Job ID = 10714377 sra ファイルのダウンロード中... Completed: 632907K bytes transferred in 15 seconds (328933K 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... Read 29109017 spots for /home/okishinya/chipatlas/results/ce10/SRX4082337/SRR7164155.sra Written 29109017 spots for /home/okishinya/chipatlas/results/ce10/SRX4082337/SRR7164155.sra 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:40 29109017 reads; of these: 29109017 (100.00%) were unpaired; of these: 816643 (2.81%) aligned 0 times 24491141 (84.14%) aligned exactly 1 time 3801233 (13.06%) aligned >1 times 97.19% overall alignment rate Time searching: 00:07:40 Overall time: 00:07:40 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 7165730 / 28292374 = 0.2533 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, 03 Jun 2018 12:45:07: # Command line: callpeak -t SRX4082337.bam -f BAM -g ce -n SRX4082337.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4082337.05 # format = BAM # ChIP-seq file = ['SRX4082337.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 03 Jun 2018 12:45:07: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:45:07: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:45:07: # Command line: callpeak -t SRX4082337.bam -f BAM -g ce -n SRX4082337.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4082337.20 # format = BAM # ChIP-seq file = ['SRX4082337.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 03 Jun 2018 12:45:07: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:45:07: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:45:07: # Command line: callpeak -t SRX4082337.bam -f BAM -g ce -n SRX4082337.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4082337.10 # format = BAM # ChIP-seq file = ['SRX4082337.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 03 Jun 2018 12:45:07: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:45:07: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:45:13: 1000000 INFO @ Sun, 03 Jun 2018 12:45:13: 1000000 INFO @ Sun, 03 Jun 2018 12:45:13: 1000000 INFO @ Sun, 03 Jun 2018 12:45:20: 2000000 INFO @ Sun, 03 Jun 2018 12:45:20: 2000000 INFO @ Sun, 03 Jun 2018 12:45:20: 2000000 INFO @ Sun, 03 Jun 2018 12:45:27: 3000000 INFO @ Sun, 03 Jun 2018 12:45:27: 3000000 INFO @ Sun, 03 Jun 2018 12:45:27: 3000000 INFO @ Sun, 03 Jun 2018 12:45:33: 4000000 INFO @ Sun, 03 Jun 2018 12:45:34: 4000000 INFO @ Sun, 03 Jun 2018 12:45:34: 4000000 INFO @ Sun, 03 Jun 2018 12:45:40: 5000000 INFO @ Sun, 03 Jun 2018 12:45:40: 5000000 INFO @ Sun, 03 Jun 2018 12:45:40: 5000000 INFO @ Sun, 03 Jun 2018 12:45:46: 6000000 INFO @ Sun, 03 Jun 2018 12:45:47: 6000000 INFO @ Sun, 03 Jun 2018 12:45:47: 6000000 INFO @ Sun, 03 Jun 2018 12:45:53: 7000000 INFO @ Sun, 03 Jun 2018 12:45:54: 7000000 INFO @ Sun, 03 Jun 2018 12:45:54: 7000000 INFO @ Sun, 03 Jun 2018 12:45:59: 8000000 INFO @ Sun, 03 Jun 2018 12:46:00: 8000000 INFO @ Sun, 03 Jun 2018 12:46:01: 8000000 INFO @ Sun, 03 Jun 2018 12:46:06: 9000000 INFO @ Sun, 03 Jun 2018 12:46:07: 9000000 INFO @ Sun, 03 Jun 2018 12:46:07: 9000000 INFO @ Sun, 03 Jun 2018 12:46:12: 10000000 INFO @ Sun, 03 Jun 2018 12:46:14: 10000000 INFO @ Sun, 03 Jun 2018 12:46:14: 10000000 INFO @ Sun, 03 Jun 2018 12:46:18: 11000000 INFO @ Sun, 03 Jun 2018 12:46:21: 11000000 INFO @ Sun, 03 Jun 2018 12:46:21: 11000000 INFO @ Sun, 03 Jun 2018 12:46:25: 12000000 INFO @ Sun, 03 Jun 2018 12:46:28: 12000000 INFO @ Sun, 03 Jun 2018 12:46:28: 12000000 INFO @ Sun, 03 Jun 2018 12:46:32: 13000000 INFO @ Sun, 03 Jun 2018 12:46:35: 13000000 INFO @ Sun, 03 Jun 2018 12:46:35: 13000000 INFO @ Sun, 03 Jun 2018 12:46:38: 14000000 INFO @ Sun, 03 Jun 2018 12:46:42: 14000000 INFO @ Sun, 03 Jun 2018 12:46:42: 14000000 INFO @ Sun, 03 Jun 2018 12:46:45: 15000000 INFO @ Sun, 03 Jun 2018 12:46:49: 15000000 INFO @ Sun, 03 Jun 2018 12:46:49: 15000000 INFO @ Sun, 03 Jun 2018 12:46:52: 16000000 INFO @ Sun, 03 Jun 2018 12:46:56: 16000000 INFO @ Sun, 03 Jun 2018 12:46:56: 16000000 INFO @ Sun, 03 Jun 2018 12:46:58: 17000000 INFO @ Sun, 03 Jun 2018 12:47:03: 17000000 INFO @ Sun, 03 Jun 2018 12:47:03: 17000000 INFO @ Sun, 03 Jun 2018 12:47:05: 18000000 INFO @ Sun, 03 Jun 2018 12:47:11: 18000000 INFO @ Sun, 03 Jun 2018 12:47:11: 18000000 INFO @ Sun, 03 Jun 2018 12:47:12: 19000000 INFO @ Sun, 03 Jun 2018 12:47:18: 19000000 INFO @ Sun, 03 Jun 2018 12:47:18: 19000000 INFO @ Sun, 03 Jun 2018 12:47:18: 20000000 INFO @ Sun, 03 Jun 2018 12:47:25: 21000000 INFO @ Sun, 03 Jun 2018 12:47:25: 20000000 INFO @ Sun, 03 Jun 2018 12:47:25: 20000000 INFO @ Sun, 03 Jun 2018 12:47:26: #1 tag size is determined as 49 bps INFO @ Sun, 03 Jun 2018 12:47:26: #1 tag size = 49 INFO @ Sun, 03 Jun 2018 12:47:26: #1 total tags in treatment: 21126644 INFO @ Sun, 03 Jun 2018 12:47:26: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:47:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:47:26: #1 tags after filtering in treatment: 21126644 INFO @ Sun, 03 Jun 2018 12:47:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:47:26: #1 finished! INFO @ Sun, 03 Jun 2018 12:47:26: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:47:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:47:28: #2 number of paired peaks: 1498 INFO @ Sun, 03 Jun 2018 12:47:28: start model_add_line... INFO @ Sun, 03 Jun 2018 12:47:29: start X-correlation... INFO @ Sun, 03 Jun 2018 12:47:29: end of X-cor INFO @ Sun, 03 Jun 2018 12:47:29: #2 finished! INFO @ Sun, 03 Jun 2018 12:47:29: #2 predicted fragment length is 149 bps INFO @ Sun, 03 Jun 2018 12:47:29: #2 alternative fragment length(s) may be 4,149 bps INFO @ Sun, 03 Jun 2018 12:47:29: #2.2 Generate R script for model : SRX4082337.20_model.r INFO @ Sun, 03 Jun 2018 12:47:29: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:47:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:47:33: 21000000 INFO @ Sun, 03 Jun 2018 12:47:33: 21000000 INFO @ Sun, 03 Jun 2018 12:47:34: #1 tag size is determined as 49 bps INFO @ Sun, 03 Jun 2018 12:47:34: #1 tag size = 49 INFO @ Sun, 03 Jun 2018 12:47:34: #1 total tags in treatment: 21126644 INFO @ Sun, 03 Jun 2018 12:47:34: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:47:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:47:34: #1 tag size is determined as 49 bps INFO @ Sun, 03 Jun 2018 12:47:34: #1 tag size = 49 INFO @ Sun, 03 Jun 2018 12:47:34: #1 total tags in treatment: 21126644 INFO @ Sun, 03 Jun 2018 12:47:34: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:47:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:47:34: #1 tags after filtering in treatment: 21126644 INFO @ Sun, 03 Jun 2018 12:47:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:47:34: #1 finished! INFO @ Sun, 03 Jun 2018 12:47:34: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:47:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:47:34: #1 tags after filtering in treatment: 21126644 INFO @ Sun, 03 Jun 2018 12:47:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:47:34: #1 finished! INFO @ Sun, 03 Jun 2018 12:47:34: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:47:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:47:36: #2 number of paired peaks: 1498 INFO @ Sun, 03 Jun 2018 12:47:36: start model_add_line... INFO @ Sun, 03 Jun 2018 12:47:36: #2 number of paired peaks: 1498 INFO @ Sun, 03 Jun 2018 12:47:36: start model_add_line... INFO @ Sun, 03 Jun 2018 12:47:36: start X-correlation... INFO @ Sun, 03 Jun 2018 12:47:36: end of X-cor INFO @ Sun, 03 Jun 2018 12:47:36: #2 finished! INFO @ Sun, 03 Jun 2018 12:47:36: #2 predicted fragment length is 149 bps INFO @ Sun, 03 Jun 2018 12:47:36: #2 alternative fragment length(s) may be 4,149 bps INFO @ Sun, 03 Jun 2018 12:47:36: #2.2 Generate R script for model : SRX4082337.05_model.r INFO @ Sun, 03 Jun 2018 12:47:36: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:47:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:47:36: start X-correlation... INFO @ Sun, 03 Jun 2018 12:47:36: end of X-cor INFO @ Sun, 03 Jun 2018 12:47:36: #2 finished! INFO @ Sun, 03 Jun 2018 12:47:36: #2 predicted fragment length is 149 bps INFO @ Sun, 03 Jun 2018 12:47:36: #2 alternative fragment length(s) may be 4,149 bps INFO @ Sun, 03 Jun 2018 12:47:36: #2.2 Generate R script for model : SRX4082337.10_model.r INFO @ Sun, 03 Jun 2018 12:47:36: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:47:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:48:19: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:48:24: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:48:26: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:48:40: #4 Write output xls file... SRX4082337.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:48:40: #4 Write peak in narrowPeak format file... SRX4082337.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:48:40: #4 Write summits bed file... SRX4082337.20_summits.bed INFO @ Sun, 03 Jun 2018 12:48:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3914 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:48:46: #4 Write output xls file... SRX4082337.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:48:46: #4 Write peak in narrowPeak format file... SRX4082337.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:48:46: #4 Write summits bed file... SRX4082337.10_summits.bed INFO @ Sun, 03 Jun 2018 12:48:46: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4956 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:48:50: #4 Write output xls file... SRX4082337.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:48:51: #4 Write peak in narrowPeak format file... SRX4082337.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:48:51: #4 Write summits bed file... SRX4082337.05_summits.bed INFO @ Sun, 03 Jun 2018 12:48:51: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6261 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。