Job ID = 10194829 sra ファイルのダウンロード中... Completed: 777388K bytes transferred in 13 seconds (489833K 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 40184488 spots for /home/okishinya/chipatlas/results/rn6/SRX1977119/SRR3952251.sra Written 40184488 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:18:04 40184488 reads; of these: 40184488 (100.00%) were unpaired; of these: 7399016 (18.41%) aligned 0 times 17270576 (42.98%) aligned exactly 1 time 15514896 (38.61%) aligned >1 times 81.59% overall alignment rate Time searching: 01:18:07 Overall time: 01:18:07 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] 4230912 / 32785472 = 0.1290 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 02:28:26: # Command line: callpeak -t SRX1977119.bam -f BAM -g 2.15e9 -n SRX1977119.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1977119.10 # format = BAM # ChIP-seq file = ['SRX1977119.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 02:28:26: #1 read tag files... INFO @ Sat, 11 Nov 2017 02:28:26: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 02:28:26: # Command line: callpeak -t SRX1977119.bam -f BAM -g 2.15e9 -n SRX1977119.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1977119.05 # format = BAM # ChIP-seq file = ['SRX1977119.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 02:28:26: #1 read tag files... INFO @ Sat, 11 Nov 2017 02:28:26: # Command line: callpeak -t SRX1977119.bam -f BAM -g 2.15e9 -n SRX1977119.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1977119.20 # format = BAM # ChIP-seq file = ['SRX1977119.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 02:28:26: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 02:28:26: #1 read tag files... INFO @ Sat, 11 Nov 2017 02:28:26: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 02:28:33: 1000000 INFO @ Sat, 11 Nov 2017 02:28:34: 1000000 INFO @ Sat, 11 Nov 2017 02:28:35: 1000000 INFO @ Sat, 11 Nov 2017 02:28:40: 2000000 INFO @ Sat, 11 Nov 2017 02:28:42: 2000000 INFO @ Sat, 11 Nov 2017 02:28:43: 2000000 INFO @ Sat, 11 Nov 2017 02:28:48: 3000000 INFO @ Sat, 11 Nov 2017 02:28:49: 3000000 INFO @ Sat, 11 Nov 2017 02:28:49: 3000000 INFO @ Sat, 11 Nov 2017 02:28:55: 4000000 INFO @ Sat, 11 Nov 2017 02:28:56: 4000000 INFO @ Sat, 11 Nov 2017 02:28:56: 4000000 INFO @ Sat, 11 Nov 2017 02:29:02: 5000000 INFO @ Sat, 11 Nov 2017 02:29:02: 5000000 INFO @ Sat, 11 Nov 2017 02:29:03: 5000000 INFO @ Sat, 11 Nov 2017 02:29:08: 6000000 INFO @ Sat, 11 Nov 2017 02:29:09: 6000000 INFO @ Sat, 11 Nov 2017 02:29:09: 6000000 INFO @ Sat, 11 Nov 2017 02:29:15: 7000000 INFO @ Sat, 11 Nov 2017 02:29:16: 7000000 INFO @ Sat, 11 Nov 2017 02:29:16: 7000000 INFO @ Sat, 11 Nov 2017 02:29:21: 8000000 INFO @ Sat, 11 Nov 2017 02:29:23: 8000000 INFO @ Sat, 11 Nov 2017 02:29:23: 8000000 INFO @ Sat, 11 Nov 2017 02:29:27: 9000000 INFO @ Sat, 11 Nov 2017 02:29:30: 9000000 INFO @ Sat, 11 Nov 2017 02:29:30: 9000000 INFO @ Sat, 11 Nov 2017 02:29:34: 10000000 INFO @ Sat, 11 Nov 2017 02:29:36: 10000000 INFO @ Sat, 11 Nov 2017 02:29:37: 10000000 INFO @ Sat, 11 Nov 2017 02:29:42: 11000000 INFO @ Sat, 11 Nov 2017 02:29:43: 11000000 INFO @ Sat, 11 Nov 2017 02:29:43: 11000000 INFO @ Sat, 11 Nov 2017 02:29:49: 12000000 INFO @ Sat, 11 Nov 2017 02:29:49: 12000000 INFO @ Sat, 11 Nov 2017 02:29:50: 12000000 INFO @ Sat, 11 Nov 2017 02:29:56: 13000000 INFO @ Sat, 11 Nov 2017 02:29:56: 13000000 INFO @ Sat, 11 Nov 2017 02:29:57: 13000000 INFO @ Sat, 11 Nov 2017 02:30:02: 14000000 INFO @ Sat, 11 Nov 2017 02:30:02: 14000000 INFO @ Sat, 11 Nov 2017 02:30:04: 14000000 INFO @ Sat, 11 Nov 2017 02:30:09: 15000000 INFO @ Sat, 11 Nov 2017 02:30:09: 15000000 INFO @ Sat, 11 Nov 2017 02:30:10: 15000000 INFO @ Sat, 11 Nov 2017 02:30:15: 16000000 INFO @ Sat, 11 Nov 2017 02:30:15: 16000000 INFO @ Sat, 11 Nov 2017 02:30:16: 16000000 INFO @ Sat, 11 Nov 2017 02:30:22: 17000000 INFO @ Sat, 11 Nov 2017 02:30:22: 17000000 INFO @ Sat, 11 Nov 2017 02:30:23: 17000000 INFO @ Sat, 11 Nov 2017 02:30:28: 18000000 INFO @ Sat, 11 Nov 2017 02:30:28: 18000000 INFO @ Sat, 11 Nov 2017 02:30:29: 18000000 INFO @ Sat, 11 Nov 2017 02:30:34: 19000000 INFO @ Sat, 11 Nov 2017 02:30:35: 19000000 INFO @ Sat, 11 Nov 2017 02:30:37: 19000000 INFO @ Sat, 11 Nov 2017 02:30:41: 20000000 INFO @ Sat, 11 Nov 2017 02:30:42: 20000000 INFO @ Sat, 11 Nov 2017 02:30:44: 20000000 INFO @ Sat, 11 Nov 2017 02:30:47: 21000000 INFO @ Sat, 11 Nov 2017 02:30:50: 21000000 INFO @ Sat, 11 Nov 2017 02:30:51: 21000000 INFO @ Sat, 11 Nov 2017 02:30:53: 22000000 INFO @ Sat, 11 Nov 2017 02:30:57: 22000000 INFO @ Sat, 11 Nov 2017 02:30:58: 22000000 INFO @ Sat, 11 Nov 2017 02:30:59: 23000000 INFO @ Sat, 11 Nov 2017 02:31:05: 23000000 INFO @ Sat, 11 Nov 2017 02:31:05: 23000000 INFO @ Sat, 11 Nov 2017 02:31:06: 24000000 INFO @ Sat, 11 Nov 2017 02:31:11: 24000000 INFO @ Sat, 11 Nov 2017 02:31:11: 24000000 INFO @ Sat, 11 Nov 2017 02:31:12: 25000000 INFO @ Sat, 11 Nov 2017 02:31:17: 25000000 INFO @ Sat, 11 Nov 2017 02:31:18: 25000000 INFO @ Sat, 11 Nov 2017 02:31:18: 26000000 INFO @ Sat, 11 Nov 2017 02:31:24: 26000000 INFO @ Sat, 11 Nov 2017 02:31:24: 26000000 INFO @ Sat, 11 Nov 2017 02:31:24: 27000000 INFO @ Sat, 11 Nov 2017 02:31:30: 27000000 INFO @ Sat, 11 Nov 2017 02:31:31: 27000000 INFO @ Sat, 11 Nov 2017 02:31:31: 28000000 INFO @ Sat, 11 Nov 2017 02:31:34: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 02:31:34: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 02:31:34: #1 total tags in treatment: 28554560 INFO @ Sat, 11 Nov 2017 02:31:34: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 02:31:34: #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 02:31:35: #1 tags after filtering in treatment: 28554478 INFO @ Sat, 11 Nov 2017 02:31:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 02:31:35: #1 finished! INFO @ Sat, 11 Nov 2017 02:31:35: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 02:31:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 02:31:37: 28000000 INFO @ Sat, 11 Nov 2017 02:31:37: 28000000 INFO @ Sat, 11 Nov 2017 02:31:40: #2 number of paired peaks: 36583 INFO @ Sat, 11 Nov 2017 02:31:40: start model_add_line... INFO @ Sat, 11 Nov 2017 02:31:40: start X-correlation... INFO @ Sat, 11 Nov 2017 02:31:40: end of X-cor INFO @ Sat, 11 Nov 2017 02:31:40: #2 finished! INFO @ Sat, 11 Nov 2017 02:31:40: #2 predicted fragment length is 162 bps INFO @ Sat, 11 Nov 2017 02:31:40: #2 alternative fragment length(s) may be 162 bps INFO @ Sat, 11 Nov 2017 02:31:40: #2.2 Generate R script for model : SRX1977119.20_model.r INFO @ Sat, 11 Nov 2017 02:31:40: #3 Call peaks... INFO @ Sat, 11 Nov 2017 02:31:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 02:31:40: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 02:31:40: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 02:31:40: #1 total tags in treatment: 28554560 INFO @ Sat, 11 Nov 2017 02:31:40: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 02:31:40: #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 02:31:41: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 02:31:41: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 02:31:41: #1 total tags in treatment: 28554560 INFO @ Sat, 11 Nov 2017 02:31:41: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 02:31:41: #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 02:31:41: #1 tags after filtering in treatment: 28554478 INFO @ Sat, 11 Nov 2017 02:31:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 02:31:41: #1 finished! INFO @ Sat, 11 Nov 2017 02:31:41: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 02:31:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 02:31:42: #1 tags after filtering in treatment: 28554478 INFO @ Sat, 11 Nov 2017 02:31:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 02:31:42: #1 finished! INFO @ Sat, 11 Nov 2017 02:31:42: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 02:31:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 02:31:46: #2 number of paired peaks: 36583 INFO @ Sat, 11 Nov 2017 02:31:46: start model_add_line... INFO @ Sat, 11 Nov 2017 02:31:46: start X-correlation... INFO @ Sat, 11 Nov 2017 02:31:46: end of X-cor INFO @ Sat, 11 Nov 2017 02:31:46: #2 finished! INFO @ Sat, 11 Nov 2017 02:31:46: #2 predicted fragment length is 162 bps INFO @ Sat, 11 Nov 2017 02:31:46: #2 alternative fragment length(s) may be 162 bps INFO @ Sat, 11 Nov 2017 02:31:46: #2.2 Generate R script for model : SRX1977119.10_model.r INFO @ Sat, 11 Nov 2017 02:31:46: #3 Call peaks... INFO @ Sat, 11 Nov 2017 02:31:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 02:31:46: #2 number of paired peaks: 36583 INFO @ Sat, 11 Nov 2017 02:31:46: start model_add_line... INFO @ Sat, 11 Nov 2017 02:31:47: start X-correlation... INFO @ Sat, 11 Nov 2017 02:31:47: end of X-cor INFO @ Sat, 11 Nov 2017 02:31:47: #2 finished! INFO @ Sat, 11 Nov 2017 02:31:47: #2 predicted fragment length is 162 bps INFO @ Sat, 11 Nov 2017 02:31:47: #2 alternative fragment length(s) may be 162 bps INFO @ Sat, 11 Nov 2017 02:31:47: #2.2 Generate R script for model : SRX1977119.05_model.r INFO @ Sat, 11 Nov 2017 02:31:47: #3 Call peaks... INFO @ Sat, 11 Nov 2017 02:31:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 02:32:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 02:32:59: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 02:33:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 02:33:43: #4 Write output xls file... SRX1977119.20_peaks.xls INFO @ Sat, 11 Nov 2017 02:33:43: #4 Write peak in narrowPeak format file... SRX1977119.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 02:33:43: #4 Write summits bed file... SRX1977119.20_summits.bed INFO @ Sat, 11 Nov 2017 02:33:43: Done! pass1 - making usageList (66 chroms): 1 millis pass2 - checking and writing primary data (3421 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 02:33:48: #4 Write output xls file... SRX1977119.05_peaks.xls INFO @ Sat, 11 Nov 2017 02:33:49: #4 Write peak in narrowPeak format file... SRX1977119.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 02:33:49: #4 Write summits bed file... SRX1977119.05_summits.bed INFO @ Sat, 11 Nov 2017 02:33:49: Done! pass1 - making usageList (199 chroms): 9 millis pass2 - checking and writing primary data (47988 records, 4 fields): 60 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 02:33:51: #4 Write output xls file... SRX1977119.10_peaks.xls INFO @ Sat, 11 Nov 2017 02:33:51: #4 Write peak in narrowPeak format file... SRX1977119.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 02:33:51: #4 Write summits bed file... SRX1977119.10_summits.bed INFO @ Sat, 11 Nov 2017 02:33:51: Done! pass1 - making usageList (117 chroms): 3 millis pass2 - checking and writing primary data (14148 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。