Job ID = 9157402 sra ファイルのダウンロード中... Completed: 711304K bytes transferred in 9 seconds (630698K 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: PAIRED fastq に変換中... Written 15852792 spots for /home/okishinya/chipatlas/results/ce10/SRX1995068/SRR3994000.sra Written 15852792 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: 00:21:17 15852792 reads; of these: 15852792 (100.00%) were paired; of these: 4338325 (27.37%) aligned concordantly 0 times 7731767 (48.77%) aligned concordantly exactly 1 time 3782700 (23.86%) aligned concordantly >1 times ---- 4338325 pairs aligned concordantly 0 times; of these: 1598125 (36.84%) aligned discordantly 1 time ---- 2740200 pairs aligned 0 times concordantly or discordantly; of these: 5480400 mates make up the pairs; of these: 2574982 (46.99%) aligned 0 times 1090750 (19.90%) aligned exactly 1 time 1814668 (33.11%) aligned >1 times 91.88% overall alignment rate Time searching: 00:21:17 Overall time: 00:21:17 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 12 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 5026540 / 13102593 = 0.3836 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 12:13:01: # Command line: callpeak -t SRX1995068.bam -f BAM -g ce -n SRX1995068.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1995068.05 # format = BAM # ChIP-seq file = ['SRX1995068.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 12:13:01: #1 read tag files... INFO @ Tue, 27 Jun 2017 12:13:01: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 12:13:01: # Command line: callpeak -t SRX1995068.bam -f BAM -g ce -n SRX1995068.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1995068.20 # format = BAM # ChIP-seq file = ['SRX1995068.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 12:13:01: #1 read tag files... INFO @ Tue, 27 Jun 2017 12:13:01: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 12:13:01: # Command line: callpeak -t SRX1995068.bam -f BAM -g ce -n SRX1995068.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1995068.10 # format = BAM # ChIP-seq file = ['SRX1995068.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 12:13:01: #1 read tag files... INFO @ Tue, 27 Jun 2017 12:13:01: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 12:13:09: 1000000 INFO @ Tue, 27 Jun 2017 12:13:10: 1000000 INFO @ Tue, 27 Jun 2017 12:13:10: 1000000 INFO @ Tue, 27 Jun 2017 12:13:17: 2000000 INFO @ Tue, 27 Jun 2017 12:13:18: 2000000 INFO @ Tue, 27 Jun 2017 12:13:18: 2000000 INFO @ Tue, 27 Jun 2017 12:13:24: 3000000 INFO @ Tue, 27 Jun 2017 12:13:26: 3000000 INFO @ Tue, 27 Jun 2017 12:13:26: 3000000 INFO @ Tue, 27 Jun 2017 12:13:32: 4000000 INFO @ Tue, 27 Jun 2017 12:13:34: 4000000 INFO @ Tue, 27 Jun 2017 12:13:36: 4000000 INFO @ Tue, 27 Jun 2017 12:13:40: 5000000 INFO @ Tue, 27 Jun 2017 12:13:41: 5000000 INFO @ Tue, 27 Jun 2017 12:13:45: 5000000 INFO @ Tue, 27 Jun 2017 12:13:48: 6000000 INFO @ Tue, 27 Jun 2017 12:13:49: 6000000 INFO @ Tue, 27 Jun 2017 12:13:55: 6000000 INFO @ Tue, 27 Jun 2017 12:13:56: 7000000 INFO @ Tue, 27 Jun 2017 12:13:57: 7000000 INFO @ Tue, 27 Jun 2017 12:14:04: 8000000 INFO @ Tue, 27 Jun 2017 12:14:04: 8000000 INFO @ Tue, 27 Jun 2017 12:14:05: 7000000 INFO @ Tue, 27 Jun 2017 12:14:11: 9000000 INFO @ Tue, 27 Jun 2017 12:14:12: 9000000 INFO @ Tue, 27 Jun 2017 12:14:13: 8000000 INFO @ Tue, 27 Jun 2017 12:14:17: 10000000 INFO @ Tue, 27 Jun 2017 12:14:19: 10000000 INFO @ Tue, 27 Jun 2017 12:14:20: 9000000 INFO @ Tue, 27 Jun 2017 12:14:24: 11000000 INFO @ Tue, 27 Jun 2017 12:14:26: 11000000 INFO @ Tue, 27 Jun 2017 12:14:28: 10000000 INFO @ Tue, 27 Jun 2017 12:14:30: 12000000 INFO @ Tue, 27 Jun 2017 12:14:33: 12000000 INFO @ Tue, 27 Jun 2017 12:14:35: 11000000 INFO @ Tue, 27 Jun 2017 12:14:37: 13000000 INFO @ Tue, 27 Jun 2017 12:14:40: 13000000 INFO @ Tue, 27 Jun 2017 12:14:42: 12000000 INFO @ Tue, 27 Jun 2017 12:14:43: 14000000 INFO @ Tue, 27 Jun 2017 12:14:46: 14000000 INFO @ Tue, 27 Jun 2017 12:14:49: 15000000 INFO @ Tue, 27 Jun 2017 12:14:50: 13000000 INFO @ Tue, 27 Jun 2017 12:14:53: 15000000 INFO @ Tue, 27 Jun 2017 12:14:55: 16000000 INFO @ Tue, 27 Jun 2017 12:14:57: 14000000 INFO @ Tue, 27 Jun 2017 12:15:00: 16000000 INFO @ Tue, 27 Jun 2017 12:15:02: 17000000 INFO @ Tue, 27 Jun 2017 12:15:04: 15000000 INFO @ Tue, 27 Jun 2017 12:15:07: 17000000 INFO @ Tue, 27 Jun 2017 12:15:08: 18000000 INFO @ Tue, 27 Jun 2017 12:15:11: 16000000 INFO @ Tue, 27 Jun 2017 12:15:13: 18000000 INFO @ Tue, 27 Jun 2017 12:15:14: 19000000 INFO @ Tue, 27 Jun 2017 12:15:15: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 12:15:15: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 12:15:15: #1 total tags in treatment: 6916486 INFO @ Tue, 27 Jun 2017 12:15:15: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:15:15: #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 12:15:15: #1 tags after filtering in treatment: 4492355 INFO @ Tue, 27 Jun 2017 12:15:15: #1 Redundant rate of treatment: 0.35 INFO @ Tue, 27 Jun 2017 12:15:15: #1 finished! INFO @ Tue, 27 Jun 2017 12:15:15: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:15:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:15:16: #2 number of paired peaks: 7440 INFO @ Tue, 27 Jun 2017 12:15:16: start model_add_line... INFO @ Tue, 27 Jun 2017 12:15:16: start X-correlation... INFO @ Tue, 27 Jun 2017 12:15:16: end of X-cor INFO @ Tue, 27 Jun 2017 12:15:16: #2 finished! INFO @ Tue, 27 Jun 2017 12:15:16: #2 predicted fragment length is 266 bps INFO @ Tue, 27 Jun 2017 12:15:16: #2 alternative fragment length(s) may be 266 bps INFO @ Tue, 27 Jun 2017 12:15:16: #2.2 Generate R script for model : SRX1995068.10_model.r INFO @ Tue, 27 Jun 2017 12:15:16: #3 Call peaks... INFO @ Tue, 27 Jun 2017 12:15:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:15:18: 17000000 INFO @ Tue, 27 Jun 2017 12:15:20: 19000000 INFO @ Tue, 27 Jun 2017 12:15:21: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 12:15:21: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 12:15:21: #1 total tags in treatment: 6916486 INFO @ Tue, 27 Jun 2017 12:15:21: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:15:21: #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 12:15:21: #1 tags after filtering in treatment: 4492355 INFO @ Tue, 27 Jun 2017 12:15:21: #1 Redundant rate of treatment: 0.35 INFO @ Tue, 27 Jun 2017 12:15:21: #1 finished! INFO @ Tue, 27 Jun 2017 12:15:21: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:15:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:15:22: #2 number of paired peaks: 7440 INFO @ Tue, 27 Jun 2017 12:15:22: start model_add_line... INFO @ Tue, 27 Jun 2017 12:15:22: start X-correlation... INFO @ Tue, 27 Jun 2017 12:15:22: end of X-cor INFO @ Tue, 27 Jun 2017 12:15:22: #2 finished! INFO @ Tue, 27 Jun 2017 12:15:22: #2 predicted fragment length is 266 bps INFO @ Tue, 27 Jun 2017 12:15:22: #2 alternative fragment length(s) may be 266 bps INFO @ Tue, 27 Jun 2017 12:15:22: #2.2 Generate R script for model : SRX1995068.20_model.r INFO @ Tue, 27 Jun 2017 12:15:22: #3 Call peaks... INFO @ Tue, 27 Jun 2017 12:15:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:15:24: 18000000 INFO @ Tue, 27 Jun 2017 12:15:30: 19000000 INFO @ Tue, 27 Jun 2017 12:15:31: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 12:15:31: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 12:15:31: #1 total tags in treatment: 6916486 INFO @ Tue, 27 Jun 2017 12:15:31: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:15:31: #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 12:15:31: #1 tags after filtering in treatment: 4492355 INFO @ Tue, 27 Jun 2017 12:15:31: #1 Redundant rate of treatment: 0.35 INFO @ Tue, 27 Jun 2017 12:15:31: #1 finished! INFO @ Tue, 27 Jun 2017 12:15:31: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:15:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:15:32: #2 number of paired peaks: 7440 INFO @ Tue, 27 Jun 2017 12:15:32: start model_add_line... INFO @ Tue, 27 Jun 2017 12:15:32: start X-correlation... INFO @ Tue, 27 Jun 2017 12:15:32: end of X-cor INFO @ Tue, 27 Jun 2017 12:15:32: #2 finished! INFO @ Tue, 27 Jun 2017 12:15:32: #2 predicted fragment length is 266 bps INFO @ Tue, 27 Jun 2017 12:15:32: #2 alternative fragment length(s) may be 266 bps INFO @ Tue, 27 Jun 2017 12:15:32: #2.2 Generate R script for model : SRX1995068.05_model.r INFO @ Tue, 27 Jun 2017 12:15:32: #3 Call peaks... INFO @ Tue, 27 Jun 2017 12:15:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:15:46: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:15:52: #4 Write output xls file... SRX1995068.10_peaks.xls INFO @ Tue, 27 Jun 2017 12:15:52: #4 Write peak in narrowPeak format file... SRX1995068.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:15:52: #4 Write summits bed file... SRX1995068.10_summits.bed INFO @ Tue, 27 Jun 2017 12:15:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2863 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 12:15:52: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:15:58: #4 Write output xls file... SRX1995068.20_peaks.xls INFO @ Tue, 27 Jun 2017 12:15:58: #4 Write peak in narrowPeak format file... SRX1995068.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:15:58: #4 Write summits bed file... SRX1995068.20_summits.bed INFO @ Tue, 27 Jun 2017 12:15:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1653 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 12:16:02: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:16:09: #4 Write output xls file... SRX1995068.05_peaks.xls INFO @ Tue, 27 Jun 2017 12:16:09: #4 Write peak in narrowPeak format file... SRX1995068.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:16:09: #4 Write summits bed file... SRX1995068.05_summits.bed INFO @ Tue, 27 Jun 2017 12:16:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4145 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。