Job ID = 10487598 sra ファイルのダウンロード中... Completed: 4013395K bytes transferred in 140 seconds (233707K 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 59555599 spots for /home/okishinya/chipatlas/results/rn6/SRX2611120/SRR5311164.sra Written 59555599 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: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 02:59:52 59555599 reads; of these: 59555599 (100.00%) were unpaired; of these: 24558019 (41.24%) aligned 0 times 30144988 (50.62%) aligned exactly 1 time 4852592 (8.15%) aligned >1 times 58.76% overall alignment rate Time searching: 02:59:54 Overall time: 02:59:54 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 28 files... [bam_rmdupse_core] 9382845 / 34997580 = 0.2681 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 @ Sun, 18 Mar 2018 13:11:31: # Command line: callpeak -t SRX2611120.bam -f BAM -g 2.15e9 -n SRX2611120.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2611120.20 # format = BAM # ChIP-seq file = ['SRX2611120.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 @ Sun, 18 Mar 2018 13:11:31: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:11:31: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:11:31: # Command line: callpeak -t SRX2611120.bam -f BAM -g 2.15e9 -n SRX2611120.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2611120.05 # format = BAM # ChIP-seq file = ['SRX2611120.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 @ Sun, 18 Mar 2018 13:11:31: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:11:31: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:11:31: # Command line: callpeak -t SRX2611120.bam -f BAM -g 2.15e9 -n SRX2611120.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2611120.10 # format = BAM # ChIP-seq file = ['SRX2611120.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 @ Sun, 18 Mar 2018 13:11:31: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:11:31: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:11:40: 1000000 INFO @ Sun, 18 Mar 2018 13:11:41: 1000000 INFO @ Sun, 18 Mar 2018 13:11:41: 1000000 INFO @ Sun, 18 Mar 2018 13:11:50: 2000000 INFO @ Sun, 18 Mar 2018 13:11:50: 2000000 INFO @ Sun, 18 Mar 2018 13:11:51: 2000000 INFO @ Sun, 18 Mar 2018 13:11:59: 3000000 INFO @ Sun, 18 Mar 2018 13:12:00: 3000000 INFO @ Sun, 18 Mar 2018 13:12:01: 3000000 INFO @ Sun, 18 Mar 2018 13:12:09: 4000000 INFO @ Sun, 18 Mar 2018 13:12:10: 4000000 INFO @ Sun, 18 Mar 2018 13:12:10: 4000000 INFO @ Sun, 18 Mar 2018 13:12:18: 5000000 INFO @ Sun, 18 Mar 2018 13:12:19: 5000000 INFO @ Sun, 18 Mar 2018 13:12:21: 5000000 INFO @ Sun, 18 Mar 2018 13:12:27: 6000000 INFO @ Sun, 18 Mar 2018 13:12:29: 6000000 INFO @ Sun, 18 Mar 2018 13:12:31: 6000000 INFO @ Sun, 18 Mar 2018 13:12:37: 7000000 INFO @ Sun, 18 Mar 2018 13:12:39: 7000000 INFO @ Sun, 18 Mar 2018 13:12:41: 7000000 INFO @ Sun, 18 Mar 2018 13:12:46: 8000000 INFO @ Sun, 18 Mar 2018 13:12:48: 8000000 INFO @ Sun, 18 Mar 2018 13:12:51: 8000000 INFO @ Sun, 18 Mar 2018 13:12:56: 9000000 INFO @ Sun, 18 Mar 2018 13:12:58: 9000000 INFO @ Sun, 18 Mar 2018 13:13:03: 9000000 INFO @ Sun, 18 Mar 2018 13:13:05: 10000000 INFO @ Sun, 18 Mar 2018 13:13:08: 10000000 INFO @ Sun, 18 Mar 2018 13:13:13: 10000000 INFO @ Sun, 18 Mar 2018 13:13:14: 11000000 INFO @ Sun, 18 Mar 2018 13:13:18: 11000000 INFO @ Sun, 18 Mar 2018 13:13:23: 11000000 INFO @ Sun, 18 Mar 2018 13:13:24: 12000000 INFO @ Sun, 18 Mar 2018 13:13:28: 12000000 INFO @ Sun, 18 Mar 2018 13:13:33: 13000000 INFO @ Sun, 18 Mar 2018 13:13:33: 12000000 INFO @ Sun, 18 Mar 2018 13:13:37: 13000000 INFO @ Sun, 18 Mar 2018 13:13:43: 14000000 INFO @ Sun, 18 Mar 2018 13:13:44: 13000000 INFO @ Sun, 18 Mar 2018 13:13:47: 14000000 INFO @ Sun, 18 Mar 2018 13:13:52: 15000000 INFO @ Sun, 18 Mar 2018 13:13:54: 14000000 INFO @ Sun, 18 Mar 2018 13:13:57: 15000000 INFO @ Sun, 18 Mar 2018 13:14:01: 16000000 INFO @ Sun, 18 Mar 2018 13:14:04: 15000000 INFO @ Sun, 18 Mar 2018 13:14:06: 16000000 INFO @ Sun, 18 Mar 2018 13:14:11: 17000000 INFO @ Sun, 18 Mar 2018 13:14:15: 16000000 INFO @ Sun, 18 Mar 2018 13:14:16: 17000000 INFO @ Sun, 18 Mar 2018 13:14:20: 18000000 INFO @ Sun, 18 Mar 2018 13:14:25: 17000000 INFO @ Sun, 18 Mar 2018 13:14:26: 18000000 INFO @ Sun, 18 Mar 2018 13:14:30: 19000000 INFO @ Sun, 18 Mar 2018 13:14:36: 18000000 INFO @ Sun, 18 Mar 2018 13:14:36: 19000000 INFO @ Sun, 18 Mar 2018 13:14:41: 20000000 INFO @ Sun, 18 Mar 2018 13:14:46: 20000000 INFO @ Sun, 18 Mar 2018 13:14:46: 19000000 INFO @ Sun, 18 Mar 2018 13:14:50: 21000000 INFO @ Sun, 18 Mar 2018 13:14:55: 21000000 INFO @ Sun, 18 Mar 2018 13:14:56: 20000000 INFO @ Sun, 18 Mar 2018 13:15:00: 22000000 INFO @ Sun, 18 Mar 2018 13:15:05: 22000000 INFO @ Sun, 18 Mar 2018 13:15:07: 21000000 INFO @ Sun, 18 Mar 2018 13:15:11: 23000000 INFO @ Sun, 18 Mar 2018 13:15:15: 23000000 INFO @ Sun, 18 Mar 2018 13:15:18: 22000000 INFO @ Sun, 18 Mar 2018 13:15:20: 24000000 INFO @ Sun, 18 Mar 2018 13:15:25: 24000000 INFO @ Sun, 18 Mar 2018 13:15:29: 23000000 INFO @ Sun, 18 Mar 2018 13:15:31: 25000000 INFO @ Sun, 18 Mar 2018 13:15:35: 25000000 INFO @ Sun, 18 Mar 2018 13:15:38: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:15:38: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:15:38: #1 total tags in treatment: 25614735 INFO @ Sun, 18 Mar 2018 13:15:38: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:15:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 13:15:38: #1 tags after filtering in treatment: 25614611 INFO @ Sun, 18 Mar 2018 13:15:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:15:38: #1 finished! INFO @ Sun, 18 Mar 2018 13:15:38: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:15:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:15:39: 24000000 INFO @ Sun, 18 Mar 2018 13:15:41: #2 number of paired peaks: 6361 INFO @ Sun, 18 Mar 2018 13:15:41: start model_add_line... INFO @ Sun, 18 Mar 2018 13:15:41: start X-correlation... INFO @ Sun, 18 Mar 2018 13:15:41: end of X-cor INFO @ Sun, 18 Mar 2018 13:15:41: #2 finished! INFO @ Sun, 18 Mar 2018 13:15:41: #2 predicted fragment length is 156 bps INFO @ Sun, 18 Mar 2018 13:15:41: #2 alternative fragment length(s) may be 156 bps INFO @ Sun, 18 Mar 2018 13:15:41: #2.2 Generate R script for model : SRX2611120.05_model.r WARNING @ Sun, 18 Mar 2018 13:15:41: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 13:15:41: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Sun, 18 Mar 2018 13:15:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 13:15:41: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:15:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:15:41: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:15:41: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:15:41: #1 total tags in treatment: 25614735 INFO @ Sun, 18 Mar 2018 13:15:41: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:15:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 13:15:42: #1 tags after filtering in treatment: 25614611 INFO @ Sun, 18 Mar 2018 13:15:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:15:42: #1 finished! INFO @ Sun, 18 Mar 2018 13:15:42: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:15:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:15:45: #2 number of paired peaks: 6361 INFO @ Sun, 18 Mar 2018 13:15:45: start model_add_line... INFO @ Sun, 18 Mar 2018 13:15:45: start X-correlation... INFO @ Sun, 18 Mar 2018 13:15:45: end of X-cor INFO @ Sun, 18 Mar 2018 13:15:45: #2 finished! INFO @ Sun, 18 Mar 2018 13:15:45: #2 predicted fragment length is 156 bps INFO @ Sun, 18 Mar 2018 13:15:45: #2 alternative fragment length(s) may be 156 bps INFO @ Sun, 18 Mar 2018 13:15:45: #2.2 Generate R script for model : SRX2611120.20_model.r WARNING @ Sun, 18 Mar 2018 13:15:45: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 13:15:45: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Sun, 18 Mar 2018 13:15:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 13:15:45: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:15:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:15:49: 25000000 INFO @ Sun, 18 Mar 2018 13:15:55: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:15:55: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:15:55: #1 total tags in treatment: 25614735 INFO @ Sun, 18 Mar 2018 13:15:55: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:15:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 13:15:56: #1 tags after filtering in treatment: 25614611 INFO @ Sun, 18 Mar 2018 13:15:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:15:56: #1 finished! INFO @ Sun, 18 Mar 2018 13:15:56: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:15:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:15:58: #2 number of paired peaks: 6361 INFO @ Sun, 18 Mar 2018 13:15:58: start model_add_line... INFO @ Sun, 18 Mar 2018 13:15:59: start X-correlation... INFO @ Sun, 18 Mar 2018 13:15:59: end of X-cor INFO @ Sun, 18 Mar 2018 13:15:59: #2 finished! INFO @ Sun, 18 Mar 2018 13:15:59: #2 predicted fragment length is 156 bps INFO @ Sun, 18 Mar 2018 13:15:59: #2 alternative fragment length(s) may be 156 bps INFO @ Sun, 18 Mar 2018 13:15:59: #2.2 Generate R script for model : SRX2611120.10_model.r WARNING @ Sun, 18 Mar 2018 13:15:59: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 13:15:59: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Sun, 18 Mar 2018 13:15:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 13:15:59: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:15:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:16:45: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:16:50: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:17:05: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:17:18: #4 Write output xls file... SRX2611120.05_peaks.xls INFO @ Sun, 18 Mar 2018 13:17:18: #4 Write peak in narrowPeak format file... SRX2611120.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:17:18: #4 Write summits bed file... SRX2611120.05_summits.bed INFO @ Sun, 18 Mar 2018 13:17:18: Done! pass1 - making usageList (47 chroms): 1 millis pass2 - checking and writing primary data (1324 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 13:17:25: #4 Write output xls file... SRX2611120.20_peaks.xls INFO @ Sun, 18 Mar 2018 13:17:25: #4 Write peak in narrowPeak format file... SRX2611120.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:17:25: #4 Write summits bed file... SRX2611120.20_summits.bed INFO @ Sun, 18 Mar 2018 13:17:25: Done! pass1 - making usageList (33 chroms): 1 millis pass2 - checking and writing primary data (279 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 13:17:40: #4 Write output xls file... SRX2611120.10_peaks.xls INFO @ Sun, 18 Mar 2018 13:17:40: #4 Write peak in narrowPeak format file... SRX2611120.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:17:40: #4 Write summits bed file... SRX2611120.10_summits.bed INFO @ Sun, 18 Mar 2018 13:17:40: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (589 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。