Job ID = 10175235 sra ファイルのダウンロード中... Completed: 476614K bytes transferred in 37 seconds (104239K 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 26750825 spots for /home/okishinya/chipatlas/results/dm3/SRX2804214/SRR5534642.sra Written 26750825 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:46 26750825 reads; of these: 26750825 (100.00%) were unpaired; of these: 9915466 (37.07%) aligned 0 times 12314589 (46.03%) aligned exactly 1 time 4520770 (16.90%) aligned >1 times 62.93% overall alignment rate Time searching: 00:08:46 Overall time: 00:08:46 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] 3376004 / 16835359 = 0.2005 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 @ Mon, 06 Nov 2017 11:56:32: # Command line: callpeak -t SRX2804214.bam -f BAM -g dm -n SRX2804214.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2804214.10 # format = BAM # ChIP-seq file = ['SRX2804214.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 @ Mon, 06 Nov 2017 11:56:32: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:56:32: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:56:32: # Command line: callpeak -t SRX2804214.bam -f BAM -g dm -n SRX2804214.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2804214.20 # format = BAM # ChIP-seq file = ['SRX2804214.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 @ Mon, 06 Nov 2017 11:56:32: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:56:32: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:56:32: # Command line: callpeak -t SRX2804214.bam -f BAM -g dm -n SRX2804214.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2804214.05 # format = BAM # ChIP-seq file = ['SRX2804214.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 @ Mon, 06 Nov 2017 11:56:32: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:56:32: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:56:38: 1000000 INFO @ Mon, 06 Nov 2017 11:56:38: 1000000 INFO @ Mon, 06 Nov 2017 11:56:39: 1000000 INFO @ Mon, 06 Nov 2017 11:56:45: 2000000 INFO @ Mon, 06 Nov 2017 11:56:45: 2000000 INFO @ Mon, 06 Nov 2017 11:56:46: 2000000 INFO @ Mon, 06 Nov 2017 11:56:51: 3000000 INFO @ Mon, 06 Nov 2017 11:56:51: 3000000 INFO @ Mon, 06 Nov 2017 11:56:53: 3000000 INFO @ Mon, 06 Nov 2017 11:56:57: 4000000 INFO @ Mon, 06 Nov 2017 11:56:58: 4000000 INFO @ Mon, 06 Nov 2017 11:57:00: 4000000 INFO @ Mon, 06 Nov 2017 11:57:04: 5000000 INFO @ Mon, 06 Nov 2017 11:57:05: 5000000 INFO @ Mon, 06 Nov 2017 11:57:07: 5000000 INFO @ Mon, 06 Nov 2017 11:57:10: 6000000 INFO @ Mon, 06 Nov 2017 11:57:11: 6000000 INFO @ Mon, 06 Nov 2017 11:57:14: 6000000 INFO @ Mon, 06 Nov 2017 11:57:17: 7000000 INFO @ Mon, 06 Nov 2017 11:57:18: 7000000 INFO @ Mon, 06 Nov 2017 11:57:21: 7000000 INFO @ Mon, 06 Nov 2017 11:57:24: 8000000 INFO @ Mon, 06 Nov 2017 11:57:24: 8000000 INFO @ Mon, 06 Nov 2017 11:57:27: 8000000 INFO @ Mon, 06 Nov 2017 11:57:30: 9000000 INFO @ Mon, 06 Nov 2017 11:57:30: 9000000 INFO @ Mon, 06 Nov 2017 11:57:34: 9000000 INFO @ Mon, 06 Nov 2017 11:57:37: 10000000 INFO @ Mon, 06 Nov 2017 11:57:37: 10000000 INFO @ Mon, 06 Nov 2017 11:57:41: 10000000 INFO @ Mon, 06 Nov 2017 11:57:43: 11000000 INFO @ Mon, 06 Nov 2017 11:57:43: 11000000 INFO @ Mon, 06 Nov 2017 11:57:48: 11000000 INFO @ Mon, 06 Nov 2017 11:57:50: 12000000 INFO @ Mon, 06 Nov 2017 11:57:50: 12000000 INFO @ Mon, 06 Nov 2017 11:57:55: 12000000 INFO @ Mon, 06 Nov 2017 11:57:56: 13000000 INFO @ Mon, 06 Nov 2017 11:57:56: 13000000 INFO @ Mon, 06 Nov 2017 11:57:59: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 11:57:59: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 11:57:59: #1 total tags in treatment: 13459355 INFO @ Mon, 06 Nov 2017 11:57:59: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:57:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 11:57:59: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 11:57:59: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 11:57:59: #1 total tags in treatment: 13459355 INFO @ Mon, 06 Nov 2017 11:57:59: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:57:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 11:57:59: #1 tags after filtering in treatment: 13459355 INFO @ Mon, 06 Nov 2017 11:57:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:57:59: #1 finished! INFO @ Mon, 06 Nov 2017 11:57:59: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:57:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:57:59: #1 tags after filtering in treatment: 13459355 INFO @ Mon, 06 Nov 2017 11:57:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:57:59: #1 finished! INFO @ Mon, 06 Nov 2017 11:57:59: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:57:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:58:00: #2 number of paired peaks: 1837 INFO @ Mon, 06 Nov 2017 11:58:00: start model_add_line... INFO @ Mon, 06 Nov 2017 11:58:00: start X-correlation... INFO @ Mon, 06 Nov 2017 11:58:01: #2 number of paired peaks: 1837 INFO @ Mon, 06 Nov 2017 11:58:01: start model_add_line... INFO @ Mon, 06 Nov 2017 11:58:01: end of X-cor INFO @ Mon, 06 Nov 2017 11:58:01: #2 finished! INFO @ Mon, 06 Nov 2017 11:58:01: #2 predicted fragment length is 288 bps INFO @ Mon, 06 Nov 2017 11:58:01: #2 alternative fragment length(s) may be 288 bps INFO @ Mon, 06 Nov 2017 11:58:01: #2.2 Generate R script for model : SRX2804214.05_model.r INFO @ Mon, 06 Nov 2017 11:58:01: #3 Call peaks... INFO @ Mon, 06 Nov 2017 11:58:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 11:58:01: start X-correlation... INFO @ Mon, 06 Nov 2017 11:58:01: end of X-cor INFO @ Mon, 06 Nov 2017 11:58:01: #2 finished! INFO @ Mon, 06 Nov 2017 11:58:01: #2 predicted fragment length is 288 bps INFO @ Mon, 06 Nov 2017 11:58:01: #2 alternative fragment length(s) may be 288 bps INFO @ Mon, 06 Nov 2017 11:58:01: #2.2 Generate R script for model : SRX2804214.10_model.r INFO @ Mon, 06 Nov 2017 11:58:01: #3 Call peaks... INFO @ Mon, 06 Nov 2017 11:58:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 11:58:01: 13000000 INFO @ Mon, 06 Nov 2017 11:58:04: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 11:58:04: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 11:58:04: #1 total tags in treatment: 13459355 INFO @ Mon, 06 Nov 2017 11:58:04: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:58:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 11:58:05: #1 tags after filtering in treatment: 13459355 INFO @ Mon, 06 Nov 2017 11:58:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:58:05: #1 finished! INFO @ Mon, 06 Nov 2017 11:58:05: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:58:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:58:06: #2 number of paired peaks: 1837 INFO @ Mon, 06 Nov 2017 11:58:06: start model_add_line... INFO @ Mon, 06 Nov 2017 11:58:06: start X-correlation... INFO @ Mon, 06 Nov 2017 11:58:06: end of X-cor INFO @ Mon, 06 Nov 2017 11:58:06: #2 finished! INFO @ Mon, 06 Nov 2017 11:58:06: #2 predicted fragment length is 288 bps INFO @ Mon, 06 Nov 2017 11:58:06: #2 alternative fragment length(s) may be 288 bps INFO @ Mon, 06 Nov 2017 11:58:06: #2.2 Generate R script for model : SRX2804214.20_model.r INFO @ Mon, 06 Nov 2017 11:58:06: #3 Call peaks... INFO @ Mon, 06 Nov 2017 11:58:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 11:58:38: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:58:41: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:58:44: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:58:54: #4 Write output xls file... SRX2804214.10_peaks.xls INFO @ Mon, 06 Nov 2017 11:58:54: #4 Write peak in narrowPeak format file... SRX2804214.10_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:58:54: #4 Write summits bed file... SRX2804214.10_summits.bed INFO @ Mon, 06 Nov 2017 11:58:54: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4855 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 11:58:58: #4 Write output xls file... SRX2804214.05_peaks.xls INFO @ Mon, 06 Nov 2017 11:58:58: #4 Write peak in narrowPeak format file... SRX2804214.05_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:58:58: #4 Write summits bed file... SRX2804214.05_summits.bed INFO @ Mon, 06 Nov 2017 11:58:58: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6109 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 11:59:01: #4 Write output xls file... SRX2804214.20_peaks.xls INFO @ Mon, 06 Nov 2017 11:59:01: #4 Write peak in narrowPeak format file... SRX2804214.20_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:59:01: #4 Write summits bed file... SRX2804214.20_summits.bed INFO @ Mon, 06 Nov 2017 11:59:01: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3693 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。