Job ID = 10609512 sra ファイルのダウンロード中... Completed: 600150K bytes transferred in 50 seconds (96996K 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 18962244 spots for /home/okishinya/chipatlas/results/dm3/SRX3011239/SRR5834716.sra Written 18962244 spots for /home/okishinya/chipatlas/results/dm3/SRX3011239/SRR5834716.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: 00:00:01 Multiseed full-index search: 00:06:29 18962244 reads; of these: 18962244 (100.00%) were unpaired; of these: 538904 (2.84%) aligned 0 times 15465417 (81.56%) aligned exactly 1 time 2957923 (15.60%) aligned >1 times 97.16% overall alignment rate Time searching: 00:06:30 Overall time: 00:06:30 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] 9833616 / 18423340 = 0.5338 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, 07 May 2018 11:07:14: # Command line: callpeak -t SRX3011239.bam -f BAM -g dm -n SRX3011239.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3011239.20 # format = BAM # ChIP-seq file = ['SRX3011239.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, 07 May 2018 11:07:14: #1 read tag files... INFO @ Mon, 07 May 2018 11:07:14: #1 read treatment tags... INFO @ Mon, 07 May 2018 11:07:14: # Command line: callpeak -t SRX3011239.bam -f BAM -g dm -n SRX3011239.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3011239.10 # format = BAM # ChIP-seq file = ['SRX3011239.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, 07 May 2018 11:07:14: #1 read tag files... INFO @ Mon, 07 May 2018 11:07:14: #1 read treatment tags... INFO @ Mon, 07 May 2018 11:07:14: # Command line: callpeak -t SRX3011239.bam -f BAM -g dm -n SRX3011239.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3011239.05 # format = BAM # ChIP-seq file = ['SRX3011239.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, 07 May 2018 11:07:14: #1 read tag files... INFO @ Mon, 07 May 2018 11:07:14: #1 read treatment tags... INFO @ Mon, 07 May 2018 11:07:23: 1000000 INFO @ Mon, 07 May 2018 11:07:23: 1000000 INFO @ Mon, 07 May 2018 11:07:23: 1000000 INFO @ Mon, 07 May 2018 11:07:31: 2000000 INFO @ Mon, 07 May 2018 11:07:31: 2000000 INFO @ Mon, 07 May 2018 11:07:31: 2000000 INFO @ Mon, 07 May 2018 11:07:39: 3000000 INFO @ Mon, 07 May 2018 11:07:40: 3000000 INFO @ Mon, 07 May 2018 11:07:40: 3000000 INFO @ Mon, 07 May 2018 11:07:47: 4000000 INFO @ Mon, 07 May 2018 11:07:48: 4000000 INFO @ Mon, 07 May 2018 11:07:48: 4000000 INFO @ Mon, 07 May 2018 11:07:55: 5000000 INFO @ Mon, 07 May 2018 11:07:56: 5000000 INFO @ Mon, 07 May 2018 11:07:56: 5000000 INFO @ Mon, 07 May 2018 11:08:04: 6000000 INFO @ Mon, 07 May 2018 11:08:05: 6000000 INFO @ Mon, 07 May 2018 11:08:05: 6000000 INFO @ Mon, 07 May 2018 11:08:12: 7000000 INFO @ Mon, 07 May 2018 11:08:13: 7000000 INFO @ Mon, 07 May 2018 11:08:13: 7000000 INFO @ Mon, 07 May 2018 11:08:20: 8000000 INFO @ Mon, 07 May 2018 11:08:21: 8000000 INFO @ Mon, 07 May 2018 11:08:21: 8000000 INFO @ Mon, 07 May 2018 11:08:25: #1 tag size is determined as 80 bps INFO @ Mon, 07 May 2018 11:08:25: #1 tag size = 80 INFO @ Mon, 07 May 2018 11:08:25: #1 total tags in treatment: 8589724 INFO @ Mon, 07 May 2018 11:08:25: #1 user defined the maximum tags... INFO @ Mon, 07 May 2018 11:08:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 May 2018 11:08:25: #1 tags after filtering in treatment: 8589724 INFO @ Mon, 07 May 2018 11:08:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 May 2018 11:08:25: #1 finished! INFO @ Mon, 07 May 2018 11:08:25: #2 Build Peak Model... INFO @ Mon, 07 May 2018 11:08:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 07 May 2018 11:08:26: #2 number of paired peaks: 4745 INFO @ Mon, 07 May 2018 11:08:26: start model_add_line... INFO @ Mon, 07 May 2018 11:08:26: start X-correlation... INFO @ Mon, 07 May 2018 11:08:26: end of X-cor INFO @ Mon, 07 May 2018 11:08:26: #2 finished! INFO @ Mon, 07 May 2018 11:08:26: #2 predicted fragment length is 173 bps INFO @ Mon, 07 May 2018 11:08:26: #2 alternative fragment length(s) may be 173 bps INFO @ Mon, 07 May 2018 11:08:26: #2.2 Generate R script for model : SRX3011239.20_model.r INFO @ Mon, 07 May 2018 11:08:26: #1 tag size is determined as 80 bps INFO @ Mon, 07 May 2018 11:08:26: #1 tag size = 80 INFO @ Mon, 07 May 2018 11:08:26: #1 total tags in treatment: 8589724 INFO @ Mon, 07 May 2018 11:08:26: #1 user defined the maximum tags... INFO @ Mon, 07 May 2018 11:08:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 May 2018 11:08:26: #1 tag size is determined as 80 bps INFO @ Mon, 07 May 2018 11:08:26: #1 tag size = 80 INFO @ Mon, 07 May 2018 11:08:26: #1 total tags in treatment: 8589724 INFO @ Mon, 07 May 2018 11:08:26: #1 user defined the maximum tags... INFO @ Mon, 07 May 2018 11:08:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 May 2018 11:08:26: #3 Call peaks... INFO @ Mon, 07 May 2018 11:08:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 May 2018 11:08:27: #1 tags after filtering in treatment: 8589724 INFO @ Mon, 07 May 2018 11:08:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 May 2018 11:08:27: #1 finished! INFO @ Mon, 07 May 2018 11:08:27: #2 Build Peak Model... INFO @ Mon, 07 May 2018 11:08:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 07 May 2018 11:08:27: #1 tags after filtering in treatment: 8589724 INFO @ Mon, 07 May 2018 11:08:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 May 2018 11:08:27: #1 finished! INFO @ Mon, 07 May 2018 11:08:27: #2 Build Peak Model... INFO @ Mon, 07 May 2018 11:08:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 07 May 2018 11:08:28: #2 number of paired peaks: 4745 INFO @ Mon, 07 May 2018 11:08:28: start model_add_line... INFO @ Mon, 07 May 2018 11:08:28: #2 number of paired peaks: 4745 INFO @ Mon, 07 May 2018 11:08:28: start model_add_line... INFO @ Mon, 07 May 2018 11:08:28: start X-correlation... INFO @ Mon, 07 May 2018 11:08:28: end of X-cor INFO @ Mon, 07 May 2018 11:08:28: #2 finished! INFO @ Mon, 07 May 2018 11:08:28: #2 predicted fragment length is 173 bps INFO @ Mon, 07 May 2018 11:08:28: #2 alternative fragment length(s) may be 173 bps INFO @ Mon, 07 May 2018 11:08:28: #2.2 Generate R script for model : SRX3011239.05_model.r INFO @ Mon, 07 May 2018 11:08:28: #3 Call peaks... INFO @ Mon, 07 May 2018 11:08:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 May 2018 11:08:28: start X-correlation... INFO @ Mon, 07 May 2018 11:08:28: end of X-cor INFO @ Mon, 07 May 2018 11:08:28: #2 finished! INFO @ Mon, 07 May 2018 11:08:28: #2 predicted fragment length is 173 bps INFO @ Mon, 07 May 2018 11:08:28: #2 alternative fragment length(s) may be 173 bps INFO @ Mon, 07 May 2018 11:08:28: #2.2 Generate R script for model : SRX3011239.10_model.r INFO @ Mon, 07 May 2018 11:08:28: #3 Call peaks... INFO @ Mon, 07 May 2018 11:08:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 May 2018 11:08:53: #3 Call peaks for each chromosome... INFO @ Mon, 07 May 2018 11:08:53: #3 Call peaks for each chromosome... INFO @ Mon, 07 May 2018 11:08:54: #3 Call peaks for each chromosome... INFO @ Mon, 07 May 2018 11:09:05: #4 Write output xls file... SRX3011239.05_peaks.xls INFO @ Mon, 07 May 2018 11:09:06: #4 Write peak in narrowPeak format file... SRX3011239.05_peaks.narrowPeak INFO @ Mon, 07 May 2018 11:09:06: #4 Write summits bed file... SRX3011239.05_summits.bed INFO @ Mon, 07 May 2018 11:09:06: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (9699 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 07 May 2018 11:09:06: #4 Write output xls file... SRX3011239.20_peaks.xls INFO @ Mon, 07 May 2018 11:09:06: #4 Write peak in narrowPeak format file... SRX3011239.20_peaks.narrowPeak INFO @ Mon, 07 May 2018 11:09:06: #4 Write summits bed file... SRX3011239.20_summits.bed INFO @ Mon, 07 May 2018 11:09:06: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5095 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 07 May 2018 11:09:07: #4 Write output xls file... SRX3011239.10_peaks.xls INFO @ Mon, 07 May 2018 11:09:07: #4 Write peak in narrowPeak format file... SRX3011239.10_peaks.narrowPeak INFO @ Mon, 07 May 2018 11:09:07: #4 Write summits bed file... SRX3011239.10_summits.bed INFO @ Mon, 07 May 2018 11:09:07: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7362 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。