Job ID = 10194778 sra ファイルのダウンロード中... Completed: 509527K bytes transferred in 7 seconds (576997K 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 22280235 spots for /home/okishinya/chipatlas/results/rn6/SRX1774911/SRR3544942.sra Written 22280235 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: 00:00:01 Multiseed full-index search: 00:17:00 22280235 reads; of these: 22280235 (100.00%) were unpaired; of these: 816186 (3.66%) aligned 0 times 16716723 (75.03%) aligned exactly 1 time 4747326 (21.31%) aligned >1 times 96.34% overall alignment rate Time searching: 00:17:04 Overall time: 00:17:05 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] 3299894 / 21464049 = 0.1537 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, 10 Nov 2017 17:14:58: # Command line: callpeak -t SRX1774911.bam -f BAM -g 2.15e9 -n SRX1774911.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1774911.05 # format = BAM # ChIP-seq file = ['SRX1774911.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, 10 Nov 2017 17:14:58: # Command line: callpeak -t SRX1774911.bam -f BAM -g 2.15e9 -n SRX1774911.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1774911.20 # format = BAM # ChIP-seq file = ['SRX1774911.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, 10 Nov 2017 17:14:58: # Command line: callpeak -t SRX1774911.bam -f BAM -g 2.15e9 -n SRX1774911.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1774911.10 # format = BAM # ChIP-seq file = ['SRX1774911.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, 10 Nov 2017 17:14:58: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:14:58: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:14:58: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:14:58: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:14:58: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:14:58: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:15:04: 1000000 INFO @ Fri, 10 Nov 2017 17:15:04: 1000000 INFO @ Fri, 10 Nov 2017 17:15:04: 1000000 INFO @ Fri, 10 Nov 2017 17:15:10: 2000000 INFO @ Fri, 10 Nov 2017 17:15:10: 2000000 INFO @ Fri, 10 Nov 2017 17:15:10: 2000000 INFO @ Fri, 10 Nov 2017 17:15:16: 3000000 INFO @ Fri, 10 Nov 2017 17:15:17: 3000000 INFO @ Fri, 10 Nov 2017 17:15:17: 3000000 INFO @ Fri, 10 Nov 2017 17:15:22: 4000000 INFO @ Fri, 10 Nov 2017 17:15:23: 4000000 INFO @ Fri, 10 Nov 2017 17:15:23: 4000000 INFO @ Fri, 10 Nov 2017 17:15:28: 5000000 INFO @ Fri, 10 Nov 2017 17:15:29: 5000000 INFO @ Fri, 10 Nov 2017 17:15:29: 5000000 INFO @ Fri, 10 Nov 2017 17:15:35: 6000000 INFO @ Fri, 10 Nov 2017 17:15:35: 6000000 INFO @ Fri, 10 Nov 2017 17:15:36: 6000000 INFO @ Fri, 10 Nov 2017 17:15:41: 7000000 INFO @ Fri, 10 Nov 2017 17:15:42: 7000000 INFO @ Fri, 10 Nov 2017 17:15:42: 7000000 INFO @ Fri, 10 Nov 2017 17:15:47: 8000000 INFO @ Fri, 10 Nov 2017 17:15:48: 8000000 INFO @ Fri, 10 Nov 2017 17:15:49: 8000000 INFO @ Fri, 10 Nov 2017 17:15:53: 9000000 INFO @ Fri, 10 Nov 2017 17:15:55: 9000000 INFO @ Fri, 10 Nov 2017 17:15:55: 9000000 INFO @ Fri, 10 Nov 2017 17:15:59: 10000000 INFO @ Fri, 10 Nov 2017 17:16:01: 10000000 INFO @ Fri, 10 Nov 2017 17:16:02: 10000000 INFO @ Fri, 10 Nov 2017 17:16:05: 11000000 INFO @ Fri, 10 Nov 2017 17:16:08: 11000000 INFO @ Fri, 10 Nov 2017 17:16:09: 11000000 INFO @ Fri, 10 Nov 2017 17:16:11: 12000000 INFO @ Fri, 10 Nov 2017 17:16:15: 12000000 INFO @ Fri, 10 Nov 2017 17:16:16: 12000000 INFO @ Fri, 10 Nov 2017 17:16:18: 13000000 INFO @ Fri, 10 Nov 2017 17:16:21: 13000000 INFO @ Fri, 10 Nov 2017 17:16:22: 13000000 INFO @ Fri, 10 Nov 2017 17:16:24: 14000000 INFO @ Fri, 10 Nov 2017 17:16:28: 14000000 INFO @ Fri, 10 Nov 2017 17:16:29: 14000000 INFO @ Fri, 10 Nov 2017 17:16:30: 15000000 INFO @ Fri, 10 Nov 2017 17:16:34: 15000000 INFO @ Fri, 10 Nov 2017 17:16:35: 15000000 INFO @ Fri, 10 Nov 2017 17:16:36: 16000000 INFO @ Fri, 10 Nov 2017 17:16:41: 16000000 INFO @ Fri, 10 Nov 2017 17:16:42: 16000000 INFO @ Fri, 10 Nov 2017 17:16:42: 17000000 INFO @ Fri, 10 Nov 2017 17:16:48: 17000000 INFO @ Fri, 10 Nov 2017 17:16:49: 18000000 INFO @ Fri, 10 Nov 2017 17:16:49: 17000000 INFO @ Fri, 10 Nov 2017 17:16:50: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:16:50: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:16:50: #1 total tags in treatment: 18164155 INFO @ Fri, 10 Nov 2017 17:16:50: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:16:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 17:16:51: #1 tags after filtering in treatment: 18163982 INFO @ Fri, 10 Nov 2017 17:16:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:16:51: #1 finished! INFO @ Fri, 10 Nov 2017 17:16:51: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:16:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:16:54: #2 number of paired peaks: 37881 INFO @ Fri, 10 Nov 2017 17:16:54: start model_add_line... INFO @ Fri, 10 Nov 2017 17:16:54: start X-correlation... INFO @ Fri, 10 Nov 2017 17:16:54: end of X-cor INFO @ Fri, 10 Nov 2017 17:16:54: #2 finished! INFO @ Fri, 10 Nov 2017 17:16:54: #2 predicted fragment length is 175 bps INFO @ Fri, 10 Nov 2017 17:16:54: #2 alternative fragment length(s) may be 175 bps INFO @ Fri, 10 Nov 2017 17:16:54: #2.2 Generate R script for model : SRX1774911.10_model.r INFO @ Fri, 10 Nov 2017 17:16:54: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:16:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:16:55: 18000000 INFO @ Fri, 10 Nov 2017 17:16:56: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:16:56: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:16:56: #1 total tags in treatment: 18164155 INFO @ Fri, 10 Nov 2017 17:16:56: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:16:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 17:16:56: 18000000 INFO @ Fri, 10 Nov 2017 17:16:56: #1 tags after filtering in treatment: 18163982 INFO @ Fri, 10 Nov 2017 17:16:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:16:56: #1 finished! INFO @ Fri, 10 Nov 2017 17:16:56: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:16:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:16:57: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:16:57: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:16:57: #1 total tags in treatment: 18164155 INFO @ Fri, 10 Nov 2017 17:16:57: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:16:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 17:16:58: #1 tags after filtering in treatment: 18163982 INFO @ Fri, 10 Nov 2017 17:16:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:16:58: #1 finished! INFO @ Fri, 10 Nov 2017 17:16:58: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:16:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:16:59: #2 number of paired peaks: 37881 INFO @ Fri, 10 Nov 2017 17:16:59: start model_add_line... INFO @ Fri, 10 Nov 2017 17:17:00: start X-correlation... INFO @ Fri, 10 Nov 2017 17:17:00: end of X-cor INFO @ Fri, 10 Nov 2017 17:17:00: #2 finished! INFO @ Fri, 10 Nov 2017 17:17:00: #2 predicted fragment length is 175 bps INFO @ Fri, 10 Nov 2017 17:17:00: #2 alternative fragment length(s) may be 175 bps INFO @ Fri, 10 Nov 2017 17:17:00: #2.2 Generate R script for model : SRX1774911.05_model.r INFO @ Fri, 10 Nov 2017 17:17:00: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:17:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:17:01: #2 number of paired peaks: 37881 INFO @ Fri, 10 Nov 2017 17:17:01: start model_add_line... INFO @ Fri, 10 Nov 2017 17:17:01: start X-correlation... INFO @ Fri, 10 Nov 2017 17:17:01: end of X-cor INFO @ Fri, 10 Nov 2017 17:17:01: #2 finished! INFO @ Fri, 10 Nov 2017 17:17:01: #2 predicted fragment length is 175 bps INFO @ Fri, 10 Nov 2017 17:17:01: #2 alternative fragment length(s) may be 175 bps INFO @ Fri, 10 Nov 2017 17:17:01: #2.2 Generate R script for model : SRX1774911.20_model.r INFO @ Fri, 10 Nov 2017 17:17:01: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:17:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:17:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:17:48: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:17:49: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:18:07: #4 Write output xls file... SRX1774911.10_peaks.xls INFO @ Fri, 10 Nov 2017 17:18:07: #4 Write peak in narrowPeak format file... SRX1774911.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:18:07: #4 Write summits bed file... SRX1774911.10_summits.bed INFO @ Fri, 10 Nov 2017 17:18:07: Done! pass1 - making usageList (63 chroms): 2 millis pass2 - checking and writing primary data (11086 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:18:15: #4 Write output xls file... SRX1774911.20_peaks.xls INFO @ Fri, 10 Nov 2017 17:18:15: #4 Write peak in narrowPeak format file... SRX1774911.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:18:15: #4 Write summits bed file... SRX1774911.20_summits.bed INFO @ Fri, 10 Nov 2017 17:18:15: Done! INFO @ Fri, 10 Nov 2017 17:18:15: #4 Write output xls file... SRX1774911.05_peaks.xls pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (4694 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:18:15: #4 Write peak in narrowPeak format file... SRX1774911.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:18:16: #4 Write summits bed file... SRX1774911.05_summits.bed INFO @ Fri, 10 Nov 2017 17:18:16: Done! pass1 - making usageList (82 chroms): 4 millis pass2 - checking and writing primary data (20899 records, 4 fields): 27 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。