFO @ Wed, 12 Dec 2018 23:48:27: 8000000 INFO @ Wed, 12 Dec 2018 23:48:28: 8000000 INFO @ Wed, 12 Dec 2018 23:48:33: 9000000 INFO @ Wed, 12 Dec 2018 23:48:39: 9000000 INFO @ Wed, 12 Dec 2018 23:48:41: 9000000 INFO @ Wed, 12 Dec 2018 23:48:44: 10000000 INFO @ Wed, 12 Dec 2018 23:48:51: 10000000 INFO @ Wed, 12 Dec 2018 23:48:53: 10000000 INFO @ Wed, 12 Dec 2018 23:48:57: 11000000 INFO @ Wed, 12 Dec 2018 23:49:03: 11000000 INFO @ Wed, 12 Dec 2018 23:49:06: 11000000 INFO @ Wed, 12 Dec 2018 23:49:09: 12000000 INFO @ Wed, 12 Dec 2018 23:49:15: 12000000 INFO @ Wed, 12 Dec 2018 23:49:20: 12000000 INFO @ Wed, 12 Dec 2018 23:49:20: 13000000 INFO @ Wed, 12 Dec 2018 23:49:29: 13000000 INFO @ Wed, 12 Dec 2018 23:49:30: 14000000 INFO @ Wed, 12 Dec 2018 23:49:33: 13000000 INFO @ Wed, 12 Dec 2018 23:49:41: 15000000 INFO @ Wed, 12 Dec 2018 23:49:44: 14000000 INFO @ Wed, 12 Dec 2018 23:49:46: 14000000 INFO @ Wed, 12 Dec 2018 23:49:52: 16000000 INFO @ Wed, 12 Dec 2018 23:49:57: 15000000 INFO @ Wed, 12 Dec 2018 23:49:57: 15000000 INFO @ Wed, 12 Dec 2018 23:50:02: 17000000 INFO @ Wed, 12 Dec 2018 23:50:08: 16000000 INFO @ Wed, 12 Dec 2018 23:50:10: 16000000 INFO @ Wed, 12 Dec 2018 23:50:12: 18000000 INFO @ Wed, 12 Dec 2018 23:50:19: 17000000 INFO @ Wed, 12 Dec 2018 23:50:22: 17000000 INFO @ Wed, 12 Dec 2018 23:50:23: 19000000 INFO @ Wed, 12 Dec 2018 23:50:31: 18000000 INFO @ Wed, 12 Dec 2018 23:50:33: 18000000 INFO @ Wed, 12 Dec 2018 23:50:34: 20000000 INFO @ Wed, 12 Dec 2018 23:50:37: #1 tag size is determined as 50 bps INFO @ Wed, 12 Dec 2018 23:50:37: #1 tag size = 50 INFO @ Wed, 12 Dec 2018 23:50:37: #1 total tags in treatment: 20311532 INFO @ Wed, 12 Dec 2018 23:50:37: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:50:37: #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 23:50:38: #1 tags after filtering in treatment: 20311403 INFO @ Wed, 12 Dec 2018 23:50:38: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:50:38: #1 finished! INFO @ Wed, 12 Dec 2018 23:50:38: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:50:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:50:41: #2 number of paired peaks: 5519 INFO @ Wed, 12 Dec 2018 23:50:41: start model_add_line... INFO @ Wed, 12 Dec 2018 23:50:41: start X-correlation... INFO @ Wed, 12 Dec 2018 23:50:41: end of X-cor INFO @ Wed, 12 Dec 2018 23:50:41: #2 finished! INFO @ Wed, 12 Dec 2018 23:50:41: #2 predicted fragment length is 49 bps INFO @ Wed, 12 Dec 2018 23:50:41: #2 alternative fragment length(s) may be 49,393,481,496 bps INFO @ Wed, 12 Dec 2018 23:50:41: #2.2 Generate R script for model : SRX3657371.20_model.r WARNING @ Wed, 12 Dec 2018 23:50:41: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:50:41: #2 You may need to consider one of the other alternative d(s): 49,393,481,496 WARNING @ Wed, 12 Dec 2018 23:50:41: #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 23:50:41: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:50:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:50:43: 19000000 INFO @ Wed, 12 Dec 2018 23:50:44: 19000000 INFO @ Wed, 12 Dec 2018 23:50:54: 20000000 INFO @ Wed, 12 Dec 2018 23:50:58: 20000000 INFO @ Wed, 12 Dec 2018 23:50:58: #1 tag size is determined as 50 bps INFO @ Wed, 12 Dec 2018 23:50:58: #1 tag size = 50 INFO @ Wed, 12 Dec 2018 23:50:58: #1 total tags in treatment: 20311532 INFO @ Wed, 12 Dec 2018 23:50:58: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:50:58: #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 23:50:59: #1 tags after filtering in treatment: 20311403 INFO @ Wed, 12 Dec 2018 23:50:59: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:50:59: #1 finished! INFO @ Wed, 12 Dec 2018 23:50:59: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:50:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:51:02: #2 number of paired peaks: 5519 INFO @ Wed, 12 Dec 2018 23:51:02: start model_add_line... INFO @ Wed, 12 Dec 2018 23:51:02: start X-correlation... INFO @ Wed, 12 Dec 2018 23:51:02: end of X-cor INFO @ Wed, 12 Dec 2018 23:51:02: #2 finished! INFO @ Wed, 12 Dec 2018 23:51:02: #2 predicted fragment length is 49 bps INFO @ Wed, 12 Dec 2018 23:51:02: #2 alternative fragment length(s) may be 49,393,481,496 bps INFO @ Wed, 12 Dec 2018 23:51:02: #2.2 Generate R script for model : SRX3657371.10_model.r WARNING @ Wed, 12 Dec 2018 23:51:02: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:51:02: #2 You may need to consider one of the other alternative d(s): 49,393,481,496 WARNING @ Wed, 12 Dec 2018 23:51:02: #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 23:51:02: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:51:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:51:02: #1 tag size is determined as 50 bps INFO @ Wed, 12 Dec 2018 23:51:02: #1 tag size = 50 INFO @ Wed, 12 Dec 2018 23:51:02: #1 total tags in treatment: 20311532 INFO @ Wed, 12 Dec 2018 23:51:02: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:51:02: #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 23:51:03: #1 tags after filtering in treatment: 20311403 INFO @ Wed, 12 Dec 2018 23:51:03: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:51:03: #1 finished! INFO @ Wed, 12 Dec 2018 23:51:03: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:51:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:51:06: #2 number of paired peaks: 5519 INFO @ Wed, 12 Dec 2018 23:51:06: start model_add_line... INFO @ Wed, 12 Dec 2018 23:51:06: start X-correlation... INFO @ Wed, 12 Dec 2018 23:51:06: end of X-cor INFO @ Wed, 12 Dec 2018 23:51:06: #2 finished! INFO @ Wed, 12 Dec 2018 23:51:06: #2 predicted fragment length is 49 bps INFO @ Wed, 12 Dec 2018 23:51:06: #2 alternative fragment length(s) may be 49,393,481,496 bps INFO @ Wed, 12 Dec 2018 23:51:06: #2.2 Generate R script for model : SRX3657371.05_model.r WARNING @ Wed, 12 Dec 2018 23:51:06: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:51:06: #2 You may need to consider one of the other alternative d(s): 49,393,481,496 WARNING @ Wed, 12 Dec 2018 23:51:06: #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 23:51:06: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:51:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:51:43: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:52:04: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:52:11: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:52:19: #4 Write output xls file... SRX3657371.20_peaks.xls INFO @ Wed, 12 Dec 2018 23:52:19: #4 Write peak in narrowPeak format file... SRX3657371.20_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:52:19: #4 Write summits bed file... SRX3657371.20_summits.bed INFO @ Wed, 12 Dec 2018 23:52:19: Done! pass1 - making usageList (34 chroms): 5 millis pass2 - checking and writing primary data (439 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 23:52:40: #4 Write output xls file... SRX3657371.10_peaks.xls INFO @ Wed, 12 Dec 2018 23:52:40: #4 Write peak in narrowPeak format file... SRX3657371.10_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:52:40: #4 Write summits bed file... SRX3657371.10_summits.bed INFO @ Wed, 12 Dec 2018 23:52:40: Done! pass1 - making usageList (44 chroms): 5 millis pass2 - checking and writing primary data (886 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 23:52:49: #4 Write output xls file... SRX3657371.05_peaks.xls INFO @ Wed, 12 Dec 2018 23:52:49: #4 Write peak in narrowPeak format file... SRX3657371.05_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:52:49: #4 Write summits bed file... SRX3657371.05_summits.bed INFO @ Wed, 12 Dec 2018 23:52:49: Done! pass1 - making usageList (54 chroms): 9 millis pass2 - checking and writing primary data (1516 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。