Job ID = 10487589 sra ファイルのダウンロード中... Completed: 3993264K bytes transferred in 149 seconds (218566K 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 59189111 spots for /home/okishinya/chipatlas/results/rn6/SRX2611112/SRR5311156.sra Written 59189111 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: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 03:15:40 59189111 reads; of these: 59189111 (100.00%) were unpaired; of these: 17279911 (29.19%) aligned 0 times 31695988 (53.55%) aligned exactly 1 time 10213212 (17.26%) aligned >1 times 70.81% overall alignment rate Time searching: 03:15:42 Overall time: 03:15:42 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 32 files... [bam_rmdupse_core] 10667946 / 41909200 = 0.2545 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 13:24:03: # Command line: callpeak -t SRX2611112.bam -f BAM -g 2.15e9 -n SRX2611112.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2611112.05 # format = BAM # ChIP-seq file = ['SRX2611112.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 13:24:03: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:24:03: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:24:03: # Command line: callpeak -t SRX2611112.bam -f BAM -g 2.15e9 -n SRX2611112.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2611112.20 # format = BAM # ChIP-seq file = ['SRX2611112.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 13:24:03: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:24:03: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:24:03: # Command line: callpeak -t SRX2611112.bam -f BAM -g 2.15e9 -n SRX2611112.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2611112.10 # format = BAM # ChIP-seq file = ['SRX2611112.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 13:24:03: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:24:03: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:24:14: 1000000 INFO @ Sun, 18 Mar 2018 13:24:15: 1000000 INFO @ Sun, 18 Mar 2018 13:24:15: 1000000 INFO @ Sun, 18 Mar 2018 13:24:25: 2000000 INFO @ Sun, 18 Mar 2018 13:24:27: 2000000 INFO @ Sun, 18 Mar 2018 13:24:27: 2000000 INFO @ Sun, 18 Mar 2018 13:24:36: 3000000 INFO @ Sun, 18 Mar 2018 13:24:38: 3000000 INFO @ Sun, 18 Mar 2018 13:24:38: 3000000 INFO @ Sun, 18 Mar 2018 13:24:47: 4000000 INFO @ Sun, 18 Mar 2018 13:24:50: 4000000 INFO @ Sun, 18 Mar 2018 13:24:50: 4000000 INFO @ Sun, 18 Mar 2018 13:24:58: 5000000 INFO @ Sun, 18 Mar 2018 13:25:02: 5000000 INFO @ Sun, 18 Mar 2018 13:25:02: 5000000 INFO @ Sun, 18 Mar 2018 13:25:10: 6000000 INFO @ Sun, 18 Mar 2018 13:25:13: 6000000 INFO @ Sun, 18 Mar 2018 13:25:14: 6000000 INFO @ Sun, 18 Mar 2018 13:25:22: 7000000 INFO @ Sun, 18 Mar 2018 13:25:24: 7000000 INFO @ Sun, 18 Mar 2018 13:25:26: 7000000 INFO @ Sun, 18 Mar 2018 13:25:34: 8000000 INFO @ Sun, 18 Mar 2018 13:25:36: 8000000 INFO @ Sun, 18 Mar 2018 13:25:38: 8000000 INFO @ Sun, 18 Mar 2018 13:25:45: 9000000 INFO @ Sun, 18 Mar 2018 13:25:47: 9000000 INFO @ Sun, 18 Mar 2018 13:25:50: 9000000 INFO @ Sun, 18 Mar 2018 13:25:57: 10000000 INFO @ Sun, 18 Mar 2018 13:25:59: 10000000 INFO @ Sun, 18 Mar 2018 13:26:02: 10000000 INFO @ Sun, 18 Mar 2018 13:26:08: 11000000 INFO @ Sun, 18 Mar 2018 13:26:10: 11000000 INFO @ Sun, 18 Mar 2018 13:26:14: 11000000 INFO @ Sun, 18 Mar 2018 13:26:19: 12000000 INFO @ Sun, 18 Mar 2018 13:26:22: 12000000 INFO @ Sun, 18 Mar 2018 13:26:26: 12000000 INFO @ Sun, 18 Mar 2018 13:26:31: 13000000 INFO @ Sun, 18 Mar 2018 13:26:34: 13000000 INFO @ Sun, 18 Mar 2018 13:26:38: 13000000 INFO @ Sun, 18 Mar 2018 13:26:43: 14000000 INFO @ Sun, 18 Mar 2018 13:26:45: 14000000 INFO @ Sun, 18 Mar 2018 13:26:51: 14000000 INFO @ Sun, 18 Mar 2018 13:26:55: 15000000 INFO @ Sun, 18 Mar 2018 13:26:56: 15000000 INFO @ Sun, 18 Mar 2018 13:27:03: 15000000 INFO @ Sun, 18 Mar 2018 13:27:07: 16000000 INFO @ Sun, 18 Mar 2018 13:27:07: 16000000 INFO @ Sun, 18 Mar 2018 13:27:15: 16000000 INFO @ Sun, 18 Mar 2018 13:27:19: 17000000 INFO @ Sun, 18 Mar 2018 13:27:19: 17000000 INFO @ Sun, 18 Mar 2018 13:27:28: 17000000 INFO @ Sun, 18 Mar 2018 13:27:30: 18000000 INFO @ Sun, 18 Mar 2018 13:27:31: 18000000 INFO @ Sun, 18 Mar 2018 13:27:40: 18000000 INFO @ Sun, 18 Mar 2018 13:27:41: 19000000 INFO @ Sun, 18 Mar 2018 13:27:43: 19000000 INFO @ Sun, 18 Mar 2018 13:27:52: 20000000 INFO @ Sun, 18 Mar 2018 13:27:52: 19000000 INFO @ Sun, 18 Mar 2018 13:27:55: 20000000 INFO @ Sun, 18 Mar 2018 13:28:04: 21000000 INFO @ Sun, 18 Mar 2018 13:28:04: 20000000 INFO @ Sun, 18 Mar 2018 13:28:06: 21000000 INFO @ Sun, 18 Mar 2018 13:28:16: 22000000 INFO @ Sun, 18 Mar 2018 13:28:16: 21000000 INFO @ Sun, 18 Mar 2018 13:28:17: 22000000 INFO @ Sun, 18 Mar 2018 13:28:27: 23000000 INFO @ Sun, 18 Mar 2018 13:28:28: 22000000 INFO @ Sun, 18 Mar 2018 13:28:29: 23000000 INFO @ Sun, 18 Mar 2018 13:28:39: 24000000 INFO @ Sun, 18 Mar 2018 13:28:40: 23000000 INFO @ Sun, 18 Mar 2018 13:28:41: 24000000 INFO @ Sun, 18 Mar 2018 13:28:50: 25000000 INFO @ Sun, 18 Mar 2018 13:28:53: 24000000 INFO @ Sun, 18 Mar 2018 13:28:53: 25000000 INFO @ Sun, 18 Mar 2018 13:29:02: 26000000 INFO @ Sun, 18 Mar 2018 13:29:05: 26000000 INFO @ Sun, 18 Mar 2018 13:29:05: 25000000 INFO @ Sun, 18 Mar 2018 13:29:13: 27000000 INFO @ Sun, 18 Mar 2018 13:29:17: 27000000 INFO @ Sun, 18 Mar 2018 13:29:17: 26000000 INFO @ Sun, 18 Mar 2018 13:29:24: 28000000 INFO @ Sun, 18 Mar 2018 13:29:29: 28000000 INFO @ Sun, 18 Mar 2018 13:29:30: 27000000 INFO @ Sun, 18 Mar 2018 13:29:36: 29000000 INFO @ Sun, 18 Mar 2018 13:29:40: 29000000 INFO @ Sun, 18 Mar 2018 13:29:42: 28000000 INFO @ Sun, 18 Mar 2018 13:29:48: 30000000 INFO @ Sun, 18 Mar 2018 13:29:51: 30000000 INFO @ Sun, 18 Mar 2018 13:29:53: 29000000 INFO @ Sun, 18 Mar 2018 13:30:00: 31000000 INFO @ Sun, 18 Mar 2018 13:30:02: 31000000 INFO @ Sun, 18 Mar 2018 13:30:03: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:30:03: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:30:03: #1 total tags in treatment: 31241254 INFO @ Sun, 18 Mar 2018 13:30:03: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:30:03: #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 13:30:04: #1 tags after filtering in treatment: 31241164 INFO @ Sun, 18 Mar 2018 13:30:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:30:04: #1 finished! INFO @ Sun, 18 Mar 2018 13:30:04: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:30:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:30:05: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:30:05: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:30:05: #1 total tags in treatment: 31241254 INFO @ Sun, 18 Mar 2018 13:30:05: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:30:05: #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 13:30:05: 30000000 INFO @ Sun, 18 Mar 2018 13:30:06: #1 tags after filtering in treatment: 31241164 INFO @ Sun, 18 Mar 2018 13:30:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:30:06: #1 finished! INFO @ Sun, 18 Mar 2018 13:30:06: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:30:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:30:07: #2 number of paired peaks: 7529 INFO @ Sun, 18 Mar 2018 13:30:07: start model_add_line... INFO @ Sun, 18 Mar 2018 13:30:07: start X-correlation... INFO @ Sun, 18 Mar 2018 13:30:07: end of X-cor INFO @ Sun, 18 Mar 2018 13:30:07: #2 finished! INFO @ Sun, 18 Mar 2018 13:30:07: #2 predicted fragment length is 148 bps INFO @ Sun, 18 Mar 2018 13:30:07: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 18 Mar 2018 13:30:07: #2.2 Generate R script for model : SRX2611112.05_model.r WARNING @ Sun, 18 Mar 2018 13:30:07: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 13:30:07: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Sun, 18 Mar 2018 13:30:07: #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 13:30:07: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:30:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:30:09: #2 number of paired peaks: 7529 INFO @ Sun, 18 Mar 2018 13:30:09: start model_add_line... INFO @ Sun, 18 Mar 2018 13:30:09: start X-correlation... INFO @ Sun, 18 Mar 2018 13:30:09: end of X-cor INFO @ Sun, 18 Mar 2018 13:30:09: #2 finished! INFO @ Sun, 18 Mar 2018 13:30:09: #2 predicted fragment length is 148 bps INFO @ Sun, 18 Mar 2018 13:30:09: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 18 Mar 2018 13:30:09: #2.2 Generate R script for model : SRX2611112.10_model.r WARNING @ Sun, 18 Mar 2018 13:30:09: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 13:30:09: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Sun, 18 Mar 2018 13:30:09: #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 13:30:09: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:30:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:30:16: 31000000 INFO @ Sun, 18 Mar 2018 13:30:18: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:30:18: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:30:18: #1 total tags in treatment: 31241254 INFO @ Sun, 18 Mar 2018 13:30:18: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:30:18: #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 13:30:19: #1 tags after filtering in treatment: 31241164 INFO @ Sun, 18 Mar 2018 13:30:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:30:19: #1 finished! INFO @ Sun, 18 Mar 2018 13:30:19: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:30:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:30:22: #2 number of paired peaks: 7529 INFO @ Sun, 18 Mar 2018 13:30:22: start model_add_line... INFO @ Sun, 18 Mar 2018 13:30:23: start X-correlation... INFO @ Sun, 18 Mar 2018 13:30:23: end of X-cor INFO @ Sun, 18 Mar 2018 13:30:23: #2 finished! INFO @ Sun, 18 Mar 2018 13:30:23: #2 predicted fragment length is 148 bps INFO @ Sun, 18 Mar 2018 13:30:23: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 18 Mar 2018 13:30:23: #2.2 Generate R script for model : SRX2611112.20_model.r WARNING @ Sun, 18 Mar 2018 13:30:23: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 13:30:23: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Sun, 18 Mar 2018 13:30:23: #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 13:30:23: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:30:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:31:23: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:31:27: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:31:47: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:32:06: #4 Write output xls file... SRX2611112.10_peaks.xls INFO @ Sun, 18 Mar 2018 13:32:06: #4 Write peak in narrowPeak format file... SRX2611112.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:32:06: #4 Write summits bed file... SRX2611112.10_summits.bed INFO @ Sun, 18 Mar 2018 13:32:06: Done! pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (1664 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 13:32:14: #4 Write output xls file... SRX2611112.05_peaks.xls INFO @ Sun, 18 Mar 2018 13:32:14: #4 Write peak in narrowPeak format file... SRX2611112.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:32:14: #4 Write summits bed file... SRX2611112.05_summits.bed INFO @ Sun, 18 Mar 2018 13:32:14: Done! pass1 - making usageList (70 chroms): 1 millis pass2 - checking and writing primary data (3641 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 13:32:33: #4 Write output xls file... SRX2611112.20_peaks.xls INFO @ Sun, 18 Mar 2018 13:32:33: #4 Write peak in narrowPeak format file... SRX2611112.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:32:33: #4 Write summits bed file... SRX2611112.20_summits.bed INFO @ Sun, 18 Mar 2018 13:32:33: Done! pass1 - making usageList (39 chroms): 1 millis pass2 - checking and writing primary data (801 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。