Job ID = 11632699 sra ファイルのダウンロード中... Completed: 680714K bytes transferred in 9 seconds (581068K 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 46345023 spots for /home/okishinya/chipatlas/results/rn6/SRX3782458/SRR6826276.sra Written 46345023 spots for /home/okishinya/chipatlas/results/rn6/SRX3782458/SRR6826276.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 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: 00:00:00 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:20:45 46345023 reads; of these: 46345023 (100.00%) were unpaired; of these: 2775062 (5.99%) aligned 0 times 33140633 (71.51%) aligned exactly 1 time 10429328 (22.50%) aligned >1 times 94.01% overall alignment rate Time searching: 00:20:48 Overall time: 00:20:48 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] 1485016 / 43569961 = 0.0341 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 @ Fri, 15 Feb 2019 07:48:29: # Command line: callpeak -t SRX3782458.bam -f BAM -g 2.15e9 -n SRX3782458.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3782458.10 # format = BAM # ChIP-seq file = ['SRX3782458.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 @ Fri, 15 Feb 2019 07:48:29: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:48:29: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:48:29: # Command line: callpeak -t SRX3782458.bam -f BAM -g 2.15e9 -n SRX3782458.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3782458.05 # format = BAM # ChIP-seq file = ['SRX3782458.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 @ Fri, 15 Feb 2019 07:48:29: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:48:29: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:48:29: # Command line: callpeak -t SRX3782458.bam -f BAM -g 2.15e9 -n SRX3782458.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3782458.20 # format = BAM # ChIP-seq file = ['SRX3782458.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 @ Fri, 15 Feb 2019 07:48:29: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:48:29: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:48:35: 1000000 INFO @ Fri, 15 Feb 2019 07:48:35: 1000000 INFO @ Fri, 15 Feb 2019 07:48:35: 1000000 INFO @ Fri, 15 Feb 2019 07:48:41: 2000000 INFO @ Fri, 15 Feb 2019 07:48:41: 2000000 INFO @ Fri, 15 Feb 2019 07:48:41: 2000000 INFO @ Fri, 15 Feb 2019 07:48:46: 3000000 INFO @ Fri, 15 Feb 2019 07:48:47: 3000000 INFO @ Fri, 15 Feb 2019 07:48:47: 3000000 INFO @ Fri, 15 Feb 2019 07:48:52: 4000000 INFO @ Fri, 15 Feb 2019 07:48:53: 4000000 INFO @ Fri, 15 Feb 2019 07:48:53: 4000000 INFO @ Fri, 15 Feb 2019 07:48:58: 5000000 INFO @ Fri, 15 Feb 2019 07:48:59: 5000000 INFO @ Fri, 15 Feb 2019 07:49:00: 5000000 INFO @ Fri, 15 Feb 2019 07:49:04: 6000000 INFO @ Fri, 15 Feb 2019 07:49:05: 6000000 INFO @ Fri, 15 Feb 2019 07:49:06: 6000000 INFO @ Fri, 15 Feb 2019 07:49:10: 7000000 INFO @ Fri, 15 Feb 2019 07:49:12: 7000000 INFO @ Fri, 15 Feb 2019 07:49:12: 7000000 INFO @ Fri, 15 Feb 2019 07:49:17: 8000000 INFO @ Fri, 15 Feb 2019 07:49:18: 8000000 INFO @ Fri, 15 Feb 2019 07:49:18: 8000000 INFO @ Fri, 15 Feb 2019 07:49:23: 9000000 INFO @ Fri, 15 Feb 2019 07:49:24: 9000000 INFO @ Fri, 15 Feb 2019 07:49:24: 9000000 INFO @ Fri, 15 Feb 2019 07:49:29: 10000000 INFO @ Fri, 15 Feb 2019 07:49:30: 10000000 INFO @ Fri, 15 Feb 2019 07:49:30: 10000000 INFO @ Fri, 15 Feb 2019 07:49:35: 11000000 INFO @ Fri, 15 Feb 2019 07:49:36: 11000000 INFO @ Fri, 15 Feb 2019 07:49:37: 11000000 INFO @ Fri, 15 Feb 2019 07:49:41: 12000000 INFO @ Fri, 15 Feb 2019 07:49:43: 12000000 INFO @ Fri, 15 Feb 2019 07:49:43: 12000000 INFO @ Fri, 15 Feb 2019 07:49:47: 13000000 INFO @ Fri, 15 Feb 2019 07:49:49: 13000000 INFO @ Fri, 15 Feb 2019 07:49:49: 13000000 INFO @ Fri, 15 Feb 2019 07:49:53: 14000000 INFO @ Fri, 15 Feb 2019 07:49:55: 14000000 INFO @ Fri, 15 Feb 2019 07:49:55: 14000000 INFO @ Fri, 15 Feb 2019 07:49:59: 15000000 INFO @ Fri, 15 Feb 2019 07:50:01: 15000000 INFO @ Fri, 15 Feb 2019 07:50:01: 15000000 INFO @ Fri, 15 Feb 2019 07:50:05: 16000000 INFO @ Fri, 15 Feb 2019 07:50:07: 16000000 INFO @ Fri, 15 Feb 2019 07:50:08: 16000000 INFO @ Fri, 15 Feb 2019 07:50:11: 17000000 INFO @ Fri, 15 Feb 2019 07:50:13: 17000000 INFO @ Fri, 15 Feb 2019 07:50:14: 17000000 INFO @ Fri, 15 Feb 2019 07:50:17: 18000000 INFO @ Fri, 15 Feb 2019 07:50:19: 18000000 INFO @ Fri, 15 Feb 2019 07:50:20: 18000000 INFO @ Fri, 15 Feb 2019 07:50:23: 19000000 INFO @ Fri, 15 Feb 2019 07:50:25: 19000000 INFO @ Fri, 15 Feb 2019 07:50:26: 19000000 INFO @ Fri, 15 Feb 2019 07:50:29: 20000000 INFO @ Fri, 15 Feb 2019 07:50:31: 20000000 INFO @ Fri, 15 Feb 2019 07:50:33: 20000000 INFO @ Fri, 15 Feb 2019 07:50:35: 21000000 INFO @ Fri, 15 Feb 2019 07:50:37: 21000000 INFO @ Fri, 15 Feb 2019 07:50:39: 21000000 INFO @ Fri, 15 Feb 2019 07:50:41: 22000000 INFO @ Fri, 15 Feb 2019 07:50:43: 22000000 INFO @ Fri, 15 Feb 2019 07:50:45: 22000000 INFO @ Fri, 15 Feb 2019 07:50:47: 23000000 INFO @ Fri, 15 Feb 2019 07:50:49: 23000000 INFO @ Fri, 15 Feb 2019 07:50:51: 23000000 INFO @ Fri, 15 Feb 2019 07:50:53: 24000000 INFO @ Fri, 15 Feb 2019 07:50:55: 24000000 INFO @ Fri, 15 Feb 2019 07:50:57: 24000000 INFO @ Fri, 15 Feb 2019 07:51:00: 25000000 INFO @ Fri, 15 Feb 2019 07:51:02: 25000000 INFO @ Fri, 15 Feb 2019 07:51:04: 25000000 INFO @ Fri, 15 Feb 2019 07:51:07: 26000000 INFO @ Fri, 15 Feb 2019 07:51:10: 26000000 INFO @ Fri, 15 Feb 2019 07:51:11: 26000000 INFO @ Fri, 15 Feb 2019 07:51:14: 27000000 INFO @ Fri, 15 Feb 2019 07:51:17: 27000000 INFO @ Fri, 15 Feb 2019 07:51:18: 27000000 INFO @ Fri, 15 Feb 2019 07:51:20: 28000000 INFO @ Fri, 15 Feb 2019 07:51:23: 28000000 INFO @ Fri, 15 Feb 2019 07:51:24: 28000000 INFO @ Fri, 15 Feb 2019 07:51:26: 29000000 INFO @ Fri, 15 Feb 2019 07:51:29: 29000000 INFO @ Fri, 15 Feb 2019 07:51:30: 29000000 INFO @ Fri, 15 Feb 2019 07:51:32: 30000000 INFO @ Fri, 15 Feb 2019 07:51:35: 30000000 INFO @ Fri, 15 Feb 2019 07:51:37: 30000000 INFO @ Fri, 15 Feb 2019 07:51:38: 31000000 INFO @ Fri, 15 Feb 2019 07:51:41: 31000000 INFO @ Fri, 15 Feb 2019 07:51:43: 31000000 INFO @ Fri, 15 Feb 2019 07:51:44: 32000000 INFO @ Fri, 15 Feb 2019 07:51:47: 32000000 INFO @ Fri, 15 Feb 2019 07:51:49: 32000000 INFO @ Fri, 15 Feb 2019 07:51:50: 33000000 INFO @ Fri, 15 Feb 2019 07:51:53: 33000000 INFO @ Fri, 15 Feb 2019 07:51:55: 33000000 INFO @ Fri, 15 Feb 2019 07:51:56: 34000000 INFO @ Fri, 15 Feb 2019 07:51:59: 34000000 INFO @ Fri, 15 Feb 2019 07:52:01: 34000000 INFO @ Fri, 15 Feb 2019 07:52:02: 35000000 INFO @ Fri, 15 Feb 2019 07:52:05: 35000000 INFO @ Fri, 15 Feb 2019 07:52:07: 35000000 INFO @ Fri, 15 Feb 2019 07:52:08: 36000000 INFO @ Fri, 15 Feb 2019 07:52:11: 36000000 INFO @ Fri, 15 Feb 2019 07:52:13: 36000000 INFO @ Fri, 15 Feb 2019 07:52:14: 37000000 INFO @ Fri, 15 Feb 2019 07:52:17: 37000000 INFO @ Fri, 15 Feb 2019 07:52:20: 37000000 INFO @ Fri, 15 Feb 2019 07:52:20: 38000000 INFO @ Fri, 15 Feb 2019 07:52:23: 38000000 INFO @ Fri, 15 Feb 2019 07:52:26: 38000000 INFO @ Fri, 15 Feb 2019 07:52:26: 39000000 INFO @ Fri, 15 Feb 2019 07:52:29: 39000000 INFO @ Fri, 15 Feb 2019 07:52:32: 40000000 INFO @ Fri, 15 Feb 2019 07:52:32: 39000000 INFO @ Fri, 15 Feb 2019 07:52:35: 40000000 INFO @ Fri, 15 Feb 2019 07:52:38: 40000000 INFO @ Fri, 15 Feb 2019 07:52:38: 41000000 INFO @ Fri, 15 Feb 2019 07:52:41: 41000000 INFO @ Fri, 15 Feb 2019 07:52:44: 42000000 INFO @ Fri, 15 Feb 2019 07:52:44: 41000000 INFO @ Fri, 15 Feb 2019 07:52:45: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:52:45: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:52:45: #1 total tags in treatment: 42084945 INFO @ Fri, 15 Feb 2019 07:52:45: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:52:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:52:46: #1 tags after filtering in treatment: 42084872 INFO @ Fri, 15 Feb 2019 07:52:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:52:46: #1 finished! INFO @ Fri, 15 Feb 2019 07:52:46: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:52:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:52:47: 42000000 INFO @ Fri, 15 Feb 2019 07:52:48: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:52:48: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:52:48: #1 total tags in treatment: 42084945 INFO @ Fri, 15 Feb 2019 07:52:48: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:52:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:52:49: #1 tags after filtering in treatment: 42084872 INFO @ Fri, 15 Feb 2019 07:52:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:52:49: #1 finished! INFO @ Fri, 15 Feb 2019 07:52:49: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:52:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:52:50: #2 number of paired peaks: 4255 INFO @ Fri, 15 Feb 2019 07:52:50: start model_add_line... INFO @ Fri, 15 Feb 2019 07:52:50: 42000000 INFO @ Fri, 15 Feb 2019 07:52:50: start X-correlation... INFO @ Fri, 15 Feb 2019 07:52:50: end of X-cor INFO @ Fri, 15 Feb 2019 07:52:50: #2 finished! INFO @ Fri, 15 Feb 2019 07:52:50: #2 predicted fragment length is 40 bps INFO @ Fri, 15 Feb 2019 07:52:50: #2 alternative fragment length(s) may be 40,120,201,385,583 bps INFO @ Fri, 15 Feb 2019 07:52:50: #2.2 Generate R script for model : SRX3782458.20_model.r WARNING @ Fri, 15 Feb 2019 07:52:50: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 07:52:50: #2 You may need to consider one of the other alternative d(s): 40,120,201,385,583 WARNING @ Fri, 15 Feb 2019 07:52:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 07:52:50: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:52:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:52:51: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:52:51: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:52:51: #1 total tags in treatment: 42084945 INFO @ Fri, 15 Feb 2019 07:52:51: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:52:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:52:52: #1 tags after filtering in treatment: 42084872 INFO @ Fri, 15 Feb 2019 07:52:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:52:52: #1 finished! INFO @ Fri, 15 Feb 2019 07:52:52: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:52:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:52:52: #2 number of paired peaks: 4255 INFO @ Fri, 15 Feb 2019 07:52:52: start model_add_line... INFO @ Fri, 15 Feb 2019 07:52:53: start X-correlation... INFO @ Fri, 15 Feb 2019 07:52:53: end of X-cor INFO @ Fri, 15 Feb 2019 07:52:53: #2 finished! INFO @ Fri, 15 Feb 2019 07:52:53: #2 predicted fragment length is 40 bps INFO @ Fri, 15 Feb 2019 07:52:53: #2 alternative fragment length(s) may be 40,120,201,385,583 bps INFO @ Fri, 15 Feb 2019 07:52:53: #2.2 Generate R script for model : SRX3782458.10_model.r WARNING @ Fri, 15 Feb 2019 07:52:53: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 07:52:53: #2 You may need to consider one of the other alternative d(s): 40,120,201,385,583 WARNING @ Fri, 15 Feb 2019 07:52:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 07:52:53: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:52:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:52:56: #2 number of paired peaks: 4255 INFO @ Fri, 15 Feb 2019 07:52:56: start model_add_line... INFO @ Fri, 15 Feb 2019 07:52:56: start X-correlation... INFO @ Fri, 15 Feb 2019 07:52:56: end of X-cor INFO @ Fri, 15 Feb 2019 07:52:56: #2 finished! INFO @ Fri, 15 Feb 2019 07:52:56: #2 predicted fragment length is 40 bps INFO @ Fri, 15 Feb 2019 07:52:56: #2 alternative fragment length(s) may be 40,120,201,385,583 bps INFO @ Fri, 15 Feb 2019 07:52:56: #2.2 Generate R script for model : SRX3782458.05_model.r WARNING @ Fri, 15 Feb 2019 07:52:56: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 07:52:56: #2 You may need to consider one of the other alternative d(s): 40,120,201,385,583 WARNING @ Fri, 15 Feb 2019 07:52:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 07:52:56: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:52:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:54:29: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:54:31: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:54:36: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:55:29: #4 Write output xls file... SRX3782458.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:55:29: #4 Write peak in narrowPeak format file... SRX3782458.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:55:29: #4 Write summits bed file... SRX3782458.20_summits.bed INFO @ Fri, 15 Feb 2019 07:55:29: Done! pass1 - making usageList (29 chroms): 3 millis pass2 - checking and writing primary data (473 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:55:30: #4 Write output xls file... SRX3782458.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:55:30: #4 Write peak in narrowPeak format file... SRX3782458.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:55:30: #4 Write summits bed file... SRX3782458.10_summits.bed INFO @ Fri, 15 Feb 2019 07:55:30: Done! pass1 - making usageList (39 chroms): 3 millis pass2 - checking and writing primary data (1057 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:55:32: #4 Write output xls file... SRX3782458.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:55:32: #4 Write peak in narrowPeak format file... SRX3782458.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:55:32: #4 Write summits bed file... SRX3782458.05_summits.bed INFO @ Fri, 15 Feb 2019 07:55:32: Done! pass1 - making usageList (48 chroms): 4 millis pass2 - checking and writing primary data (1842 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。