Job ID = 10924604 sra ファイルのダウンロード中... Completed: 402051K bytes transferred in 11 seconds (294647K 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: PAIRED fastq に変換中... Read 6572922 spots for /home/okishinya/chipatlas/results/dm3/SRX2396691/SRR5078061.sra Written 6572922 spots for /home/okishinya/chipatlas/results/dm3/SRX2396691/SRR5078061.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: 00:06:34 6572922 reads; of these: 6572922 (100.00%) were paired; of these: 3800686 (57.82%) aligned concordantly 0 times 2495718 (37.97%) aligned concordantly exactly 1 time 276518 (4.21%) aligned concordantly >1 times ---- 3800686 pairs aligned concordantly 0 times; of these: 477063 (12.55%) aligned discordantly 1 time ---- 3323623 pairs aligned 0 times concordantly or discordantly; of these: 6647246 mates make up the pairs; of these: 4805805 (72.30%) aligned 0 times 1348244 (20.28%) aligned exactly 1 time 493197 (7.42%) aligned >1 times 63.44% overall alignment rate Time searching: 00:06:35 Overall time: 00:06:35 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 425153 / 2948385 = 0.1442 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 Aug 2018 10:35:04: # Command line: callpeak -t SRX2396691.bam -f BAM -g dm -n SRX2396691.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2396691.10 # format = BAM # ChIP-seq file = ['SRX2396691.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 Aug 2018 10:35:04: # Command line: callpeak -t SRX2396691.bam -f BAM -g dm -n SRX2396691.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2396691.20 # format = BAM # ChIP-seq file = ['SRX2396691.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 Aug 2018 10:35:04: # Command line: callpeak -t SRX2396691.bam -f BAM -g dm -n SRX2396691.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2396691.05 # format = BAM # ChIP-seq file = ['SRX2396691.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 Aug 2018 10:35:04: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:35:04: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:35:04: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:35:04: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:35:04: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:35:04: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:35:09: 1000000 INFO @ Mon, 06 Aug 2018 10:35:09: 1000000 INFO @ Mon, 06 Aug 2018 10:35:09: 1000000 INFO @ Mon, 06 Aug 2018 10:35:14: 2000000 INFO @ Mon, 06 Aug 2018 10:35:14: 2000000 INFO @ Mon, 06 Aug 2018 10:35:14: 2000000 INFO @ Mon, 06 Aug 2018 10:35:19: 3000000 INFO @ Mon, 06 Aug 2018 10:35:19: 3000000 INFO @ Mon, 06 Aug 2018 10:35:20: 3000000 INFO @ Mon, 06 Aug 2018 10:35:24: 4000000 INFO @ Mon, 06 Aug 2018 10:35:25: 4000000 INFO @ Mon, 06 Aug 2018 10:35:25: 4000000 INFO @ Mon, 06 Aug 2018 10:35:30: 5000000 INFO @ Mon, 06 Aug 2018 10:35:30: 5000000 INFO @ Mon, 06 Aug 2018 10:35:30: 5000000 INFO @ Mon, 06 Aug 2018 10:35:35: 6000000 INFO @ Mon, 06 Aug 2018 10:35:35: 6000000 INFO @ Mon, 06 Aug 2018 10:35:35: 6000000 INFO @ Mon, 06 Aug 2018 10:35:40: 7000000 INFO @ Mon, 06 Aug 2018 10:35:40: 7000000 INFO @ Mon, 06 Aug 2018 10:35:41: 7000000 INFO @ Mon, 06 Aug 2018 10:35:42: #1 tag size is determined as 50 bps INFO @ Mon, 06 Aug 2018 10:35:42: #1 tag size = 50 INFO @ Mon, 06 Aug 2018 10:35:42: #1 total tags in treatment: 2368238 INFO @ Mon, 06 Aug 2018 10:35:42: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:35:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:35:42: #1 tags after filtering in treatment: 2210701 INFO @ Mon, 06 Aug 2018 10:35:42: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 06 Aug 2018 10:35:42: #1 finished! INFO @ Mon, 06 Aug 2018 10:35:42: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:35:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:35:42: #1 tag size is determined as 50 bps INFO @ Mon, 06 Aug 2018 10:35:42: #1 tag size = 50 INFO @ Mon, 06 Aug 2018 10:35:42: #1 total tags in treatment: 2368238 INFO @ Mon, 06 Aug 2018 10:35:42: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:35:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:35:42: #1 tags after filtering in treatment: 2210701 INFO @ Mon, 06 Aug 2018 10:35:42: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 06 Aug 2018 10:35:42: #1 finished! INFO @ Mon, 06 Aug 2018 10:35:42: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:35:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:35:43: #2 number of paired peaks: 4517 INFO @ Mon, 06 Aug 2018 10:35:43: start model_add_line... INFO @ Mon, 06 Aug 2018 10:35:43: start X-correlation... INFO @ Mon, 06 Aug 2018 10:35:43: end of X-cor INFO @ Mon, 06 Aug 2018 10:35:43: #2 finished! INFO @ Mon, 06 Aug 2018 10:35:43: #2 predicted fragment length is 255 bps INFO @ Mon, 06 Aug 2018 10:35:43: #2 alternative fragment length(s) may be 255 bps INFO @ Mon, 06 Aug 2018 10:35:43: #2.2 Generate R script for model : SRX2396691.10_model.r INFO @ Mon, 06 Aug 2018 10:35:43: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:35:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:35:43: #2 number of paired peaks: 4517 INFO @ Mon, 06 Aug 2018 10:35:43: start model_add_line... INFO @ Mon, 06 Aug 2018 10:35:43: start X-correlation... INFO @ Mon, 06 Aug 2018 10:35:43: end of X-cor INFO @ Mon, 06 Aug 2018 10:35:43: #2 finished! INFO @ Mon, 06 Aug 2018 10:35:43: #2 predicted fragment length is 255 bps INFO @ Mon, 06 Aug 2018 10:35:43: #2 alternative fragment length(s) may be 255 bps INFO @ Mon, 06 Aug 2018 10:35:43: #2.2 Generate R script for model : SRX2396691.05_model.r INFO @ Mon, 06 Aug 2018 10:35:43: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:35:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:35:43: #1 tag size is determined as 50 bps INFO @ Mon, 06 Aug 2018 10:35:43: #1 tag size = 50 INFO @ Mon, 06 Aug 2018 10:35:43: #1 total tags in treatment: 2368238 INFO @ Mon, 06 Aug 2018 10:35:43: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:35:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:35:43: #1 tags after filtering in treatment: 2210701 INFO @ Mon, 06 Aug 2018 10:35:43: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 06 Aug 2018 10:35:43: #1 finished! INFO @ Mon, 06 Aug 2018 10:35:43: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:35:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:35:44: #2 number of paired peaks: 4517 INFO @ Mon, 06 Aug 2018 10:35:44: start model_add_line... INFO @ Mon, 06 Aug 2018 10:35:44: start X-correlation... INFO @ Mon, 06 Aug 2018 10:35:44: end of X-cor INFO @ Mon, 06 Aug 2018 10:35:44: #2 finished! INFO @ Mon, 06 Aug 2018 10:35:44: #2 predicted fragment length is 255 bps INFO @ Mon, 06 Aug 2018 10:35:44: #2 alternative fragment length(s) may be 255 bps INFO @ Mon, 06 Aug 2018 10:35:44: #2.2 Generate R script for model : SRX2396691.20_model.r INFO @ Mon, 06 Aug 2018 10:35:44: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:35:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:35:49: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:35:49: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:35:50: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:35:52: #4 Write output xls file... SRX2396691.05_peaks.xls INFO @ Mon, 06 Aug 2018 10:35:52: #4 Write peak in narrowPeak format file... SRX2396691.05_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:35:52: #4 Write summits bed file... SRX2396691.05_summits.bed INFO @ Mon, 06 Aug 2018 10:35:52: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (4623 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 06 Aug 2018 10:35:53: #4 Write output xls file... SRX2396691.10_peaks.xls INFO @ Mon, 06 Aug 2018 10:35:53: #4 Write peak in narrowPeak format file... SRX2396691.10_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:35:53: #4 Write summits bed file... SRX2396691.10_summits.bed INFO @ Mon, 06 Aug 2018 10:35:53: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (2690 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 06 Aug 2018 10:35:53: #4 Write output xls file... SRX2396691.20_peaks.xls INFO @ Mon, 06 Aug 2018 10:35:53: #4 Write peak in narrowPeak format file... SRX2396691.20_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:35:53: #4 Write summits bed file... SRX2396691.20_summits.bed INFO @ Mon, 06 Aug 2018 10:35:53: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1206 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。