Job ID = 2236859 sra ファイルのダウンロード中... Completed: 314075K bytes transferred in 13 seconds (188755K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 35211 0 35211 0 0 49233 0 --:--:-- --:--:-- --:--:-- 67325 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 15514273 spots for /home/okishinya/chipatlas/results/ce10/SRX059235/SRR190675.sra Written 15514273 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: 00:02:58 15514273 reads; of these: 15514273 (100.00%) were unpaired; of these: 1190770 (7.68%) aligned 0 times 11744903 (75.70%) aligned exactly 1 time 2578600 (16.62%) aligned >1 times 92.32% overall alignment rate Time searching: 00:02:58 Overall time: 00:02:58 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] 2909376 / 14323503 = 0.2031 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 @ Thu, 30 Apr 2015 11:17:07: # Command line: callpeak -t SRX059235.bam -f BAM -g ce -n SRX059235.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX059235.20 # format = BAM # ChIP-seq file = ['SRX059235.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 INFO @ Thu, 30 Apr 2015 11:17:07: # Command line: callpeak -t SRX059235.bam -f BAM -g ce -n SRX059235.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX059235.05 # format = BAM # ChIP-seq file = ['SRX059235.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 INFO @ Thu, 30 Apr 2015 11:17:07: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:17:07: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:17:07: # Command line: callpeak -t SRX059235.bam -f BAM -g ce -n SRX059235.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX059235.10 # format = BAM # ChIP-seq file = ['SRX059235.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 INFO @ Thu, 30 Apr 2015 11:17:07: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:17:07: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:17:07: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:17:07: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:17:12: 1000000 INFO @ Thu, 30 Apr 2015 11:17:13: 1000000 INFO @ Thu, 30 Apr 2015 11:17:13: 1000000 INFO @ Thu, 30 Apr 2015 11:17:18: 2000000 INFO @ Thu, 30 Apr 2015 11:17:19: 2000000 INFO @ Thu, 30 Apr 2015 11:17:19: 2000000 INFO @ Thu, 30 Apr 2015 11:17:23: 3000000 INFO @ Thu, 30 Apr 2015 11:17:25: 3000000 INFO @ Thu, 30 Apr 2015 11:17:25: 3000000 INFO @ Thu, 30 Apr 2015 11:17:29: 4000000 INFO @ Thu, 30 Apr 2015 11:17:31: 4000000 INFO @ Thu, 30 Apr 2015 11:17:31: 4000000 INFO @ Thu, 30 Apr 2015 11:17:34: 5000000 INFO @ Thu, 30 Apr 2015 11:17:37: 5000000 INFO @ Thu, 30 Apr 2015 11:17:37: 5000000 INFO @ Thu, 30 Apr 2015 11:17:39: 6000000 INFO @ Thu, 30 Apr 2015 11:17:42: 6000000 INFO @ Thu, 30 Apr 2015 11:17:42: 6000000 INFO @ Thu, 30 Apr 2015 11:17:44: 7000000 INFO @ Thu, 30 Apr 2015 11:17:47: 7000000 INFO @ Thu, 30 Apr 2015 11:17:47: 7000000 INFO @ Thu, 30 Apr 2015 11:17:49: 8000000 INFO @ Thu, 30 Apr 2015 11:17:51: 8000000 INFO @ Thu, 30 Apr 2015 11:17:52: 8000000 INFO @ Thu, 30 Apr 2015 11:17:54: 9000000 INFO @ Thu, 30 Apr 2015 11:17:56: 9000000 INFO @ Thu, 30 Apr 2015 11:17:57: 9000000 INFO @ Thu, 30 Apr 2015 11:17:59: 10000000 INFO @ Thu, 30 Apr 2015 11:18:02: 10000000 INFO @ Thu, 30 Apr 2015 11:18:02: 10000000 INFO @ Thu, 30 Apr 2015 11:18:03: 11000000 INFO @ Thu, 30 Apr 2015 11:18:06: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:18:06: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:18:06: #1 total tags in treatment: 11414127 INFO @ Thu, 30 Apr 2015 11:18:06: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:18:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:18:07: 11000000 INFO @ Thu, 30 Apr 2015 11:18:07: 11000000 INFO @ Thu, 30 Apr 2015 11:18:08: #1 tags after filtering in treatment: 11412878 INFO @ Thu, 30 Apr 2015 11:18:08: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:18:08: #1 finished! INFO @ Thu, 30 Apr 2015 11:18:08: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:18:09: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:18:09: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:18:09: #1 total tags in treatment: 11414127 INFO @ Thu, 30 Apr 2015 11:18:09: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:18:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:18:09: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:18:09: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:18:09: #1 total tags in treatment: 11414127 INFO @ Thu, 30 Apr 2015 11:18:09: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:18:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:18:10: #2 number of paired peaks: 1445 INFO @ Thu, 30 Apr 2015 11:18:10: start model_add_line... INFO @ Thu, 30 Apr 2015 11:18:11: #1 tags after filtering in treatment: 11412878 INFO @ Thu, 30 Apr 2015 11:18:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:18:11: #1 finished! INFO @ Thu, 30 Apr 2015 11:18:11: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:18:11: #1 tags after filtering in treatment: 11412878 INFO @ Thu, 30 Apr 2015 11:18:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:18:11: #1 finished! INFO @ Thu, 30 Apr 2015 11:18:11: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:18:13: #2 number of paired peaks: 1445 INFO @ Thu, 30 Apr 2015 11:18:13: start model_add_line... INFO @ Thu, 30 Apr 2015 11:18:13: #2 number of paired peaks: 1445 INFO @ Thu, 30 Apr 2015 11:18:13: start model_add_line... INFO @ Thu, 30 Apr 2015 11:18:26: start X-correlation... INFO @ Thu, 30 Apr 2015 11:18:26: end of X-cor INFO @ Thu, 30 Apr 2015 11:18:26: #2 finished! INFO @ Thu, 30 Apr 2015 11:18:26: #2 predicted fragment length is 101 bps INFO @ Thu, 30 Apr 2015 11:18:26: #2 alternative fragment length(s) may be 101 bps INFO @ Thu, 30 Apr 2015 11:18:26: #2.2 Generate R script for model : SRX059235.10_model.r INFO @ Thu, 30 Apr 2015 11:18:26: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:18:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:18:28: start X-correlation... INFO @ Thu, 30 Apr 2015 11:18:28: end of X-cor INFO @ Thu, 30 Apr 2015 11:18:28: #2 finished! INFO @ Thu, 30 Apr 2015 11:18:28: #2 predicted fragment length is 101 bps INFO @ Thu, 30 Apr 2015 11:18:28: #2 alternative fragment length(s) may be 101 bps INFO @ Thu, 30 Apr 2015 11:18:28: #2.2 Generate R script for model : SRX059235.20_model.r INFO @ Thu, 30 Apr 2015 11:18:28: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:18:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:18:30: start X-correlation... INFO @ Thu, 30 Apr 2015 11:18:30: end of X-cor INFO @ Thu, 30 Apr 2015 11:18:30: #2 finished! INFO @ Thu, 30 Apr 2015 11:18:30: #2 predicted fragment length is 101 bps INFO @ Thu, 30 Apr 2015 11:18:30: #2 alternative fragment length(s) may be 101 bps INFO @ Thu, 30 Apr 2015 11:18:30: #2.2 Generate R script for model : SRX059235.05_model.r INFO @ Thu, 30 Apr 2015 11:18:30: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:18:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:19:28: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:19:29: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:19:30: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:20:12: #4 Write output xls file... SRX059235.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:20:12: #4 Write peak in narrowPeak format file... SRX059235.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:20:12: #4 Write summits bed file... SRX059235.20_summits.bed INFO @ Thu, 30 Apr 2015 11:20:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1778 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:20:14: #4 Write output xls file... SRX059235.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:20:14: #4 Write peak in narrowPeak format file... SRX059235.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:20:14: #4 Write summits bed file... SRX059235.10_summits.bed INFO @ Thu, 30 Apr 2015 11:20:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2839 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:20:17: #4 Write output xls file... SRX059235.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:20:17: #4 Write peak in narrowPeak format file... SRX059235.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:20:17: #4 Write summits bed file... SRX059235.05_summits.bed INFO @ Thu, 30 Apr 2015 11:20:17: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4393 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。