Job ID = 11171261 sra ファイルのダウンロード中... Completed: 1436274K bytes transferred in 61 seconds (191184K 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 21595570 spots for /home/okishinya/chipatlas/results/dm3/SRX2985881/SRR5806896.sra Written 21595570 spots for /home/okishinya/chipatlas/results/dm3/SRX2985881/SRR5806896.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: 00:00:00 Multiseed full-index search: 00:51:33 21595570 reads; of these: 21595570 (100.00%) were paired; of these: 3958080 (18.33%) aligned concordantly 0 times 13712980 (63.50%) aligned concordantly exactly 1 time 3924510 (18.17%) aligned concordantly >1 times ---- 3958080 pairs aligned concordantly 0 times; of these: 23891 (0.60%) aligned discordantly 1 time ---- 3934189 pairs aligned 0 times concordantly or discordantly; of these: 7868378 mates make up the pairs; of these: 6944946 (88.26%) aligned 0 times 553283 (7.03%) aligned exactly 1 time 370149 (4.70%) aligned >1 times 83.92% overall alignment rate Time searching: 00:51:33 Overall time: 00:51:33 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 16 files... [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] 10597603 / 17642656 = 0.6007 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 @ Sat, 08 Sep 2018 14:24:07: # Command line: callpeak -t SRX2985881.bam -f BAM -g dm -n SRX2985881.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2985881.10 # format = BAM # ChIP-seq file = ['SRX2985881.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 @ Sat, 08 Sep 2018 14:24:07: # Command line: callpeak -t SRX2985881.bam -f BAM -g dm -n SRX2985881.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2985881.05 # format = BAM # ChIP-seq file = ['SRX2985881.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 @ Sat, 08 Sep 2018 14:24:07: # Command line: callpeak -t SRX2985881.bam -f BAM -g dm -n SRX2985881.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2985881.20 # format = BAM # ChIP-seq file = ['SRX2985881.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 @ Sat, 08 Sep 2018 14:24:07: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:24:07: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:24:07: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:24:07: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:24:07: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:24:07: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:24:14: 1000000 INFO @ Sat, 08 Sep 2018 14:24:14: 1000000 INFO @ Sat, 08 Sep 2018 14:24:14: 1000000 INFO @ Sat, 08 Sep 2018 14:24:20: 2000000 INFO @ Sat, 08 Sep 2018 14:24:21: 2000000 INFO @ Sat, 08 Sep 2018 14:24:21: 2000000 INFO @ Sat, 08 Sep 2018 14:24:26: 3000000 INFO @ Sat, 08 Sep 2018 14:24:27: 3000000 INFO @ Sat, 08 Sep 2018 14:24:27: 3000000 INFO @ Sat, 08 Sep 2018 14:24:33: 4000000 INFO @ Sat, 08 Sep 2018 14:24:34: 4000000 INFO @ Sat, 08 Sep 2018 14:24:34: 4000000 INFO @ Sat, 08 Sep 2018 14:24:39: 5000000 INFO @ Sat, 08 Sep 2018 14:24:41: 5000000 INFO @ Sat, 08 Sep 2018 14:24:41: 5000000 INFO @ Sat, 08 Sep 2018 14:24:45: 6000000 INFO @ Sat, 08 Sep 2018 14:24:47: 6000000 INFO @ Sat, 08 Sep 2018 14:24:47: 6000000 INFO @ Sat, 08 Sep 2018 14:24:51: 7000000 INFO @ Sat, 08 Sep 2018 14:24:54: 7000000 INFO @ Sat, 08 Sep 2018 14:24:54: 7000000 INFO @ Sat, 08 Sep 2018 14:24:58: 8000000 INFO @ Sat, 08 Sep 2018 14:25:01: 8000000 INFO @ Sat, 08 Sep 2018 14:25:01: 8000000 INFO @ Sat, 08 Sep 2018 14:25:04: 9000000 INFO @ Sat, 08 Sep 2018 14:25:07: 9000000 INFO @ Sat, 08 Sep 2018 14:25:08: 9000000 INFO @ Sat, 08 Sep 2018 14:25:10: 10000000 INFO @ Sat, 08 Sep 2018 14:25:14: 10000000 INFO @ Sat, 08 Sep 2018 14:25:14: 10000000 INFO @ Sat, 08 Sep 2018 14:25:16: 11000000 INFO @ Sat, 08 Sep 2018 14:25:21: 11000000 INFO @ Sat, 08 Sep 2018 14:25:21: 11000000 INFO @ Sat, 08 Sep 2018 14:25:23: 12000000 INFO @ Sat, 08 Sep 2018 14:25:28: 12000000 INFO @ Sat, 08 Sep 2018 14:25:28: 12000000 INFO @ Sat, 08 Sep 2018 14:25:29: 13000000 INFO @ Sat, 08 Sep 2018 14:25:35: 13000000 INFO @ Sat, 08 Sep 2018 14:25:35: 14000000 INFO @ Sat, 08 Sep 2018 14:25:35: 13000000 INFO @ Sat, 08 Sep 2018 14:25:41: 15000000 INFO @ Sat, 08 Sep 2018 14:25:42: 14000000 INFO @ Sat, 08 Sep 2018 14:25:42: #1 tag size is determined as 78 bps INFO @ Sat, 08 Sep 2018 14:25:42: #1 tag size = 78 INFO @ Sat, 08 Sep 2018 14:25:42: #1 total tags in treatment: 7049801 INFO @ Sat, 08 Sep 2018 14:25:42: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:25:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:25:42: #1 tags after filtering in treatment: 6715548 INFO @ Sat, 08 Sep 2018 14:25:42: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 08 Sep 2018 14:25:42: #1 finished! INFO @ Sat, 08 Sep 2018 14:25:42: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:25:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:25:42: 14000000 INFO @ Sat, 08 Sep 2018 14:25:43: #2 number of paired peaks: 1136 INFO @ Sat, 08 Sep 2018 14:25:43: start model_add_line... INFO @ Sat, 08 Sep 2018 14:25:43: start X-correlation... INFO @ Sat, 08 Sep 2018 14:25:43: end of X-cor INFO @ Sat, 08 Sep 2018 14:25:43: #2 finished! INFO @ Sat, 08 Sep 2018 14:25:43: #2 predicted fragment length is 215 bps INFO @ Sat, 08 Sep 2018 14:25:43: #2 alternative fragment length(s) may be 215 bps INFO @ Sat, 08 Sep 2018 14:25:43: #2.2 Generate R script for model : SRX2985881.20_model.r INFO @ Sat, 08 Sep 2018 14:25:43: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:25:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:25:49: 15000000 INFO @ Sat, 08 Sep 2018 14:25:49: #1 tag size is determined as 78 bps INFO @ Sat, 08 Sep 2018 14:25:49: #1 tag size = 78 INFO @ Sat, 08 Sep 2018 14:25:49: #1 total tags in treatment: 7049801 INFO @ Sat, 08 Sep 2018 14:25:49: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:25:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:25:49: #1 tags after filtering in treatment: 6715548 INFO @ Sat, 08 Sep 2018 14:25:49: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 08 Sep 2018 14:25:49: #1 finished! INFO @ Sat, 08 Sep 2018 14:25:49: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:25:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:25:49: 15000000 INFO @ Sat, 08 Sep 2018 14:25:50: #1 tag size is determined as 78 bps INFO @ Sat, 08 Sep 2018 14:25:50: #1 tag size = 78 INFO @ Sat, 08 Sep 2018 14:25:50: #1 total tags in treatment: 7049801 INFO @ Sat, 08 Sep 2018 14:25:50: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:25:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:25:50: #2 number of paired peaks: 1136 INFO @ Sat, 08 Sep 2018 14:25:50: start model_add_line... INFO @ Sat, 08 Sep 2018 14:25:50: start X-correlation... INFO @ Sat, 08 Sep 2018 14:25:50: end of X-cor INFO @ Sat, 08 Sep 2018 14:25:50: #2 finished! INFO @ Sat, 08 Sep 2018 14:25:50: #2 predicted fragment length is 215 bps INFO @ Sat, 08 Sep 2018 14:25:50: #2 alternative fragment length(s) may be 215 bps INFO @ Sat, 08 Sep 2018 14:25:50: #2.2 Generate R script for model : SRX2985881.10_model.r INFO @ Sat, 08 Sep 2018 14:25:50: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:25:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:25:50: #1 tags after filtering in treatment: 6715548 INFO @ Sat, 08 Sep 2018 14:25:50: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 08 Sep 2018 14:25:50: #1 finished! INFO @ Sat, 08 Sep 2018 14:25:50: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:25:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:25:51: #2 number of paired peaks: 1136 INFO @ Sat, 08 Sep 2018 14:25:51: start model_add_line... INFO @ Sat, 08 Sep 2018 14:25:51: start X-correlation... INFO @ Sat, 08 Sep 2018 14:25:51: end of X-cor INFO @ Sat, 08 Sep 2018 14:25:51: #2 finished! INFO @ Sat, 08 Sep 2018 14:25:51: #2 predicted fragment length is 215 bps INFO @ Sat, 08 Sep 2018 14:25:51: #2 alternative fragment length(s) may be 215 bps INFO @ Sat, 08 Sep 2018 14:25:51: #2.2 Generate R script for model : SRX2985881.05_model.r INFO @ Sat, 08 Sep 2018 14:25:51: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:25:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:26:02: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:26:09: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:26:09: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:26:11: #4 Write output xls file... SRX2985881.20_peaks.xls INFO @ Sat, 08 Sep 2018 14:26:11: #4 Write peak in narrowPeak format file... SRX2985881.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:26:11: #4 Write summits bed file... SRX2985881.20_summits.bed INFO @ Sat, 08 Sep 2018 14:26:11: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (915 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 14:26:17: #4 Write output xls file... SRX2985881.05_peaks.xls INFO @ Sat, 08 Sep 2018 14:26:17: #4 Write peak in narrowPeak format file... SRX2985881.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:26:17: #4 Write summits bed file... SRX2985881.05_summits.bed INFO @ Sat, 08 Sep 2018 14:26:17: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5012 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 14:26:18: #4 Write output xls file... SRX2985881.10_peaks.xls INFO @ Sat, 08 Sep 2018 14:26:18: #4 Write peak in narrowPeak format file... SRX2985881.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:26:18: #4 Write summits bed file... SRX2985881.10_summits.bed INFO @ Sat, 08 Sep 2018 14:26:18: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2441 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。