Job ID = 10194838 sra ファイルのダウンロード中... Completed: 908763K bytes transferred in 20 seconds (370857K 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 48727199 spots for /home/okishinya/chipatlas/results/rn6/SRX1977127/SRR3952259.sra Written 48727199 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: 01:27:12 48727199 reads; of these: 48727199 (100.00%) were unpaired; of these: 9668039 (19.84%) aligned 0 times 21330775 (43.78%) aligned exactly 1 time 17728385 (36.38%) aligned >1 times 80.16% overall alignment rate Time searching: 01:27:15 Overall time: 01:27:15 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 16 files... [bam_rmdupse_core] 5259038 / 39059160 = 0.1346 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 @ Sat, 11 Nov 2017 03:25:43: # Command line: callpeak -t SRX1977127.bam -f BAM -g 2.15e9 -n SRX1977127.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1977127.05 # format = BAM # ChIP-seq file = ['SRX1977127.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 @ Sat, 11 Nov 2017 03:25:43: # Command line: callpeak -t SRX1977127.bam -f BAM -g 2.15e9 -n SRX1977127.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1977127.10 # format = BAM # ChIP-seq file = ['SRX1977127.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 @ Sat, 11 Nov 2017 03:25:43: # Command line: callpeak -t SRX1977127.bam -f BAM -g 2.15e9 -n SRX1977127.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1977127.20 # format = BAM # ChIP-seq file = ['SRX1977127.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 @ Sat, 11 Nov 2017 03:25:43: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:25:43: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:25:43: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:25:43: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:25:43: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:25:43: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:25:50: 1000000 INFO @ Sat, 11 Nov 2017 03:25:50: 1000000 INFO @ Sat, 11 Nov 2017 03:25:50: 1000000 INFO @ Sat, 11 Nov 2017 03:25:56: 2000000 INFO @ Sat, 11 Nov 2017 03:25:56: 2000000 INFO @ Sat, 11 Nov 2017 03:25:56: 2000000 INFO @ Sat, 11 Nov 2017 03:26:03: 3000000 INFO @ Sat, 11 Nov 2017 03:26:03: 3000000 INFO @ Sat, 11 Nov 2017 03:26:03: 3000000 INFO @ Sat, 11 Nov 2017 03:26:10: 4000000 INFO @ Sat, 11 Nov 2017 03:26:10: 4000000 INFO @ Sat, 11 Nov 2017 03:26:10: 4000000 INFO @ Sat, 11 Nov 2017 03:26:16: 5000000 INFO @ Sat, 11 Nov 2017 03:26:16: 5000000 INFO @ Sat, 11 Nov 2017 03:26:16: 5000000 INFO @ Sat, 11 Nov 2017 03:26:23: 6000000 INFO @ Sat, 11 Nov 2017 03:26:23: 6000000 INFO @ Sat, 11 Nov 2017 03:26:23: 6000000 INFO @ Sat, 11 Nov 2017 03:26:29: 7000000 INFO @ Sat, 11 Nov 2017 03:26:29: 7000000 INFO @ Sat, 11 Nov 2017 03:26:29: 7000000 INFO @ Sat, 11 Nov 2017 03:26:36: 8000000 INFO @ Sat, 11 Nov 2017 03:26:36: 8000000 INFO @ Sat, 11 Nov 2017 03:26:36: 8000000 INFO @ Sat, 11 Nov 2017 03:26:43: 9000000 INFO @ Sat, 11 Nov 2017 03:26:43: 9000000 INFO @ Sat, 11 Nov 2017 03:26:43: 9000000 INFO @ Sat, 11 Nov 2017 03:26:49: 10000000 INFO @ Sat, 11 Nov 2017 03:26:49: 10000000 INFO @ Sat, 11 Nov 2017 03:26:50: 10000000 INFO @ Sat, 11 Nov 2017 03:26:56: 11000000 INFO @ Sat, 11 Nov 2017 03:26:56: 11000000 INFO @ Sat, 11 Nov 2017 03:26:57: 11000000 INFO @ Sat, 11 Nov 2017 03:27:02: 12000000 INFO @ Sat, 11 Nov 2017 03:27:03: 12000000 INFO @ Sat, 11 Nov 2017 03:27:04: 12000000 INFO @ Sat, 11 Nov 2017 03:27:08: 13000000 INFO @ Sat, 11 Nov 2017 03:27:10: 13000000 INFO @ Sat, 11 Nov 2017 03:27:12: 13000000 INFO @ Sat, 11 Nov 2017 03:27:15: 14000000 INFO @ Sat, 11 Nov 2017 03:27:17: 14000000 INFO @ Sat, 11 Nov 2017 03:27:19: 14000000 INFO @ Sat, 11 Nov 2017 03:27:21: 15000000 INFO @ Sat, 11 Nov 2017 03:27:24: 15000000 INFO @ Sat, 11 Nov 2017 03:27:27: 15000000 INFO @ Sat, 11 Nov 2017 03:27:28: 16000000 INFO @ Sat, 11 Nov 2017 03:27:31: 16000000 INFO @ Sat, 11 Nov 2017 03:27:34: 17000000 INFO @ Sat, 11 Nov 2017 03:27:35: 16000000 INFO @ Sat, 11 Nov 2017 03:27:39: 17000000 INFO @ Sat, 11 Nov 2017 03:27:41: 18000000 INFO @ Sat, 11 Nov 2017 03:27:42: 17000000 INFO @ Sat, 11 Nov 2017 03:27:46: 18000000 INFO @ Sat, 11 Nov 2017 03:27:47: 19000000 INFO @ Sat, 11 Nov 2017 03:27:50: 18000000 INFO @ Sat, 11 Nov 2017 03:27:53: 19000000 INFO @ Sat, 11 Nov 2017 03:27:53: 20000000 INFO @ Sat, 11 Nov 2017 03:27:58: 19000000 INFO @ Sat, 11 Nov 2017 03:28:00: 21000000 INFO @ Sat, 11 Nov 2017 03:28:00: 20000000 INFO @ Sat, 11 Nov 2017 03:28:05: 20000000 INFO @ Sat, 11 Nov 2017 03:28:06: 22000000 INFO @ Sat, 11 Nov 2017 03:28:07: 21000000 INFO @ Sat, 11 Nov 2017 03:28:13: 21000000 INFO @ Sat, 11 Nov 2017 03:28:13: 23000000 INFO @ Sat, 11 Nov 2017 03:28:14: 22000000 INFO @ Sat, 11 Nov 2017 03:28:19: 24000000 INFO @ Sat, 11 Nov 2017 03:28:19: 22000000 INFO @ Sat, 11 Nov 2017 03:28:20: 23000000 INFO @ Sat, 11 Nov 2017 03:28:26: 25000000 INFO @ Sat, 11 Nov 2017 03:28:26: 23000000 INFO @ Sat, 11 Nov 2017 03:28:27: 24000000 INFO @ Sat, 11 Nov 2017 03:28:33: 24000000 INFO @ Sat, 11 Nov 2017 03:28:33: 26000000 INFO @ Sat, 11 Nov 2017 03:28:33: 25000000 INFO @ Sat, 11 Nov 2017 03:28:39: 25000000 INFO @ Sat, 11 Nov 2017 03:28:40: 27000000 INFO @ Sat, 11 Nov 2017 03:28:40: 26000000 INFO @ Sat, 11 Nov 2017 03:28:46: 27000000 INFO @ Sat, 11 Nov 2017 03:28:46: 26000000 INFO @ Sat, 11 Nov 2017 03:28:46: 28000000 INFO @ Sat, 11 Nov 2017 03:28:53: 28000000 INFO @ Sat, 11 Nov 2017 03:28:53: 27000000 INFO @ Sat, 11 Nov 2017 03:28:53: 29000000 INFO @ Sat, 11 Nov 2017 03:28:59: 29000000 INFO @ Sat, 11 Nov 2017 03:29:00: 28000000 INFO @ Sat, 11 Nov 2017 03:29:00: 30000000 INFO @ Sat, 11 Nov 2017 03:29:05: 30000000 INFO @ Sat, 11 Nov 2017 03:29:06: 29000000 INFO @ Sat, 11 Nov 2017 03:29:06: 31000000 INFO @ Sat, 11 Nov 2017 03:29:12: 31000000 INFO @ Sat, 11 Nov 2017 03:29:13: 30000000 INFO @ Sat, 11 Nov 2017 03:29:13: 32000000 INFO @ Sat, 11 Nov 2017 03:29:19: 32000000 INFO @ Sat, 11 Nov 2017 03:29:20: 31000000 INFO @ Sat, 11 Nov 2017 03:29:20: 33000000 INFO @ Sat, 11 Nov 2017 03:29:25: 33000000 INFO @ Sat, 11 Nov 2017 03:29:26: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:29:26: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:29:26: #1 total tags in treatment: 33800122 INFO @ Sat, 11 Nov 2017 03:29:26: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:29:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 03:29:26: #1 tags after filtering in treatment: 33800058 INFO @ Sat, 11 Nov 2017 03:29:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:29:26: #1 finished! INFO @ Sat, 11 Nov 2017 03:29:26: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:29:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:29:26: 32000000 INFO @ Sat, 11 Nov 2017 03:29:30: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:29:30: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:29:30: #1 total tags in treatment: 33800122 INFO @ Sat, 11 Nov 2017 03:29:30: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:29:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 03:29:31: #2 number of paired peaks: 36614 INFO @ Sat, 11 Nov 2017 03:29:31: start model_add_line... INFO @ Sat, 11 Nov 2017 03:29:31: #1 tags after filtering in treatment: 33800058 INFO @ Sat, 11 Nov 2017 03:29:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:29:31: #1 finished! INFO @ Sat, 11 Nov 2017 03:29:31: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:29:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:29:32: start X-correlation... INFO @ Sat, 11 Nov 2017 03:29:32: end of X-cor INFO @ Sat, 11 Nov 2017 03:29:32: #2 finished! INFO @ Sat, 11 Nov 2017 03:29:32: #2 predicted fragment length is 168 bps INFO @ Sat, 11 Nov 2017 03:29:32: #2 alternative fragment length(s) may be 168 bps INFO @ Sat, 11 Nov 2017 03:29:32: #2.2 Generate R script for model : SRX1977127.20_model.r INFO @ Sat, 11 Nov 2017 03:29:32: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:29:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:29:33: 33000000 INFO @ Sat, 11 Nov 2017 03:29:36: #2 number of paired peaks: 36614 INFO @ Sat, 11 Nov 2017 03:29:36: start model_add_line... INFO @ Sat, 11 Nov 2017 03:29:36: start X-correlation... INFO @ Sat, 11 Nov 2017 03:29:36: end of X-cor INFO @ Sat, 11 Nov 2017 03:29:36: #2 finished! INFO @ Sat, 11 Nov 2017 03:29:36: #2 predicted fragment length is 168 bps INFO @ Sat, 11 Nov 2017 03:29:36: #2 alternative fragment length(s) may be 168 bps INFO @ Sat, 11 Nov 2017 03:29:36: #2.2 Generate R script for model : SRX1977127.05_model.r INFO @ Sat, 11 Nov 2017 03:29:36: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:29:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:29:38: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:29:38: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:29:38: #1 total tags in treatment: 33800122 INFO @ Sat, 11 Nov 2017 03:29:38: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:29:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 03:29:39: #1 tags after filtering in treatment: 33800058 INFO @ Sat, 11 Nov 2017 03:29:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:29:39: #1 finished! INFO @ Sat, 11 Nov 2017 03:29:39: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:29:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:29:44: #2 number of paired peaks: 36614 INFO @ Sat, 11 Nov 2017 03:29:44: start model_add_line... INFO @ Sat, 11 Nov 2017 03:29:45: start X-correlation... INFO @ Sat, 11 Nov 2017 03:29:45: end of X-cor INFO @ Sat, 11 Nov 2017 03:29:45: #2 finished! INFO @ Sat, 11 Nov 2017 03:29:45: #2 predicted fragment length is 168 bps INFO @ Sat, 11 Nov 2017 03:29:45: #2 alternative fragment length(s) may be 168 bps INFO @ Sat, 11 Nov 2017 03:29:45: #2.2 Generate R script for model : SRX1977127.10_model.r INFO @ Sat, 11 Nov 2017 03:29:45: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:29:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:31:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:31:06: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:31:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:31:54: #4 Write output xls file... SRX1977127.05_peaks.xls INFO @ Sat, 11 Nov 2017 03:31:54: #4 Write output xls file... SRX1977127.20_peaks.xls INFO @ Sat, 11 Nov 2017 03:31:54: #4 Write peak in narrowPeak format file... SRX1977127.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:31:54: #4 Write summits bed file... SRX1977127.20_summits.bed INFO @ Sat, 11 Nov 2017 03:31:54: Done! pass1 - making usageList (83 chroms): 1 millis pass2 - checking and writing primary data (5346 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 03:31:54: #4 Write peak in narrowPeak format file... SRX1977127.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:31:55: #4 Write summits bed file... SRX1977127.05_summits.bed INFO @ Sat, 11 Nov 2017 03:31:55: #4 Write output xls file... SRX1977127.10_peaks.xls INFO @ Sat, 11 Nov 2017 03:31:55: Done! INFO @ Sat, 11 Nov 2017 03:31:55: #4 Write peak in narrowPeak format file... SRX1977127.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:31:55: #4 Write summits bed file... SRX1977127.10_summits.bed INFO @ Sat, 11 Nov 2017 03:31:56: Done! pass1 - making usageList (156 chroms): 5 millis pass2 - checking and writing primary data (24194 records, 4 fields): 34 millis CompletedMACS2peakCalling pass1 - making usageList (231 chroms): 12 millis pass2 - checking and writing primary data (67520 records, 4 fields): 82 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。