Job ID = 2236696 sra ファイルのダウンロード中... Completed: 223295K bytes transferred in 5 seconds (347946K 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 19286 0 19286 0 0 26168 0 --:--:-- --:--:-- --:--:-- 35322 100 34429 0 34429 0 0 46663 0 --:--:-- --:--:-- --:--:-- 62941 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 10435718 spots for /home/okishinya/chipatlas/results/ce10/SRX027098/SRR066370.sra Written 10435718 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:46 10435718 reads; of these: 10435718 (100.00%) were unpaired; of these: 2656146 (25.45%) aligned 0 times 6045965 (57.94%) aligned exactly 1 time 1733607 (16.61%) aligned >1 times 74.55% overall alignment rate Time searching: 00:01:47 Overall time: 00:01:47 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] 1056098 / 7779572 = 0.1358 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 10:59:32: # Command line: callpeak -t SRX027098.bam -f BAM -g ce -n SRX027098.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX027098.10 # format = BAM # ChIP-seq file = ['SRX027098.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 10:59:32: # Command line: callpeak -t SRX027098.bam -f BAM -g ce -n SRX027098.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX027098.05 # format = BAM # ChIP-seq file = ['SRX027098.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 10:59:32: #1 read tag files... INFO @ Thu, 30 Apr 2015 10:59:32: # Command line: callpeak -t SRX027098.bam -f BAM -g ce -n SRX027098.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX027098.20 # format = BAM # ChIP-seq file = ['SRX027098.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 10:59:32: #1 read tag files... INFO @ Thu, 30 Apr 2015 10:59:32: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 10:59:32: #1 read tag files... INFO @ Thu, 30 Apr 2015 10:59:32: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 10:59:32: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 10:59:37: 1000000 INFO @ Thu, 30 Apr 2015 10:59:37: 1000000 INFO @ Thu, 30 Apr 2015 10:59:38: 1000000 INFO @ Thu, 30 Apr 2015 10:59:43: 2000000 INFO @ Thu, 30 Apr 2015 10:59:43: 2000000 INFO @ Thu, 30 Apr 2015 10:59:44: 2000000 INFO @ Thu, 30 Apr 2015 10:59:49: 3000000 INFO @ Thu, 30 Apr 2015 10:59:49: 3000000 INFO @ Thu, 30 Apr 2015 10:59:50: 3000000 INFO @ Thu, 30 Apr 2015 10:59:55: 4000000 INFO @ Thu, 30 Apr 2015 10:59:55: 4000000 INFO @ Thu, 30 Apr 2015 10:59:57: 4000000 INFO @ Thu, 30 Apr 2015 11:00:00: 5000000 INFO @ Thu, 30 Apr 2015 11:00:01: 5000000 INFO @ Thu, 30 Apr 2015 11:00:03: 5000000 INFO @ Thu, 30 Apr 2015 11:00:06: 6000000 INFO @ Thu, 30 Apr 2015 11:00:07: 6000000 INFO @ Thu, 30 Apr 2015 11:00:09: 6000000 INFO @ Thu, 30 Apr 2015 11:00:10: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:00:10: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:00:10: #1 total tags in treatment: 6723474 INFO @ Thu, 30 Apr 2015 11:00:10: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:00:10: #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 11:00:11: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:00:11: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:00:11: #1 total tags in treatment: 6723474 INFO @ Thu, 30 Apr 2015 11:00:11: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:00:11: #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 11:00:12: #1 tags after filtering in treatment: 6722869 INFO @ Thu, 30 Apr 2015 11:00:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:00:12: #1 finished! INFO @ Thu, 30 Apr 2015 11:00:12: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:00:12: #1 tags after filtering in treatment: 6722869 INFO @ Thu, 30 Apr 2015 11:00:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:00:12: #1 finished! INFO @ Thu, 30 Apr 2015 11:00:12: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:00:13: #2 number of paired peaks: 551 WARNING @ Thu, 30 Apr 2015 11:00:13: Fewer paired peaks (551) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 551 pairs to build model! INFO @ Thu, 30 Apr 2015 11:00:13: start model_add_line... INFO @ Thu, 30 Apr 2015 11:00:13: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:00:13: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:00:13: #1 total tags in treatment: 6723474 INFO @ Thu, 30 Apr 2015 11:00:13: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:00:13: #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 11:00:14: #2 number of paired peaks: 551 WARNING @ Thu, 30 Apr 2015 11:00:14: Fewer paired peaks (551) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 551 pairs to build model! INFO @ Thu, 30 Apr 2015 11:00:14: start model_add_line... INFO @ Thu, 30 Apr 2015 11:00:14: #1 tags after filtering in treatment: 6722869 INFO @ Thu, 30 Apr 2015 11:00:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:00:14: #1 finished! INFO @ Thu, 30 Apr 2015 11:00:14: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:00:16: #2 number of paired peaks: 551 WARNING @ Thu, 30 Apr 2015 11:00:16: Fewer paired peaks (551) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 551 pairs to build model! INFO @ Thu, 30 Apr 2015 11:00:16: start model_add_line... INFO @ Thu, 30 Apr 2015 11:00:18: start X-correlation... INFO @ Thu, 30 Apr 2015 11:00:18: end of X-cor INFO @ Thu, 30 Apr 2015 11:00:18: #2 finished! INFO @ Thu, 30 Apr 2015 11:00:18: #2 predicted fragment length is 152 bps INFO @ Thu, 30 Apr 2015 11:00:18: #2 alternative fragment length(s) may be 4,77,121,152 bps INFO @ Thu, 30 Apr 2015 11:00:18: #2.2 Generate R script for model : SRX027098.10_model.r INFO @ Thu, 30 Apr 2015 11:00:18: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:00:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:00:18: start X-correlation... INFO @ Thu, 30 Apr 2015 11:00:18: end of X-cor INFO @ Thu, 30 Apr 2015 11:00:18: #2 finished! INFO @ Thu, 30 Apr 2015 11:00:18: #2 predicted fragment length is 152 bps INFO @ Thu, 30 Apr 2015 11:00:18: #2 alternative fragment length(s) may be 4,77,121,152 bps INFO @ Thu, 30 Apr 2015 11:00:18: #2.2 Generate R script for model : SRX027098.05_model.r INFO @ Thu, 30 Apr 2015 11:00:18: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:00:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:00:20: start X-correlation... INFO @ Thu, 30 Apr 2015 11:00:20: end of X-cor INFO @ Thu, 30 Apr 2015 11:00:20: #2 finished! INFO @ Thu, 30 Apr 2015 11:00:20: #2 predicted fragment length is 152 bps INFO @ Thu, 30 Apr 2015 11:00:20: #2 alternative fragment length(s) may be 4,77,121,152 bps INFO @ Thu, 30 Apr 2015 11:00:20: #2.2 Generate R script for model : SRX027098.20_model.r INFO @ Thu, 30 Apr 2015 11:00:20: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:00:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:00:55: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:00:55: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:00:59: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:01:21: #4 Write output xls file... SRX027098.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:01:21: #4 Write peak in narrowPeak format file... SRX027098.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:01:21: #4 Write summits bed file... SRX027098.10_summits.bed INFO @ Thu, 30 Apr 2015 11:01:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1119 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:01:26: #4 Write output xls file... SRX027098.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:01:27: #4 Write peak in narrowPeak format file... SRX027098.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:01:27: #4 Write summits bed file... SRX027098.05_summits.bed INFO @ Thu, 30 Apr 2015 11:01:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4329 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:01:27: #4 Write output xls file... SRX027098.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:01:27: #4 Write peak in narrowPeak format file... SRX027098.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:01:27: #4 Write summits bed file... SRX027098.20_summits.bed INFO @ Thu, 30 Apr 2015 11:01:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (210 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。