Job ID = 9157134 sra ファイルのダウンロード中... Completed: 259665K bytes transferred in 5 seconds (392613K 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 7769658 spots for /home/okishinya/chipatlas/results/ce10/SRX2228868/SRR4380324.sra Written 7769658 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: 00:01:50 7769658 reads; of these: 7769658 (100.00%) were unpaired; of these: 915587 (11.78%) aligned 0 times 5877425 (75.65%) aligned exactly 1 time 976646 (12.57%) aligned >1 times 88.22% overall alignment rate Time searching: 00:01:50 Overall time: 00:01:50 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_rmdupse_core] 4004330 / 6854071 = 0.5842 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 10:39:56: # Command line: callpeak -t SRX2228868.bam -f BAM -g ce -n SRX2228868.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228868.20 # format = BAM # ChIP-seq file = ['SRX2228868.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 10:39:56: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:39:56: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:39:56: # Command line: callpeak -t SRX2228868.bam -f BAM -g ce -n SRX2228868.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228868.05 # format = BAM # ChIP-seq file = ['SRX2228868.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 10:39:56: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:39:56: # Command line: callpeak -t SRX2228868.bam -f BAM -g ce -n SRX2228868.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228868.10 # format = BAM # ChIP-seq file = ['SRX2228868.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 10:39:56: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:39:56: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:39:56: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:40:04: 1000000 INFO @ Tue, 27 Jun 2017 10:40:04: 1000000 INFO @ Tue, 27 Jun 2017 10:40:04: 1000000 INFO @ Tue, 27 Jun 2017 10:40:10: 2000000 INFO @ Tue, 27 Jun 2017 10:40:12: 2000000 INFO @ Tue, 27 Jun 2017 10:40:12: 2000000 INFO @ Tue, 27 Jun 2017 10:40:16: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:40:16: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:40:16: #1 total tags in treatment: 2849741 INFO @ Tue, 27 Jun 2017 10:40:16: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:40:16: #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 10:40:16: #1 tags after filtering in treatment: 2849741 INFO @ Tue, 27 Jun 2017 10:40:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:40:16: #1 finished! INFO @ Tue, 27 Jun 2017 10:40:16: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:40:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:40:17: #2 number of paired peaks: 2479 INFO @ Tue, 27 Jun 2017 10:40:17: start model_add_line... INFO @ Tue, 27 Jun 2017 10:40:17: start X-correlation... INFO @ Tue, 27 Jun 2017 10:40:17: end of X-cor INFO @ Tue, 27 Jun 2017 10:40:17: #2 finished! INFO @ Tue, 27 Jun 2017 10:40:17: #2 predicted fragment length is 255 bps INFO @ Tue, 27 Jun 2017 10:40:17: #2 alternative fragment length(s) may be 255 bps INFO @ Tue, 27 Jun 2017 10:40:17: #2.2 Generate R script for model : SRX2228868.10_model.r INFO @ Tue, 27 Jun 2017 10:40:17: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:40:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:40:19: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:40:19: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:40:19: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:40:19: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:40:19: #1 total tags in treatment: 2849741 INFO @ Tue, 27 Jun 2017 10:40:19: #1 total tags in treatment: 2849741 INFO @ Tue, 27 Jun 2017 10:40:19: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:40:19: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:40:19: #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 10:40:19: #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 10:40:19: #1 tags after filtering in treatment: 2849741 INFO @ Tue, 27 Jun 2017 10:40:19: #1 tags after filtering in treatment: 2849741 INFO @ Tue, 27 Jun 2017 10:40:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:40:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:40:19: #1 finished! INFO @ Tue, 27 Jun 2017 10:40:19: #1 finished! INFO @ Tue, 27 Jun 2017 10:40:19: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:40:19: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:40:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:40:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:40:19: #2 number of paired peaks: 2479 INFO @ Tue, 27 Jun 2017 10:40:19: start model_add_line... INFO @ Tue, 27 Jun 2017 10:40:19: #2 number of paired peaks: 2479 INFO @ Tue, 27 Jun 2017 10:40:19: start model_add_line... INFO @ Tue, 27 Jun 2017 10:40:19: start X-correlation... INFO @ Tue, 27 Jun 2017 10:40:19: start X-correlation... INFO @ Tue, 27 Jun 2017 10:40:19: end of X-cor INFO @ Tue, 27 Jun 2017 10:40:19: #2 finished! INFO @ Tue, 27 Jun 2017 10:40:19: #2 predicted fragment length is 255 bps INFO @ Tue, 27 Jun 2017 10:40:19: #2 alternative fragment length(s) may be 255 bps INFO @ Tue, 27 Jun 2017 10:40:19: #2.2 Generate R script for model : SRX2228868.20_model.r INFO @ Tue, 27 Jun 2017 10:40:19: end of X-cor INFO @ Tue, 27 Jun 2017 10:40:19: #2 finished! INFO @ Tue, 27 Jun 2017 10:40:19: #2 predicted fragment length is 255 bps INFO @ Tue, 27 Jun 2017 10:40:19: #2 alternative fragment length(s) may be 255 bps INFO @ Tue, 27 Jun 2017 10:40:19: #2.2 Generate R script for model : SRX2228868.05_model.r INFO @ Tue, 27 Jun 2017 10:40:19: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:40:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:40:19: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:40:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:40:25: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:40:28: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:40:28: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:40:29: #4 Write output xls file... SRX2228868.10_peaks.xls INFO @ Tue, 27 Jun 2017 10:40:29: #4 Write peak in narrowPeak format file... SRX2228868.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:40:29: #4 Write summits bed file... SRX2228868.10_summits.bed INFO @ Tue, 27 Jun 2017 10:40:29: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (2329 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:40:32: #4 Write output xls file... SRX2228868.05_peaks.xls INFO @ Tue, 27 Jun 2017 10:40:32: #4 Write peak in narrowPeak format file... SRX2228868.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:40:32: #4 Write summits bed file... SRX2228868.05_summits.bed INFO @ Tue, 27 Jun 2017 10:40:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3167 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:40:32: #4 Write output xls file... SRX2228868.20_peaks.xls INFO @ Tue, 27 Jun 2017 10:40:32: #4 Write peak in narrowPeak format file... SRX2228868.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:40:32: #4 Write summits bed file... SRX2228868.20_summits.bed INFO @ Tue, 27 Jun 2017 10:40:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1220 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。