Job ID = 11632723 sra ファイルのダウンロード中... Completed: 680714K bytes transferred in 9 seconds (608535K 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/SRX3782482/SRR6829573.sra Written 46345023 spots for /home/okishinya/chipatlas/results/rn6/SRX3782482/SRR6829573.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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:19:42 46345023 reads; of these: 46345023 (100.00%) were unpaired; of these: 2775032 (5.99%) aligned 0 times 33141289 (71.51%) aligned exactly 1 time 10428702 (22.50%) aligned >1 times 94.01% overall alignment rate Time searching: 00:19:45 Overall time: 00:19:45 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] 1484400 / 43569991 = 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 07:14:46: # Command line: callpeak -t SRX3782482.bam -f BAM -g 2.15e9 -n SRX3782482.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3782482.20 # format = BAM # ChIP-seq file = ['SRX3782482.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 07:14:46: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:14:46: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:14:46: # Command line: callpeak -t SRX3782482.bam -f BAM -g 2.15e9 -n SRX3782482.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3782482.10 # format = BAM # ChIP-seq file = ['SRX3782482.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 07:14:46: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:14:46: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:14:46: # Command line: callpeak -t SRX3782482.bam -f BAM -g 2.15e9 -n SRX3782482.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3782482.05 # format = BAM # ChIP-seq file = ['SRX3782482.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 07:14:46: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:14:46: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:14:52: 1000000 INFO @ Fri, 15 Feb 2019 07:14:52: 1000000 INFO @ Fri, 15 Feb 2019 07:14:53: 1000000 INFO @ Fri, 15 Feb 2019 07:14:59: 2000000 INFO @ Fri, 15 Feb 2019 07:14:59: 2000000 INFO @ Fri, 15 Feb 2019 07:14:59: 2000000 INFO @ Fri, 15 Feb 2019 07:15:05: 3000000 INFO @ Fri, 15 Feb 2019 07:15:05: 3000000 INFO @ Fri, 15 Feb 2019 07:15:06: 3000000 INFO @ Fri, 15 Feb 2019 07:15:11: 4000000 INFO @ Fri, 15 Feb 2019 07:15:11: 4000000 INFO @ Fri, 15 Feb 2019 07:15:13: 4000000 INFO @ Fri, 15 Feb 2019 07:15:18: 5000000 INFO @ Fri, 15 Feb 2019 07:15:18: 5000000 INFO @ Fri, 15 Feb 2019 07:15:19: 5000000 INFO @ Fri, 15 Feb 2019 07:15:24: 6000000 INFO @ Fri, 15 Feb 2019 07:15:24: 6000000 INFO @ Fri, 15 Feb 2019 07:15:26: 6000000 INFO @ Fri, 15 Feb 2019 07:15:30: 7000000 INFO @ Fri, 15 Feb 2019 07:15:30: 7000000 INFO @ Fri, 15 Feb 2019 07:15:33: 7000000 INFO @ Fri, 15 Feb 2019 07:15:37: 8000000 INFO @ Fri, 15 Feb 2019 07:15:37: 8000000 INFO @ Fri, 15 Feb 2019 07:15:40: 8000000 INFO @ Fri, 15 Feb 2019 07:15:43: 9000000 INFO @ Fri, 15 Feb 2019 07:15:43: 9000000 INFO @ Fri, 15 Feb 2019 07:15:47: 9000000 INFO @ Fri, 15 Feb 2019 07:15:49: 10000000 INFO @ Fri, 15 Feb 2019 07:15:49: 10000000 INFO @ Fri, 15 Feb 2019 07:15:53: 10000000 INFO @ Fri, 15 Feb 2019 07:15:56: 11000000 INFO @ Fri, 15 Feb 2019 07:15:56: 11000000 INFO @ Fri, 15 Feb 2019 07:16:00: 11000000 INFO @ Fri, 15 Feb 2019 07:16:02: 12000000 INFO @ Fri, 15 Feb 2019 07:16:02: 12000000 INFO @ Fri, 15 Feb 2019 07:16:07: 12000000 INFO @ Fri, 15 Feb 2019 07:16:08: 13000000 INFO @ Fri, 15 Feb 2019 07:16:08: 13000000 INFO @ Fri, 15 Feb 2019 07:16:14: 13000000 INFO @ Fri, 15 Feb 2019 07:16:15: 14000000 INFO @ Fri, 15 Feb 2019 07:16:15: 14000000 INFO @ Fri, 15 Feb 2019 07:16:21: 14000000 INFO @ Fri, 15 Feb 2019 07:16:21: 15000000 INFO @ Fri, 15 Feb 2019 07:16:21: 15000000 INFO @ Fri, 15 Feb 2019 07:16:27: 15000000 INFO @ Fri, 15 Feb 2019 07:16:28: 16000000 INFO @ Fri, 15 Feb 2019 07:16:28: 16000000 INFO @ Fri, 15 Feb 2019 07:16:34: 17000000 INFO @ Fri, 15 Feb 2019 07:16:34: 17000000 INFO @ Fri, 15 Feb 2019 07:16:34: 16000000 INFO @ Fri, 15 Feb 2019 07:16:40: 18000000 INFO @ Fri, 15 Feb 2019 07:16:40: 18000000 INFO @ Fri, 15 Feb 2019 07:16:41: 17000000 INFO @ Fri, 15 Feb 2019 07:16:47: 19000000 INFO @ Fri, 15 Feb 2019 07:16:47: 19000000 INFO @ Fri, 15 Feb 2019 07:16:48: 18000000 INFO @ Fri, 15 Feb 2019 07:16:53: 20000000 INFO @ Fri, 15 Feb 2019 07:16:53: 20000000 INFO @ Fri, 15 Feb 2019 07:16:55: 19000000 INFO @ Fri, 15 Feb 2019 07:17:00: 21000000 INFO @ Fri, 15 Feb 2019 07:17:00: 21000000 INFO @ Fri, 15 Feb 2019 07:17:02: 20000000 INFO @ Fri, 15 Feb 2019 07:17:06: 22000000 INFO @ Fri, 15 Feb 2019 07:17:06: 22000000 INFO @ Fri, 15 Feb 2019 07:17:08: 21000000 INFO @ Fri, 15 Feb 2019 07:17:12: 23000000 INFO @ Fri, 15 Feb 2019 07:17:12: 23000000 INFO @ Fri, 15 Feb 2019 07:17:15: 22000000 INFO @ Fri, 15 Feb 2019 07:17:19: 24000000 INFO @ Fri, 15 Feb 2019 07:17:19: 24000000 INFO @ Fri, 15 Feb 2019 07:17:22: 23000000 INFO @ Fri, 15 Feb 2019 07:17:25: 25000000 INFO @ Fri, 15 Feb 2019 07:17:25: 25000000 INFO @ Fri, 15 Feb 2019 07:17:28: 24000000 INFO @ Fri, 15 Feb 2019 07:17:31: 26000000 INFO @ Fri, 15 Feb 2019 07:17:31: 26000000 INFO @ Fri, 15 Feb 2019 07:17:35: 25000000 INFO @ Fri, 15 Feb 2019 07:17:37: 27000000 INFO @ Fri, 15 Feb 2019 07:17:37: 27000000 INFO @ Fri, 15 Feb 2019 07:17:41: 26000000 INFO @ Fri, 15 Feb 2019 07:17:44: 28000000 INFO @ Fri, 15 Feb 2019 07:17:44: 28000000 INFO @ Fri, 15 Feb 2019 07:17:48: 27000000 INFO @ Fri, 15 Feb 2019 07:17:50: 29000000 INFO @ Fri, 15 Feb 2019 07:17:50: 29000000 INFO @ Fri, 15 Feb 2019 07:17:54: 28000000 INFO @ Fri, 15 Feb 2019 07:17:56: 30000000 INFO @ Fri, 15 Feb 2019 07:17:56: 30000000 INFO @ Fri, 15 Feb 2019 07:18:01: 29000000 INFO @ Fri, 15 Feb 2019 07:18:02: 31000000 INFO @ Fri, 15 Feb 2019 07:18:02: 31000000 INFO @ Fri, 15 Feb 2019 07:18:07: 30000000 INFO @ Fri, 15 Feb 2019 07:18:09: 32000000 INFO @ Fri, 15 Feb 2019 07:18:09: 32000000 INFO @ Fri, 15 Feb 2019 07:18:14: 31000000 INFO @ Fri, 15 Feb 2019 07:18:15: 33000000 INFO @ Fri, 15 Feb 2019 07:18:15: 33000000 INFO @ Fri, 15 Feb 2019 07:18:20: 32000000 INFO @ Fri, 15 Feb 2019 07:18:21: 34000000 INFO @ Fri, 15 Feb 2019 07:18:21: 34000000 INFO @ Fri, 15 Feb 2019 07:18:27: 33000000 INFO @ Fri, 15 Feb 2019 07:18:28: 35000000 INFO @ Fri, 15 Feb 2019 07:18:28: 35000000 INFO @ Fri, 15 Feb 2019 07:18:33: 34000000 INFO @ Fri, 15 Feb 2019 07:18:34: 36000000 INFO @ Fri, 15 Feb 2019 07:18:34: 36000000 INFO @ Fri, 15 Feb 2019 07:18:40: 35000000 INFO @ Fri, 15 Feb 2019 07:18:40: 37000000 INFO @ Fri, 15 Feb 2019 07:18:40: 37000000 INFO @ Fri, 15 Feb 2019 07:18:46: 36000000 INFO @ Fri, 15 Feb 2019 07:18:46: 38000000 INFO @ Fri, 15 Feb 2019 07:18:47: 38000000 INFO @ Fri, 15 Feb 2019 07:18:53: 39000000 INFO @ Fri, 15 Feb 2019 07:18:53: 37000000 INFO @ Fri, 15 Feb 2019 07:18:53: 39000000 INFO @ Fri, 15 Feb 2019 07:18:59: 40000000 INFO @ Fri, 15 Feb 2019 07:19:00: 38000000 INFO @ Fri, 15 Feb 2019 07:19:00: 40000000 INFO @ Fri, 15 Feb 2019 07:19:06: 41000000 INFO @ Fri, 15 Feb 2019 07:19:06: 39000000 INFO @ Fri, 15 Feb 2019 07:19:06: 41000000 INFO @ Fri, 15 Feb 2019 07:19:13: 42000000 INFO @ Fri, 15 Feb 2019 07:19:13: 40000000 INFO @ Fri, 15 Feb 2019 07:19:13: 42000000 INFO @ Fri, 15 Feb 2019 07:19:14: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:19:14: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:19:14: #1 total tags in treatment: 42085591 INFO @ Fri, 15 Feb 2019 07:19:14: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:19:14: #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 07:19:14: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:19:14: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:19:14: #1 total tags in treatment: 42085591 INFO @ Fri, 15 Feb 2019 07:19:14: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:19:14: #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 07:19:15: #1 tags after filtering in treatment: 42085506 INFO @ Fri, 15 Feb 2019 07:19:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:19:15: #1 finished! INFO @ Fri, 15 Feb 2019 07:19:15: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:19:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:19:15: #1 tags after filtering in treatment: 42085506 INFO @ Fri, 15 Feb 2019 07:19:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:19:15: #1 finished! INFO @ Fri, 15 Feb 2019 07:19:15: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:19:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:19:18: #2 number of paired peaks: 4197 INFO @ Fri, 15 Feb 2019 07:19:18: start model_add_line... INFO @ Fri, 15 Feb 2019 07:19:19: start X-correlation... INFO @ Fri, 15 Feb 2019 07:19:19: end of X-cor INFO @ Fri, 15 Feb 2019 07:19:19: #2 finished! INFO @ Fri, 15 Feb 2019 07:19:19: #2 predicted fragment length is 40 bps INFO @ Fri, 15 Feb 2019 07:19:19: #2 alternative fragment length(s) may be 40,493,585 bps INFO @ Fri, 15 Feb 2019 07:19:19: #2.2 Generate R script for model : SRX3782482.05_model.r WARNING @ Fri, 15 Feb 2019 07:19:19: #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 07:19:19: #2 You may need to consider one of the other alternative d(s): 40,493,585 WARNING @ Fri, 15 Feb 2019 07:19:19: #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 07:19:19: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:19:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:19:19: #2 number of paired peaks: 4197 INFO @ Fri, 15 Feb 2019 07:19:19: start model_add_line... INFO @ Fri, 15 Feb 2019 07:19:19: 41000000 INFO @ Fri, 15 Feb 2019 07:19:19: start X-correlation... INFO @ Fri, 15 Feb 2019 07:19:19: end of X-cor INFO @ Fri, 15 Feb 2019 07:19:19: #2 finished! INFO @ Fri, 15 Feb 2019 07:19:19: #2 predicted fragment length is 40 bps INFO @ Fri, 15 Feb 2019 07:19:19: #2 alternative fragment length(s) may be 40,493,585 bps INFO @ Fri, 15 Feb 2019 07:19:19: #2.2 Generate R script for model : SRX3782482.10_model.r WARNING @ Fri, 15 Feb 2019 07:19:19: #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 07:19:19: #2 You may need to consider one of the other alternative d(s): 40,493,585 WARNING @ Fri, 15 Feb 2019 07:19:19: #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 07:19:19: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:19:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:19:25: 42000000 INFO @ Fri, 15 Feb 2019 07:19:26: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:19:26: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:19:26: #1 total tags in treatment: 42085591 INFO @ Fri, 15 Feb 2019 07:19:26: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:19:26: #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 07:19:27: #1 tags after filtering in treatment: 42085506 INFO @ Fri, 15 Feb 2019 07:19:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:19:27: #1 finished! INFO @ Fri, 15 Feb 2019 07:19:27: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:19:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:19:31: #2 number of paired peaks: 4197 INFO @ Fri, 15 Feb 2019 07:19:31: start model_add_line... INFO @ Fri, 15 Feb 2019 07:19:31: start X-correlation... INFO @ Fri, 15 Feb 2019 07:19:31: end of X-cor INFO @ Fri, 15 Feb 2019 07:19:31: #2 finished! INFO @ Fri, 15 Feb 2019 07:19:31: #2 predicted fragment length is 40 bps INFO @ Fri, 15 Feb 2019 07:19:31: #2 alternative fragment length(s) may be 40,493,585 bps INFO @ Fri, 15 Feb 2019 07:19:31: #2.2 Generate R script for model : SRX3782482.20_model.r WARNING @ Fri, 15 Feb 2019 07:19:31: #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 07:19:31: #2 You may need to consider one of the other alternative d(s): 40,493,585 WARNING @ Fri, 15 Feb 2019 07:19:31: #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 07:19:31: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:19:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:20:59: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:21:05: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:21:16: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:21:59: #4 Write output xls file... SRX3782482.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:21:59: #4 Write peak in narrowPeak format file... SRX3782482.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:21:59: #4 Write summits bed file... SRX3782482.05_summits.bed INFO @ Fri, 15 Feb 2019 07:21:59: Done! pass1 - making usageList (45 chroms): 11 millis pass2 - checking and writing primary data (1835 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:22:04: #4 Write output xls file... SRX3782482.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:22:04: #4 Write peak in narrowPeak format file... SRX3782482.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:22:04: #4 Write summits bed file... SRX3782482.10_summits.bed INFO @ Fri, 15 Feb 2019 07:22:04: Done! pass1 - making usageList (38 chroms): 9 millis pass2 - checking and writing primary data (1039 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:22:20: #4 Write output xls file... SRX3782482.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:22:20: #4 Write peak in narrowPeak format file... SRX3782482.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:22:20: #4 Write summits bed file... SRX3782482.20_summits.bed INFO @ Fri, 15 Feb 2019 07:22:20: Done! pass1 - making usageList (28 chroms): 7 millis pass2 - checking and writing primary data (447 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。