Job ID = 2237048 sra ファイルのダウンロード中... Completed: 78038K bytes transferred in 4 seconds (128837K 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 38039 0 38039 0 0 54359 0 --:--:-- --:--:-- --:--:-- 74879 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 3231623 spots for /home/okishinya/chipatlas/results/ce10/SRX080103/SRR298923.sra Written 3231623 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: 00:00:35 3231623 reads; of these: 3231623 (100.00%) were unpaired; of these: 177041 (5.48%) aligned 0 times 2571341 (79.57%) aligned exactly 1 time 483241 (14.95%) aligned >1 times 94.52% overall alignment rate Time searching: 00:00:35 Overall time: 00:00:35 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] 131014 / 3054582 = 0.0429 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 11:26:10: # Command line: callpeak -t SRX080103.bam -f BAM -g ce -n SRX080103.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX080103.10 # format = BAM # ChIP-seq file = ['SRX080103.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 11:26:10: # Command line: callpeak -t SRX080103.bam -f BAM -g ce -n SRX080103.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX080103.05 # format = BAM # ChIP-seq file = ['SRX080103.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 11:26:10: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:26:10: # Command line: callpeak -t SRX080103.bam -f BAM -g ce -n SRX080103.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX080103.20 # format = BAM # ChIP-seq file = ['SRX080103.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 11:26:10: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:26:10: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:26:10: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:26:10: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:26:10: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:26:16: 1000000 INFO @ Thu, 30 Apr 2015 11:26:16: 1000000 INFO @ Thu, 30 Apr 2015 11:26:16: 1000000 INFO @ Thu, 30 Apr 2015 11:26:21: 2000000 INFO @ Thu, 30 Apr 2015 11:26:22: 2000000 INFO @ Thu, 30 Apr 2015 11:26:22: 2000000 INFO @ Thu, 30 Apr 2015 11:26:26: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:26:26: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:26:26: #1 total tags in treatment: 2923568 INFO @ Thu, 30 Apr 2015 11:26:26: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:26:26: #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 11:26:27: #1 tags after filtering in treatment: 2923510 INFO @ Thu, 30 Apr 2015 11:26:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:26:27: #1 finished! INFO @ Thu, 30 Apr 2015 11:26:27: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:26:28: #2 number of paired peaks: 399 WARNING @ Thu, 30 Apr 2015 11:26:28: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Thu, 30 Apr 2015 11:26:28: start model_add_line... INFO @ Thu, 30 Apr 2015 11:26:28: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:26:28: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:26:28: #1 total tags in treatment: 2923568 INFO @ Thu, 30 Apr 2015 11:26:28: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:26:28: #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 11:26:28: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:26:28: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:26:28: #1 total tags in treatment: 2923568 INFO @ Thu, 30 Apr 2015 11:26:28: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:26:28: #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 11:26:28: #1 tags after filtering in treatment: 2923510 INFO @ Thu, 30 Apr 2015 11:26:28: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:26:28: #1 finished! INFO @ Thu, 30 Apr 2015 11:26:28: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:26:28: #1 tags after filtering in treatment: 2923510 INFO @ Thu, 30 Apr 2015 11:26:28: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:26:28: #1 finished! INFO @ Thu, 30 Apr 2015 11:26:28: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:26:29: #2 number of paired peaks: 399 WARNING @ Thu, 30 Apr 2015 11:26:29: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Thu, 30 Apr 2015 11:26:29: start model_add_line... INFO @ Thu, 30 Apr 2015 11:26:29: #2 number of paired peaks: 399 WARNING @ Thu, 30 Apr 2015 11:26:29: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Thu, 30 Apr 2015 11:26:29: start model_add_line... INFO @ Thu, 30 Apr 2015 11:26:30: start X-correlation... INFO @ Thu, 30 Apr 2015 11:26:30: end of X-cor INFO @ Thu, 30 Apr 2015 11:26:30: #2 finished! INFO @ Thu, 30 Apr 2015 11:26:30: #2 predicted fragment length is 32 bps INFO @ Thu, 30 Apr 2015 11:26:30: #2 alternative fragment length(s) may be 32,200 bps INFO @ Thu, 30 Apr 2015 11:26:30: #2.2 Generate R script for model : SRX080103.10_model.r WARNING @ Thu, 30 Apr 2015 11:26:30: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:26:30: #2 You may need to consider one of the other alternative d(s): 32,200 WARNING @ Thu, 30 Apr 2015 11:26:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 11:26:30: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:26:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:26:31: start X-correlation... INFO @ Thu, 30 Apr 2015 11:26:31: end of X-cor INFO @ Thu, 30 Apr 2015 11:26:31: #2 finished! INFO @ Thu, 30 Apr 2015 11:26:31: #2 predicted fragment length is 32 bps INFO @ Thu, 30 Apr 2015 11:26:31: #2 alternative fragment length(s) may be 32,200 bps INFO @ Thu, 30 Apr 2015 11:26:31: #2.2 Generate R script for model : SRX080103.05_model.r WARNING @ Thu, 30 Apr 2015 11:26:31: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:26:31: #2 You may need to consider one of the other alternative d(s): 32,200 WARNING @ Thu, 30 Apr 2015 11:26:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 11:26:31: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:26:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:26:31: start X-correlation... INFO @ Thu, 30 Apr 2015 11:26:31: end of X-cor INFO @ Thu, 30 Apr 2015 11:26:31: #2 finished! INFO @ Thu, 30 Apr 2015 11:26:31: #2 predicted fragment length is 32 bps INFO @ Thu, 30 Apr 2015 11:26:31: #2 alternative fragment length(s) may be 32,200 bps INFO @ Thu, 30 Apr 2015 11:26:31: #2.2 Generate R script for model : SRX080103.20_model.r WARNING @ Thu, 30 Apr 2015 11:26:31: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:26:31: #2 You may need to consider one of the other alternative d(s): 32,200 WARNING @ Thu, 30 Apr 2015 11:26:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 11:26:31: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:26:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:26:47: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:26:48: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:26:48: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:26:59: #4 Write output xls file... SRX080103.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:26:59: #4 Write peak in narrowPeak format file... SRX080103.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:26:59: #4 Write summits bed file... SRX080103.10_summits.bed INFO @ Thu, 30 Apr 2015 11:26:59: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (156 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:27:00: #4 Write output xls file... SRX080103.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:27:00: #4 Write peak in narrowPeak format file... SRX080103.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:27:00: #4 Write summits bed file... SRX080103.05_summits.bed INFO @ Thu, 30 Apr 2015 11:27:00: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (373 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:27:00: #4 Write output xls file... SRX080103.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:27:00: #4 Write peak in narrowPeak format file... SRX080103.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:27:00: #4 Write summits bed file... SRX080103.20_summits.bed INFO @ Thu, 30 Apr 2015 11:27:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (35 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。