Job ID = 2237011 sra ファイルのダウンロード中... Completed: 18513K bytes transferred in 3 seconds (43621K 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 29828 0 29828 0 0 42051 0 --:--:-- --:--:-- --:--:-- 57583 100 37968 0 37968 0 0 53456 0 --:--:-- --:--:-- --:--:-- 73156 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 1161234 spots for /home/okishinya/chipatlas/results/ce10/SRX080067/SRR298887.sra Written 1161234 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: 00:00:09 1161234 reads; of these: 1161234 (100.00%) were unpaired; of these: 542423 (46.71%) aligned 0 times 512457 (44.13%) aligned exactly 1 time 106354 (9.16%) aligned >1 times 53.29% overall alignment rate Time searching: 00:00:09 Overall time: 00:00:09 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] 172492 / 618811 = 0.2787 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 11:23:03: # Command line: callpeak -t SRX080067.bam -f BAM -g ce -n SRX080067.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX080067.10 # format = BAM # ChIP-seq file = ['SRX080067.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 11:23:03: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:23:03: # Command line: callpeak -t SRX080067.bam -f BAM -g ce -n SRX080067.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX080067.05 # format = BAM # ChIP-seq file = ['SRX080067.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 11:23:03: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:23:03: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:23:03: # Command line: callpeak -t SRX080067.bam -f BAM -g ce -n SRX080067.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX080067.20 # format = BAM # ChIP-seq file = ['SRX080067.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 11:23:03: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:23:03: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:23:03: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:23:05: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:23:05: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:23:05: #1 total tags in treatment: 446319 INFO @ Thu, 30 Apr 2015 11:23:05: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:23:05: #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 11:23:05: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:23:05: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:23:05: #1 total tags in treatment: 446319 INFO @ Thu, 30 Apr 2015 11:23:05: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:23:05: #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 11:23:05: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:23:05: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:23:05: #1 total tags in treatment: 446319 INFO @ Thu, 30 Apr 2015 11:23:05: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:23:05: #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 11:23:05: #1 tags after filtering in treatment: 446313 INFO @ Thu, 30 Apr 2015 11:23:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:23:05: #1 finished! INFO @ Thu, 30 Apr 2015 11:23:05: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:23:05: #1 tags after filtering in treatment: 446313 INFO @ Thu, 30 Apr 2015 11:23:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:23:05: #1 finished! INFO @ Thu, 30 Apr 2015 11:23:05: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:23:05: #1 tags after filtering in treatment: 446313 INFO @ Thu, 30 Apr 2015 11:23:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:23:05: #1 finished! INFO @ Thu, 30 Apr 2015 11:23:05: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:23:05: #2 number of paired peaks: 543 WARNING @ Thu, 30 Apr 2015 11:23:05: Fewer paired peaks (543) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 543 pairs to build model! INFO @ Thu, 30 Apr 2015 11:23:05: start model_add_line... INFO @ Thu, 30 Apr 2015 11:23:05: #2 number of paired peaks: 543 WARNING @ Thu, 30 Apr 2015 11:23:05: Fewer paired peaks (543) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 543 pairs to build model! INFO @ Thu, 30 Apr 2015 11:23:05: start model_add_line... INFO @ Thu, 30 Apr 2015 11:23:05: #2 number of paired peaks: 543 WARNING @ Thu, 30 Apr 2015 11:23:05: Fewer paired peaks (543) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 543 pairs to build model! INFO @ Thu, 30 Apr 2015 11:23:05: start model_add_line... INFO @ Thu, 30 Apr 2015 11:23:06: start X-correlation... INFO @ Thu, 30 Apr 2015 11:23:06: end of X-cor INFO @ Thu, 30 Apr 2015 11:23:06: #2 finished! INFO @ Thu, 30 Apr 2015 11:23:06: #2 predicted fragment length is 106 bps INFO @ Thu, 30 Apr 2015 11:23:06: #2 alternative fragment length(s) may be 37,79,106,163,217 bps INFO @ Thu, 30 Apr 2015 11:23:06: #2.2 Generate R script for model : SRX080067.05_model.r INFO @ Thu, 30 Apr 2015 11:23:06: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:23:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:23:06: start X-correlation... INFO @ Thu, 30 Apr 2015 11:23:06: end of X-cor INFO @ Thu, 30 Apr 2015 11:23:06: #2 finished! INFO @ Thu, 30 Apr 2015 11:23:06: #2 predicted fragment length is 106 bps INFO @ Thu, 30 Apr 2015 11:23:06: #2 alternative fragment length(s) may be 37,79,106,163,217 bps INFO @ Thu, 30 Apr 2015 11:23:06: #2.2 Generate R script for model : SRX080067.10_model.r INFO @ Thu, 30 Apr 2015 11:23:06: start X-correlation... INFO @ Thu, 30 Apr 2015 11:23:06: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:23:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:23:06: end of X-cor INFO @ Thu, 30 Apr 2015 11:23:06: #2 finished! INFO @ Thu, 30 Apr 2015 11:23:06: #2 predicted fragment length is 106 bps INFO @ Thu, 30 Apr 2015 11:23:06: #2 alternative fragment length(s) may be 37,79,106,163,217 bps INFO @ Thu, 30 Apr 2015 11:23:06: #2.2 Generate R script for model : SRX080067.20_model.r INFO @ Thu, 30 Apr 2015 11:23:06: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:23:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:23:08: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:23:08: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:23:09: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:23:10: #4 Write output xls file... SRX080067.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:23:10: #4 Write peak in narrowPeak format file... SRX080067.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:23:10: #4 Write summits bed file... SRX080067.05_summits.bed INFO @ Thu, 30 Apr 2015 11:23:10: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (79 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:23:10: #4 Write output xls file... SRX080067.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:23:10: #4 Write peak in narrowPeak format file... SRX080067.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:23:10: #4 Write summits bed file... SRX080067.10_summits.bed INFO @ Thu, 30 Apr 2015 11:23:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (25 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:23:11: #4 Write output xls file... SRX080067.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:23:11: #4 Write peak in narrowPeak format file... SRX080067.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:23:11: #4 Write summits bed file... SRX080067.20_summits.bed INFO @ Thu, 30 Apr 2015 11:23:11: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (6 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。