Job ID = 10487617 sra ファイルのダウンロード中... Completed: 787564K bytes transferred in 53 seconds (121167K 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 17176930 spots for /home/okishinya/chipatlas/results/rn6/SRX3358573/SRR6251632.sra Written 17176930 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: 00:21:44 17176930 reads; of these: 17176930 (100.00%) were unpaired; of these: 711717 (4.14%) aligned 0 times 12935299 (75.31%) aligned exactly 1 time 3529914 (20.55%) aligned >1 times 95.86% overall alignment rate Time searching: 00:21:47 Overall time: 00:21:47 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 8 files... [bam_rmdupse_core] 408674 / 16465213 = 0.0248 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 10:47:00: # Command line: callpeak -t SRX3358573.bam -f BAM -g 2.15e9 -n SRX3358573.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3358573.05 # format = BAM # ChIP-seq file = ['SRX3358573.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 10:47:00: #1 read tag files... INFO @ Sun, 18 Mar 2018 10:47:00: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 10:47:00: # Command line: callpeak -t SRX3358573.bam -f BAM -g 2.15e9 -n SRX3358573.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3358573.20 # format = BAM # ChIP-seq file = ['SRX3358573.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 10:47:00: #1 read tag files... INFO @ Sun, 18 Mar 2018 10:47:00: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 10:47:00: # Command line: callpeak -t SRX3358573.bam -f BAM -g 2.15e9 -n SRX3358573.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3358573.10 # format = BAM # ChIP-seq file = ['SRX3358573.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 10:47:00: #1 read tag files... INFO @ Sun, 18 Mar 2018 10:47:00: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 10:47:08: 1000000 INFO @ Sun, 18 Mar 2018 10:47:08: 1000000 INFO @ Sun, 18 Mar 2018 10:47:09: 1000000 INFO @ Sun, 18 Mar 2018 10:47:16: 2000000 INFO @ Sun, 18 Mar 2018 10:47:17: 2000000 INFO @ Sun, 18 Mar 2018 10:47:17: 2000000 INFO @ Sun, 18 Mar 2018 10:47:23: 3000000 INFO @ Sun, 18 Mar 2018 10:47:26: 3000000 INFO @ Sun, 18 Mar 2018 10:47:27: 3000000 INFO @ Sun, 18 Mar 2018 10:47:31: 4000000 INFO @ Sun, 18 Mar 2018 10:47:35: 4000000 INFO @ Sun, 18 Mar 2018 10:47:36: 4000000 INFO @ Sun, 18 Mar 2018 10:47:38: 5000000 INFO @ Sun, 18 Mar 2018 10:47:43: 5000000 INFO @ Sun, 18 Mar 2018 10:47:45: 5000000 INFO @ Sun, 18 Mar 2018 10:47:46: 6000000 INFO @ Sun, 18 Mar 2018 10:47:51: 6000000 INFO @ Sun, 18 Mar 2018 10:47:54: 6000000 INFO @ Sun, 18 Mar 2018 10:47:54: 7000000 INFO @ Sun, 18 Mar 2018 10:47:59: 7000000 INFO @ Sun, 18 Mar 2018 10:48:02: 8000000 INFO @ Sun, 18 Mar 2018 10:48:03: 7000000 INFO @ Sun, 18 Mar 2018 10:48:06: 8000000 INFO @ Sun, 18 Mar 2018 10:48:10: 9000000 INFO @ Sun, 18 Mar 2018 10:48:12: 8000000 INFO @ Sun, 18 Mar 2018 10:48:15: 9000000 INFO @ Sun, 18 Mar 2018 10:48:19: 10000000 INFO @ Sun, 18 Mar 2018 10:48:21: 9000000 INFO @ Sun, 18 Mar 2018 10:48:22: 10000000 INFO @ Sun, 18 Mar 2018 10:48:27: 11000000 INFO @ Sun, 18 Mar 2018 10:48:30: 11000000 INFO @ Sun, 18 Mar 2018 10:48:30: 10000000 INFO @ Sun, 18 Mar 2018 10:48:35: 12000000 INFO @ Sun, 18 Mar 2018 10:48:38: 12000000 INFO @ Sun, 18 Mar 2018 10:48:39: 11000000 INFO @ Sun, 18 Mar 2018 10:48:44: 13000000 INFO @ Sun, 18 Mar 2018 10:48:46: 13000000 INFO @ Sun, 18 Mar 2018 10:48:48: 12000000 INFO @ Sun, 18 Mar 2018 10:48:52: 14000000 INFO @ Sun, 18 Mar 2018 10:48:54: 14000000 INFO @ Sun, 18 Mar 2018 10:48:58: 13000000 INFO @ Sun, 18 Mar 2018 10:49:00: 15000000 INFO @ Sun, 18 Mar 2018 10:49:02: 15000000 INFO @ Sun, 18 Mar 2018 10:49:07: 14000000 INFO @ Sun, 18 Mar 2018 10:49:09: 16000000 INFO @ Sun, 18 Mar 2018 10:49:09: #1 tag size is determined as 75 bps INFO @ Sun, 18 Mar 2018 10:49:09: #1 tag size = 75 INFO @ Sun, 18 Mar 2018 10:49:09: #1 total tags in treatment: 16056539 INFO @ Sun, 18 Mar 2018 10:49:09: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 10:49:09: #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 10:49:09: 16000000 INFO @ Sun, 18 Mar 2018 10:49:10: #1 tags after filtering in treatment: 16056374 INFO @ Sun, 18 Mar 2018 10:49:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 10:49:10: #1 finished! INFO @ Sun, 18 Mar 2018 10:49:10: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 10:49:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 10:49:10: #1 tag size is determined as 75 bps INFO @ Sun, 18 Mar 2018 10:49:10: #1 tag size = 75 INFO @ Sun, 18 Mar 2018 10:49:10: #1 total tags in treatment: 16056539 INFO @ Sun, 18 Mar 2018 10:49:10: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 10:49:10: #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 10:49:11: #1 tags after filtering in treatment: 16056374 INFO @ Sun, 18 Mar 2018 10:49:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 10:49:11: #1 finished! INFO @ Sun, 18 Mar 2018 10:49:11: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 10:49:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 10:49:13: #2 number of paired peaks: 50530 INFO @ Sun, 18 Mar 2018 10:49:13: start model_add_line... INFO @ Sun, 18 Mar 2018 10:49:13: start X-correlation... INFO @ Sun, 18 Mar 2018 10:49:13: end of X-cor INFO @ Sun, 18 Mar 2018 10:49:13: #2 finished! INFO @ Sun, 18 Mar 2018 10:49:13: #2 predicted fragment length is 158 bps INFO @ Sun, 18 Mar 2018 10:49:13: #2 alternative fragment length(s) may be 158 bps INFO @ Sun, 18 Mar 2018 10:49:13: #2.2 Generate R script for model : SRX3358573.05_model.r INFO @ Sun, 18 Mar 2018 10:49:13: #3 Call peaks... INFO @ Sun, 18 Mar 2018 10:49:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 10:49:14: #2 number of paired peaks: 50530 INFO @ Sun, 18 Mar 2018 10:49:14: start model_add_line... INFO @ Sun, 18 Mar 2018 10:49:14: start X-correlation... INFO @ Sun, 18 Mar 2018 10:49:14: end of X-cor INFO @ Sun, 18 Mar 2018 10:49:14: #2 finished! INFO @ Sun, 18 Mar 2018 10:49:14: #2 predicted fragment length is 158 bps INFO @ Sun, 18 Mar 2018 10:49:14: #2 alternative fragment length(s) may be 158 bps INFO @ Sun, 18 Mar 2018 10:49:14: #2.2 Generate R script for model : SRX3358573.10_model.r INFO @ Sun, 18 Mar 2018 10:49:14: #3 Call peaks... INFO @ Sun, 18 Mar 2018 10:49:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 10:49:15: 15000000 INFO @ Sun, 18 Mar 2018 10:49:23: 16000000 INFO @ Sun, 18 Mar 2018 10:49:24: #1 tag size is determined as 75 bps INFO @ Sun, 18 Mar 2018 10:49:24: #1 tag size = 75 INFO @ Sun, 18 Mar 2018 10:49:24: #1 total tags in treatment: 16056539 INFO @ Sun, 18 Mar 2018 10:49:24: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 10:49:24: #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 10:49:24: #1 tags after filtering in treatment: 16056374 INFO @ Sun, 18 Mar 2018 10:49:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 10:49:24: #1 finished! INFO @ Sun, 18 Mar 2018 10:49:24: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 10:49:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 10:49:27: #2 number of paired peaks: 50530 INFO @ Sun, 18 Mar 2018 10:49:27: start model_add_line... INFO @ Sun, 18 Mar 2018 10:49:28: start X-correlation... INFO @ Sun, 18 Mar 2018 10:49:28: end of X-cor INFO @ Sun, 18 Mar 2018 10:49:28: #2 finished! INFO @ Sun, 18 Mar 2018 10:49:28: #2 predicted fragment length is 158 bps INFO @ Sun, 18 Mar 2018 10:49:28: #2 alternative fragment length(s) may be 158 bps INFO @ Sun, 18 Mar 2018 10:49:28: #2.2 Generate R script for model : SRX3358573.20_model.r INFO @ Sun, 18 Mar 2018 10:49:28: #3 Call peaks... INFO @ Sun, 18 Mar 2018 10:49:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 10:49:56: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 10:49:57: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 10:50:08: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 10:50:22: #4 Write output xls file... SRX3358573.05_peaks.xls INFO @ Sun, 18 Mar 2018 10:50:22: #4 Write peak in narrowPeak format file... SRX3358573.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 10:50:22: #4 Write summits bed file... SRX3358573.05_summits.bed INFO @ Sun, 18 Mar 2018 10:50:22: Done! pass1 - making usageList (75 chroms): 4 millis pass2 - checking and writing primary data (17013 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 10:50:24: #4 Write output xls file... SRX3358573.10_peaks.xls INFO @ Sun, 18 Mar 2018 10:50:25: #4 Write peak in narrowPeak format file... SRX3358573.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 10:50:25: #4 Write summits bed file... SRX3358573.10_summits.bed INFO @ Sun, 18 Mar 2018 10:50:25: Done! pass1 - making usageList (51 chroms): 2 millis pass2 - checking and writing primary data (7628 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 10:50:34: #4 Write output xls file... SRX3358573.20_peaks.xls INFO @ Sun, 18 Mar 2018 10:50:34: #4 Write peak in narrowPeak format file... SRX3358573.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 10:50:34: #4 Write summits bed file... SRX3358573.20_summits.bed INFO @ Sun, 18 Mar 2018 10:50:34: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (1822 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。