Job ID = 2237007 sra ファイルのダウンロード中... Completed: 57974K bytes transferred in 4 seconds (112991K 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 6919 0 6919 0 0 12740 0 --:--:-- --:--:-- --:--:-- 19656 100 38113 0 38113 0 0 52011 0 --:--:-- --:--:-- --:--:-- 70319 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 3273507 spots for /home/okishinya/chipatlas/results/ce10/SRX080063/SRR298883.sra Written 3273507 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: 00:00:23 3273507 reads; of these: 3273507 (100.00%) were unpaired; of these: 1959375 (59.86%) aligned 0 times 1075509 (32.85%) aligned exactly 1 time 238623 (7.29%) aligned >1 times 40.14% overall alignment rate Time searching: 00:00:23 Overall time: 00:00:23 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] 141485 / 1314132 = 0.1077 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 11:23:05: # Command line: callpeak -t SRX080063.bam -f BAM -g ce -n SRX080063.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX080063.20 # format = BAM # ChIP-seq file = ['SRX080063.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 11:23:05: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:23:05: # Command line: callpeak -t SRX080063.bam -f BAM -g ce -n SRX080063.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX080063.10 # format = BAM # ChIP-seq file = ['SRX080063.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 11:23:05: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:23:05: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:23:05: # Command line: callpeak -t SRX080063.bam -f BAM -g ce -n SRX080063.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX080063.05 # format = BAM # ChIP-seq file = ['SRX080063.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 11:23:05: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:23:05: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:23:05: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:23:11: 1000000 INFO @ Thu, 30 Apr 2015 11:23:11: 1000000 INFO @ Thu, 30 Apr 2015 11:23:11: 1000000 INFO @ Thu, 30 Apr 2015 11:23:12: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:23:12: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:23:12: #1 total tags in treatment: 1172647 INFO @ Thu, 30 Apr 2015 11:23:12: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:23:12: #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 11:23:12: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:23:12: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:23:12: #1 total tags in treatment: 1172647 INFO @ Thu, 30 Apr 2015 11:23:12: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:23:12: #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 11:23:12: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:23:12: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:23:12: #1 total tags in treatment: 1172647 INFO @ Thu, 30 Apr 2015 11:23:12: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:23:12: #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 11:23:12: #1 tags after filtering in treatment: 1172618 INFO @ Thu, 30 Apr 2015 11:23:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:23:12: #1 finished! INFO @ Thu, 30 Apr 2015 11:23:12: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:23:12: #1 tags after filtering in treatment: 1172618 INFO @ Thu, 30 Apr 2015 11:23:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:23:12: #1 finished! INFO @ Thu, 30 Apr 2015 11:23:12: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:23:12: #1 tags after filtering in treatment: 1172618 INFO @ Thu, 30 Apr 2015 11:23:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:23:12: #1 finished! INFO @ Thu, 30 Apr 2015 11:23:12: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:23:13: #2 number of paired peaks: 671 WARNING @ Thu, 30 Apr 2015 11:23:13: Fewer paired peaks (671) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 671 pairs to build model! INFO @ Thu, 30 Apr 2015 11:23:13: start model_add_line... INFO @ Thu, 30 Apr 2015 11:23:13: #2 number of paired peaks: 671 WARNING @ Thu, 30 Apr 2015 11:23:13: Fewer paired peaks (671) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 671 pairs to build model! INFO @ Thu, 30 Apr 2015 11:23:13: start model_add_line... INFO @ Thu, 30 Apr 2015 11:23:13: #2 number of paired peaks: 671 WARNING @ Thu, 30 Apr 2015 11:23:13: Fewer paired peaks (671) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 671 pairs to build model! INFO @ Thu, 30 Apr 2015 11:23:13: start model_add_line... INFO @ Thu, 30 Apr 2015 11:23:14: start X-correlation... INFO @ Thu, 30 Apr 2015 11:23:14: end of X-cor INFO @ Thu, 30 Apr 2015 11:23:14: #2 finished! INFO @ Thu, 30 Apr 2015 11:23:14: #2 predicted fragment length is 138 bps INFO @ Thu, 30 Apr 2015 11:23:14: #2 alternative fragment length(s) may be 138 bps INFO @ Thu, 30 Apr 2015 11:23:14: #2.2 Generate R script for model : SRX080063.10_model.r INFO @ Thu, 30 Apr 2015 11:23:14: start X-correlation... INFO @ Thu, 30 Apr 2015 11:23:14: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:23:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:23:14: end of X-cor INFO @ Thu, 30 Apr 2015 11:23:14: #2 finished! INFO @ Thu, 30 Apr 2015 11:23:14: #2 predicted fragment length is 138 bps INFO @ Thu, 30 Apr 2015 11:23:14: #2 alternative fragment length(s) may be 138 bps INFO @ Thu, 30 Apr 2015 11:23:14: #2.2 Generate R script for model : SRX080063.05_model.r INFO @ Thu, 30 Apr 2015 11:23:14: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:23:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:23:14: start X-correlation... INFO @ Thu, 30 Apr 2015 11:23:14: end of X-cor INFO @ Thu, 30 Apr 2015 11:23:14: #2 finished! INFO @ Thu, 30 Apr 2015 11:23:14: #2 predicted fragment length is 138 bps INFO @ Thu, 30 Apr 2015 11:23:14: #2 alternative fragment length(s) may be 138 bps INFO @ Thu, 30 Apr 2015 11:23:14: #2.2 Generate R script for model : SRX080063.20_model.r INFO @ Thu, 30 Apr 2015 11:23:14: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:23:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:23:21: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:23:21: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:23:22: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:23:26: #4 Write output xls file... SRX080063.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:23:26: #4 Write peak in narrowPeak format file... SRX080063.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:23:26: #4 Write summits bed file... SRX080063.05_summits.bed INFO @ Thu, 30 Apr 2015 11:23:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (628 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:23:26: #4 Write output xls file... SRX080063.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:23:26: #4 Write peak in narrowPeak format file... SRX080063.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:23:26: #4 Write summits bed file... SRX080063.10_summits.bed INFO @ Thu, 30 Apr 2015 11:23:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (261 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:23:27: #4 Write output xls file... SRX080063.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:23:27: #4 Write peak in narrowPeak format file... SRX080063.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:23:27: #4 Write summits bed file... SRX080063.20_summits.bed INFO @ Thu, 30 Apr 2015 11:23:27: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (61 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。