Job ID = 11171221 sra ファイルのダウンロード中... Completed: 285441K bytes transferred in 15 seconds (152605K 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 14276261 spots for /home/okishinya/chipatlas/results/dm3/SRX2618530/SRR5319084.sra Written 14276261 spots for /home/okishinya/chipatlas/results/dm3/SRX2618530/SRR5319084.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: 00:04:23 14276261 reads; of these: 14276261 (100.00%) were unpaired; of these: 862859 (6.04%) aligned 0 times 11418363 (79.98%) aligned exactly 1 time 1995039 (13.97%) aligned >1 times 93.96% overall alignment rate Time searching: 00:04:23 Overall time: 00:04:23 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1594638 / 13413402 = 0.1189 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, 08 Sep 2018 13:10:24: # Command line: callpeak -t SRX2618530.bam -f BAM -g dm -n SRX2618530.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2618530.10 # format = BAM # ChIP-seq file = ['SRX2618530.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 08 Sep 2018 13:10:24: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:10:24: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:10:24: # Command line: callpeak -t SRX2618530.bam -f BAM -g dm -n SRX2618530.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2618530.05 # format = BAM # ChIP-seq file = ['SRX2618530.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 08 Sep 2018 13:10:24: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:10:24: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:10:24: # Command line: callpeak -t SRX2618530.bam -f BAM -g dm -n SRX2618530.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2618530.20 # format = BAM # ChIP-seq file = ['SRX2618530.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 08 Sep 2018 13:10:24: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:10:24: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:10:31: 1000000 INFO @ Sat, 08 Sep 2018 13:10:31: 1000000 INFO @ Sat, 08 Sep 2018 13:10:31: 1000000 INFO @ Sat, 08 Sep 2018 13:10:38: 2000000 INFO @ Sat, 08 Sep 2018 13:10:38: 2000000 INFO @ Sat, 08 Sep 2018 13:10:38: 2000000 INFO @ Sat, 08 Sep 2018 13:10:45: 3000000 INFO @ Sat, 08 Sep 2018 13:10:45: 3000000 INFO @ Sat, 08 Sep 2018 13:10:46: 3000000 INFO @ Sat, 08 Sep 2018 13:10:51: 4000000 INFO @ Sat, 08 Sep 2018 13:10:52: 4000000 INFO @ Sat, 08 Sep 2018 13:10:53: 4000000 INFO @ Sat, 08 Sep 2018 13:10:58: 5000000 INFO @ Sat, 08 Sep 2018 13:11:00: 5000000 INFO @ Sat, 08 Sep 2018 13:11:00: 5000000 INFO @ Sat, 08 Sep 2018 13:11:05: 6000000 INFO @ Sat, 08 Sep 2018 13:11:07: 6000000 INFO @ Sat, 08 Sep 2018 13:11:07: 6000000 INFO @ Sat, 08 Sep 2018 13:11:12: 7000000 INFO @ Sat, 08 Sep 2018 13:11:14: 7000000 INFO @ Sat, 08 Sep 2018 13:11:14: 7000000 INFO @ Sat, 08 Sep 2018 13:11:19: 8000000 INFO @ Sat, 08 Sep 2018 13:11:21: 8000000 INFO @ Sat, 08 Sep 2018 13:11:22: 8000000 INFO @ Sat, 08 Sep 2018 13:11:26: 9000000 INFO @ Sat, 08 Sep 2018 13:11:28: 9000000 INFO @ Sat, 08 Sep 2018 13:11:29: 9000000 INFO @ Sat, 08 Sep 2018 13:11:33: 10000000 INFO @ Sat, 08 Sep 2018 13:11:36: 10000000 INFO @ Sat, 08 Sep 2018 13:11:36: 10000000 INFO @ Sat, 08 Sep 2018 13:11:40: 11000000 INFO @ Sat, 08 Sep 2018 13:11:43: 11000000 INFO @ Sat, 08 Sep 2018 13:11:43: 11000000 INFO @ Sat, 08 Sep 2018 13:11:46: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:11:46: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:11:46: #1 total tags in treatment: 11818764 INFO @ Sat, 08 Sep 2018 13:11:46: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:11:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:11:46: #1 tags after filtering in treatment: 11818764 INFO @ Sat, 08 Sep 2018 13:11:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:11:46: #1 finished! INFO @ Sat, 08 Sep 2018 13:11:46: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:11:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:11:47: #2 number of paired peaks: 2117 INFO @ Sat, 08 Sep 2018 13:11:47: start model_add_line... INFO @ Sat, 08 Sep 2018 13:11:48: start X-correlation... INFO @ Sat, 08 Sep 2018 13:11:48: end of X-cor INFO @ Sat, 08 Sep 2018 13:11:48: #2 finished! INFO @ Sat, 08 Sep 2018 13:11:48: #2 predicted fragment length is 158 bps INFO @ Sat, 08 Sep 2018 13:11:48: #2 alternative fragment length(s) may be 158 bps INFO @ Sat, 08 Sep 2018 13:11:48: #2.2 Generate R script for model : SRX2618530.20_model.r INFO @ Sat, 08 Sep 2018 13:11:48: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:11:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:11:49: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:11:49: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:11:49: #1 total tags in treatment: 11818764 INFO @ Sat, 08 Sep 2018 13:11:49: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:11:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:11:49: #1 tags after filtering in treatment: 11818764 INFO @ Sat, 08 Sep 2018 13:11:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:11:49: #1 finished! INFO @ Sat, 08 Sep 2018 13:11:49: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:11:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:11:49: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:11:49: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:11:49: #1 total tags in treatment: 11818764 INFO @ Sat, 08 Sep 2018 13:11:49: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:11:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:11:49: #1 tags after filtering in treatment: 11818764 INFO @ Sat, 08 Sep 2018 13:11:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:11:49: #1 finished! INFO @ Sat, 08 Sep 2018 13:11:49: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:11:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:11:50: #2 number of paired peaks: 2117 INFO @ Sat, 08 Sep 2018 13:11:50: start model_add_line... INFO @ Sat, 08 Sep 2018 13:11:50: start X-correlation... INFO @ Sat, 08 Sep 2018 13:11:50: end of X-cor INFO @ Sat, 08 Sep 2018 13:11:50: #2 finished! INFO @ Sat, 08 Sep 2018 13:11:50: #2 predicted fragment length is 158 bps INFO @ Sat, 08 Sep 2018 13:11:50: #2 alternative fragment length(s) may be 158 bps INFO @ Sat, 08 Sep 2018 13:11:50: #2.2 Generate R script for model : SRX2618530.05_model.r INFO @ Sat, 08 Sep 2018 13:11:50: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:11:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:11:51: #2 number of paired peaks: 2117 INFO @ Sat, 08 Sep 2018 13:11:51: start model_add_line... INFO @ Sat, 08 Sep 2018 13:11:51: start X-correlation... INFO @ Sat, 08 Sep 2018 13:11:51: end of X-cor INFO @ Sat, 08 Sep 2018 13:11:51: #2 finished! INFO @ Sat, 08 Sep 2018 13:11:51: #2 predicted fragment length is 158 bps INFO @ Sat, 08 Sep 2018 13:11:51: #2 alternative fragment length(s) may be 158 bps INFO @ Sat, 08 Sep 2018 13:11:51: #2.2 Generate R script for model : SRX2618530.10_model.r INFO @ Sat, 08 Sep 2018 13:11:51: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:11:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:12:17: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:12:20: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:12:21: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:12:33: #4 Write output xls file... SRX2618530.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:12:33: #4 Write peak in narrowPeak format file... SRX2618530.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:12:33: #4 Write summits bed file... SRX2618530.20_summits.bed INFO @ Sat, 08 Sep 2018 13:12:33: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (2743 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:12:36: #4 Write output xls file... SRX2618530.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:12:36: #4 Write peak in narrowPeak format file... SRX2618530.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:12:36: #4 Write summits bed file... SRX2618530.05_summits.bed INFO @ Sat, 08 Sep 2018 13:12:36: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (9493 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:12:37: #4 Write output xls file... SRX2618530.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:12:37: #4 Write peak in narrowPeak format file... SRX2618530.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:12:37: #4 Write summits bed file... SRX2618530.10_summits.bed INFO @ Sat, 08 Sep 2018 13:12:37: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6169 records, 4 fields): 86 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。