Job ID = 2237046 sra ファイルのダウンロード中... Completed: 143924K bytes transferred in 5 seconds (213929K 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 --:--:-- --:--:-- --:--:-- 0 108 1087 0 1087 0 0 2086 0 --:--:-- --:--:-- --:--:-- 3293 100 38039 0 38039 0 0 53495 0 --:--:-- --:--:-- --:--:-- 73151 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 7742128 spots for /home/okishinya/chipatlas/results/ce10/SRX080101/SRR298921.sra Written 7742128 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: 00:00:01 Multiseed full-index search: 00:00:40 7742128 reads; of these: 7742128 (100.00%) were unpaired; of these: 6119636 (79.04%) aligned 0 times 1354625 (17.50%) aligned exactly 1 time 267867 (3.46%) aligned >1 times 20.96% overall alignment rate Time searching: 00:00:41 Overall time: 00:00:41 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] 125203 / 1622492 = 0.0772 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 11:26:12: # Command line: callpeak -t SRX080101.bam -f BAM -g ce -n SRX080101.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX080101.20 # format = BAM # ChIP-seq file = ['SRX080101.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 11:26:12: # Command line: callpeak -t SRX080101.bam -f BAM -g ce -n SRX080101.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX080101.05 # format = BAM # ChIP-seq file = ['SRX080101.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 11:26:12: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:26:12: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:26:12: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:26:12: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:26:12: # Command line: callpeak -t SRX080101.bam -f BAM -g ce -n SRX080101.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX080101.10 # format = BAM # ChIP-seq file = ['SRX080101.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 11:26:12: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:26:12: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:26:17: 1000000 INFO @ Thu, 30 Apr 2015 11:26:18: 1000000 INFO @ Thu, 30 Apr 2015 11:26:18: 1000000 INFO @ Thu, 30 Apr 2015 11:26:20: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:26:20: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:26:20: #1 total tags in treatment: 1497289 INFO @ Thu, 30 Apr 2015 11:26:20: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:26:20: #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 11:26:20: #1 tags after filtering in treatment: 1497262 INFO @ Thu, 30 Apr 2015 11:26:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:26:20: #1 finished! INFO @ Thu, 30 Apr 2015 11:26:20: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:26:21: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:26:21: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:26:21: #1 total tags in treatment: 1497289 INFO @ Thu, 30 Apr 2015 11:26:21: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:26:21: #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 11:26:21: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:26:21: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:26:21: #1 total tags in treatment: 1497289 INFO @ Thu, 30 Apr 2015 11:26:21: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:26:21: #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 11:26:21: #2 number of paired peaks: 397 WARNING @ Thu, 30 Apr 2015 11:26:21: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Thu, 30 Apr 2015 11:26:21: start model_add_line... INFO @ Thu, 30 Apr 2015 11:26:21: #1 tags after filtering in treatment: 1497262 INFO @ Thu, 30 Apr 2015 11:26:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:26:21: #1 finished! INFO @ Thu, 30 Apr 2015 11:26:21: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:26:21: #1 tags after filtering in treatment: 1497262 INFO @ Thu, 30 Apr 2015 11:26:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:26:21: #1 finished! INFO @ Thu, 30 Apr 2015 11:26:21: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:26:21: #2 number of paired peaks: 397 WARNING @ Thu, 30 Apr 2015 11:26:21: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Thu, 30 Apr 2015 11:26:21: start model_add_line... INFO @ Thu, 30 Apr 2015 11:26:21: #2 number of paired peaks: 397 WARNING @ Thu, 30 Apr 2015 11:26:21: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Thu, 30 Apr 2015 11:26:21: start model_add_line... INFO @ Thu, 30 Apr 2015 11:26:22: start X-correlation... INFO @ Thu, 30 Apr 2015 11:26:22: end of X-cor INFO @ Thu, 30 Apr 2015 11:26:22: #2 finished! INFO @ Thu, 30 Apr 2015 11:26:22: #2 predicted fragment length is 30 bps INFO @ Thu, 30 Apr 2015 11:26:22: #2 alternative fragment length(s) may be 30,154,500,538 bps INFO @ Thu, 30 Apr 2015 11:26:22: #2.2 Generate R script for model : SRX080101.10_model.r WARNING @ Thu, 30 Apr 2015 11:26:22: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:26:22: #2 You may need to consider one of the other alternative d(s): 30,154,500,538 WARNING @ Thu, 30 Apr 2015 11:26:22: #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 11:26:22: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:26:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:26:22: start X-correlation... INFO @ Thu, 30 Apr 2015 11:26:22: end of X-cor INFO @ Thu, 30 Apr 2015 11:26:22: #2 finished! INFO @ Thu, 30 Apr 2015 11:26:22: #2 predicted fragment length is 30 bps INFO @ Thu, 30 Apr 2015 11:26:22: #2 alternative fragment length(s) may be 30,154,500,538 bps INFO @ Thu, 30 Apr 2015 11:26:22: #2.2 Generate R script for model : SRX080101.05_model.r WARNING @ Thu, 30 Apr 2015 11:26:22: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:26:22: #2 You may need to consider one of the other alternative d(s): 30,154,500,538 WARNING @ Thu, 30 Apr 2015 11:26:22: #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 11:26:22: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:26:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:26:22: start X-correlation... INFO @ Thu, 30 Apr 2015 11:26:22: end of X-cor INFO @ Thu, 30 Apr 2015 11:26:22: #2 finished! INFO @ Thu, 30 Apr 2015 11:26:22: #2 predicted fragment length is 30 bps INFO @ Thu, 30 Apr 2015 11:26:22: #2 alternative fragment length(s) may be 30,154,500,538 bps INFO @ Thu, 30 Apr 2015 11:26:22: #2.2 Generate R script for model : SRX080101.20_model.r WARNING @ Thu, 30 Apr 2015 11:26:22: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:26:22: #2 You may need to consider one of the other alternative d(s): 30,154,500,538 WARNING @ Thu, 30 Apr 2015 11:26:22: #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 11:26:22: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:26:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:26:31: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:26:31: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:26:31: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:26:37: #4 Write output xls file... SRX080101.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:26:37: #4 Write peak in narrowPeak format file... SRX080101.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:26:37: #4 Write summits bed file... SRX080101.20_summits.bed INFO @ Thu, 30 Apr 2015 11:26:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (18 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:26:37: #4 Write output xls file... SRX080101.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:26:37: #4 Write peak in narrowPeak format file... SRX080101.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:26:37: #4 Write summits bed file... SRX080101.10_summits.bed INFO @ Thu, 30 Apr 2015 11:26:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (74 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:26:37: #4 Write output xls file... SRX080101.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:26:37: #4 Write peak in narrowPeak format file... SRX080101.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:26:37: #4 Write summits bed file... SRX080101.05_summits.bed INFO @ Thu, 30 Apr 2015 11:26:37: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (205 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。