Job ID = 2237072 sra ファイルのダウンロード中... Completed: 290796K bytes transferred in 7 seconds (322885K 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 4007 0 4007 0 0 7069 0 --:--:-- --:--:-- --:--:-- 10656 100 36871 0 36871 0 0 48734 0 --:--:-- --:--:-- --:--:-- 65143 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 14341616 spots for /home/okishinya/chipatlas/results/ce10/SRX113610/SRR393710.sra Written 14341616 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: 00:04:11 14341616 reads; of these: 14341616 (100.00%) were unpaired; of these: 911727 (6.36%) aligned 0 times 9078663 (63.30%) aligned exactly 1 time 4351226 (30.34%) aligned >1 times 93.64% overall alignment rate Time searching: 00:04:11 Overall time: 00:04:11 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] 8146506 / 13429889 = 0.6066 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 11:33:29: # Command line: callpeak -t SRX113610.bam -f BAM -g ce -n SRX113610.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX113610.05 # format = BAM # ChIP-seq file = ['SRX113610.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 11:33:29: # Command line: callpeak -t SRX113610.bam -f BAM -g ce -n SRX113610.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX113610.20 # format = BAM # ChIP-seq file = ['SRX113610.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 11:33:29: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:33:29: # Command line: callpeak -t SRX113610.bam -f BAM -g ce -n SRX113610.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX113610.10 # format = BAM # ChIP-seq file = ['SRX113610.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 11:33:29: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:33:29: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:33:29: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:33:29: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:33:29: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:33:35: 1000000 INFO @ Thu, 30 Apr 2015 11:33:35: 1000000 INFO @ Thu, 30 Apr 2015 11:33:35: 1000000 INFO @ Thu, 30 Apr 2015 11:33:42: 2000000 INFO @ Thu, 30 Apr 2015 11:33:42: 2000000 INFO @ Thu, 30 Apr 2015 11:33:42: 2000000 INFO @ Thu, 30 Apr 2015 11:33:48: 3000000 INFO @ Thu, 30 Apr 2015 11:33:48: 3000000 INFO @ Thu, 30 Apr 2015 11:33:48: 3000000 INFO @ Thu, 30 Apr 2015 11:33:54: 4000000 INFO @ Thu, 30 Apr 2015 11:33:54: 4000000 INFO @ Thu, 30 Apr 2015 11:33:54: 4000000 INFO @ Thu, 30 Apr 2015 11:34:00: 5000000 INFO @ Thu, 30 Apr 2015 11:34:00: 5000000 INFO @ Thu, 30 Apr 2015 11:34:00: 5000000 INFO @ Thu, 30 Apr 2015 11:34:02: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:34:02: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:34:02: #1 total tags in treatment: 5283383 INFO @ Thu, 30 Apr 2015 11:34:02: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:34:02: #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 11:34:02: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:34:02: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:34:02: #1 total tags in treatment: 5283383 INFO @ Thu, 30 Apr 2015 11:34:02: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:34:02: #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 11:34:02: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:34:02: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:34:02: #1 total tags in treatment: 5283383 INFO @ Thu, 30 Apr 2015 11:34:02: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:34:02: #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 11:34:03: #1 tags after filtering in treatment: 5243625 INFO @ Thu, 30 Apr 2015 11:34:03: #1 Redundant rate of treatment: 0.01 INFO @ Thu, 30 Apr 2015 11:34:03: #1 finished! INFO @ Thu, 30 Apr 2015 11:34:03: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:34:03: #1 tags after filtering in treatment: 5243625 INFO @ Thu, 30 Apr 2015 11:34:03: #1 Redundant rate of treatment: 0.01 INFO @ Thu, 30 Apr 2015 11:34:03: #1 finished! INFO @ Thu, 30 Apr 2015 11:34:03: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:34:03: #1 tags after filtering in treatment: 5243625 INFO @ Thu, 30 Apr 2015 11:34:03: #1 Redundant rate of treatment: 0.01 INFO @ Thu, 30 Apr 2015 11:34:03: #1 finished! INFO @ Thu, 30 Apr 2015 11:34:03: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:34:04: #2 number of paired peaks: 4726 INFO @ Thu, 30 Apr 2015 11:34:04: start model_add_line... INFO @ Thu, 30 Apr 2015 11:34:04: #2 number of paired peaks: 4726 INFO @ Thu, 30 Apr 2015 11:34:04: start model_add_line... INFO @ Thu, 30 Apr 2015 11:34:04: #2 number of paired peaks: 4726 INFO @ Thu, 30 Apr 2015 11:34:04: start model_add_line... INFO @ Thu, 30 Apr 2015 11:34:27: start X-correlation... INFO @ Thu, 30 Apr 2015 11:34:27: end of X-cor INFO @ Thu, 30 Apr 2015 11:34:27: #2 finished! INFO @ Thu, 30 Apr 2015 11:34:27: #2 predicted fragment length is 146 bps INFO @ Thu, 30 Apr 2015 11:34:27: #2 alternative fragment length(s) may be 2,146 bps INFO @ Thu, 30 Apr 2015 11:34:27: #2.2 Generate R script for model : SRX113610.20_model.r INFO @ Thu, 30 Apr 2015 11:34:27: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:34:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:34:27: start X-correlation... INFO @ Thu, 30 Apr 2015 11:34:27: end of X-cor INFO @ Thu, 30 Apr 2015 11:34:27: #2 finished! INFO @ Thu, 30 Apr 2015 11:34:27: #2 predicted fragment length is 146 bps INFO @ Thu, 30 Apr 2015 11:34:27: #2 alternative fragment length(s) may be 2,146 bps INFO @ Thu, 30 Apr 2015 11:34:27: #2.2 Generate R script for model : SRX113610.10_model.r INFO @ Thu, 30 Apr 2015 11:34:27: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:34:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:34:28: start X-correlation... INFO @ Thu, 30 Apr 2015 11:34:28: end of X-cor INFO @ Thu, 30 Apr 2015 11:34:28: #2 finished! INFO @ Thu, 30 Apr 2015 11:34:28: #2 predicted fragment length is 146 bps INFO @ Thu, 30 Apr 2015 11:34:28: #2 alternative fragment length(s) may be 2,146 bps INFO @ Thu, 30 Apr 2015 11:34:28: #2.2 Generate R script for model : SRX113610.05_model.r INFO @ Thu, 30 Apr 2015 11:34:28: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:34:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:34:57: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:34:59: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:34:59: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:35:16: #4 Write output xls file... SRX113610.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:35:16: #4 Write peak in narrowPeak format file... SRX113610.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:35:16: #4 Write summits bed file... SRX113610.20_summits.bed INFO @ Thu, 30 Apr 2015 11:35:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (258 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:35:19: #4 Write output xls file... SRX113610.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:35:19: #4 Write peak in narrowPeak format file... SRX113610.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:35:19: #4 Write summits bed file... SRX113610.10_summits.bed INFO @ Thu, 30 Apr 2015 11:35:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1095 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:35:23: #4 Write output xls file... SRX113610.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:35:23: #4 Write peak in narrowPeak format file... SRX113610.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:35:23: #4 Write summits bed file... SRX113610.05_summits.bed INFO @ Thu, 30 Apr 2015 11:35:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3412 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。