Job ID = 9157407 sra ファイルのダウンロード中... Completed: 478593K bytes transferred in 8 seconds (451438K bits/sec), in 1 file, 2 directories. 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 14095169 spots for /home/okishinya/chipatlas/results/ce10/SRX208771/SRR628905.sra Written 14095169 spots total 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: 00:05:26 14095169 reads; of these: 14095169 (100.00%) were unpaired; of these: 1509471 (10.71%) aligned 0 times 10443019 (74.09%) aligned exactly 1 time 2142679 (15.20%) aligned >1 times 89.29% overall alignment rate Time searching: 00:05:26 Overall time: 00:05:26 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 8 files... [bam_rmdupse_core] 6835594 / 12585698 = 0.5431 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 @ Tue, 27 Jun 2017 11:54:37: # Command line: callpeak -t SRX208771.bam -f BAM -g ce -n SRX208771.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX208771.10 # format = BAM # ChIP-seq file = ['SRX208771.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 @ Tue, 27 Jun 2017 11:54:37: # Command line: callpeak -t SRX208771.bam -f BAM -g ce -n SRX208771.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX208771.05 # format = BAM # ChIP-seq file = ['SRX208771.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 @ Tue, 27 Jun 2017 11:54:37: # Command line: callpeak -t SRX208771.bam -f BAM -g ce -n SRX208771.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX208771.20 # format = BAM # ChIP-seq file = ['SRX208771.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 @ Tue, 27 Jun 2017 11:54:37: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:54:37: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:54:37: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:54:37: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:54:37: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:54:37: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:54:46: 1000000 INFO @ Tue, 27 Jun 2017 11:54:46: 1000000 INFO @ Tue, 27 Jun 2017 11:54:46: 1000000 INFO @ Tue, 27 Jun 2017 11:54:54: 2000000 INFO @ Tue, 27 Jun 2017 11:54:55: 2000000 INFO @ Tue, 27 Jun 2017 11:54:55: 2000000 INFO @ Tue, 27 Jun 2017 11:55:02: 3000000 INFO @ Tue, 27 Jun 2017 11:55:03: 3000000 INFO @ Tue, 27 Jun 2017 11:55:03: 3000000 INFO @ Tue, 27 Jun 2017 11:55:10: 4000000 INFO @ Tue, 27 Jun 2017 11:55:11: 4000000 INFO @ Tue, 27 Jun 2017 11:55:11: 4000000 INFO @ Tue, 27 Jun 2017 11:55:18: 5000000 INFO @ Tue, 27 Jun 2017 11:55:20: 5000000 INFO @ Tue, 27 Jun 2017 11:55:20: 5000000 INFO @ Tue, 27 Jun 2017 11:55:25: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:55:25: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:55:25: #1 total tags in treatment: 5750104 INFO @ Tue, 27 Jun 2017 11:55:25: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:55:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:55:25: #1 tags after filtering in treatment: 5750104 INFO @ Tue, 27 Jun 2017 11:55:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:55:25: #1 finished! INFO @ Tue, 27 Jun 2017 11:55:25: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:55:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:55:25: #2 number of paired peaks: 1082 INFO @ Tue, 27 Jun 2017 11:55:25: start model_add_line... INFO @ Tue, 27 Jun 2017 11:55:25: start X-correlation... INFO @ Tue, 27 Jun 2017 11:55:25: end of X-cor INFO @ Tue, 27 Jun 2017 11:55:25: #2 finished! INFO @ Tue, 27 Jun 2017 11:55:25: #2 predicted fragment length is 279 bps INFO @ Tue, 27 Jun 2017 11:55:25: #2 alternative fragment length(s) may be 279 bps INFO @ Tue, 27 Jun 2017 11:55:25: #2.2 Generate R script for model : SRX208771.05_model.r INFO @ Tue, 27 Jun 2017 11:55:25: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:55:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:55:26: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:55:26: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:55:26: #1 total tags in treatment: 5750104 INFO @ Tue, 27 Jun 2017 11:55:26: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:55:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:55:26: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:55:26: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:55:26: #1 total tags in treatment: 5750104 INFO @ Tue, 27 Jun 2017 11:55:26: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:55:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:55:26: #1 tags after filtering in treatment: 5750104 INFO @ Tue, 27 Jun 2017 11:55:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:55:26: #1 finished! INFO @ Tue, 27 Jun 2017 11:55:26: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:55:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:55:26: #1 tags after filtering in treatment: 5750104 INFO @ Tue, 27 Jun 2017 11:55:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:55:26: #1 finished! INFO @ Tue, 27 Jun 2017 11:55:26: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:55:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:55:27: #2 number of paired peaks: 1082 INFO @ Tue, 27 Jun 2017 11:55:27: start model_add_line... INFO @ Tue, 27 Jun 2017 11:55:27: #2 number of paired peaks: 1082 INFO @ Tue, 27 Jun 2017 11:55:27: start model_add_line... INFO @ Tue, 27 Jun 2017 11:55:27: start X-correlation... INFO @ Tue, 27 Jun 2017 11:55:27: end of X-cor INFO @ Tue, 27 Jun 2017 11:55:27: #2 finished! INFO @ Tue, 27 Jun 2017 11:55:27: #2 predicted fragment length is 279 bps INFO @ Tue, 27 Jun 2017 11:55:27: #2 alternative fragment length(s) may be 279 bps INFO @ Tue, 27 Jun 2017 11:55:27: #2.2 Generate R script for model : SRX208771.10_model.r INFO @ Tue, 27 Jun 2017 11:55:27: start X-correlation... INFO @ Tue, 27 Jun 2017 11:55:27: end of X-cor INFO @ Tue, 27 Jun 2017 11:55:27: #2 finished! INFO @ Tue, 27 Jun 2017 11:55:27: #2 predicted fragment length is 279 bps INFO @ Tue, 27 Jun 2017 11:55:27: #2 alternative fragment length(s) may be 279 bps INFO @ Tue, 27 Jun 2017 11:55:27: #2.2 Generate R script for model : SRX208771.20_model.r INFO @ Tue, 27 Jun 2017 11:55:27: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:55:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:55:27: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:55:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:55:41: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:55:42: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:55:43: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:55:49: #4 Write output xls file... SRX208771.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:55:49: #4 Write peak in narrowPeak format file... SRX208771.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:55:49: #4 Write summits bed file... SRX208771.05_summits.bed INFO @ Tue, 27 Jun 2017 11:55:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1357 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:55:50: #4 Write output xls file... SRX208771.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:55:50: #4 Write peak in narrowPeak format file... SRX208771.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:55:50: #4 Write summits bed file... SRX208771.20_summits.bed INFO @ Tue, 27 Jun 2017 11:55:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (915 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:55:51: #4 Write output xls file... SRX208771.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:55:51: #4 Write peak in narrowPeak format file... SRX208771.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:55:51: #4 Write summits bed file... SRX208771.10_summits.bed INFO @ Tue, 27 Jun 2017 11:55:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1129 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。