Job ID = 9025502 sra ファイルのダウンロード中... Completed: 10126K bytes transferred in 2 seconds (28697K 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 --:--:-- 0:00:06 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 100 14324 0 14324 0 0 1820 0 --:--:-- 0:00:07 --:--:-- 10641 100 37486 0 37486 0 0 4228 0 --:--:-- 0:00:08 --:--:-- 16012 100 42743 0 42743 0 0 4733 0 --:--:-- 0:00:09 --:--:-- 17049 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 384962 spots for /home/okishinya/chipatlas/results/ce10/SRX1388751/SRR2832467.sra Written 384962 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: 00:00:10 384962 reads; of these: 384962 (100.00%) were unpaired; of these: 136811 (35.54%) aligned 0 times 162974 (42.34%) aligned exactly 1 time 85177 (22.13%) aligned >1 times 64.46% overall alignment rate Time searching: 00:00:10 Overall time: 00:00:10 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] 49749 / 248151 = 0.2005 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 @ Sat, 03 Jun 2017 04:08:47: # Command line: callpeak -t SRX1388751.bam -f BAM -g ce -n SRX1388751.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1388751.20 # format = BAM # ChIP-seq file = ['SRX1388751.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 @ Sat, 03 Jun 2017 04:08:47: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:08:47: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:08:47: # Command line: callpeak -t SRX1388751.bam -f BAM -g ce -n SRX1388751.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1388751.05 # format = BAM # ChIP-seq file = ['SRX1388751.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 @ Sat, 03 Jun 2017 04:08:47: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:08:47: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:08:47: # Command line: callpeak -t SRX1388751.bam -f BAM -g ce -n SRX1388751.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1388751.10 # format = BAM # ChIP-seq file = ['SRX1388751.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 @ Sat, 03 Jun 2017 04:08:47: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:08:47: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:08:48: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:08:48: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:08:48: #1 total tags in treatment: 198402 INFO @ Sat, 03 Jun 2017 04:08:48: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:08:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 04:08:48: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:08:48: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:08:48: #1 total tags in treatment: 198402 INFO @ Sat, 03 Jun 2017 04:08:48: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:08:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 04:08:48: #1 tags after filtering in treatment: 198369 INFO @ Sat, 03 Jun 2017 04:08:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:08:48: #1 finished! INFO @ Sat, 03 Jun 2017 04:08:48: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:08:48: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:08:48: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:08:48: #1 total tags in treatment: 198402 INFO @ Sat, 03 Jun 2017 04:08:48: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:08:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 04:08:48: #1 tags after filtering in treatment: 198369 INFO @ Sat, 03 Jun 2017 04:08:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:08:48: #1 finished! INFO @ Sat, 03 Jun 2017 04:08:48: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:08:48: #1 tags after filtering in treatment: 198369 INFO @ Sat, 03 Jun 2017 04:08:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:08:48: #1 finished! INFO @ Sat, 03 Jun 2017 04:08:48: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:08:49: #2 number of paired peaks: 1157 INFO @ Sat, 03 Jun 2017 04:08:49: start model_add_line... INFO @ Sat, 03 Jun 2017 04:08:49: #2 number of paired peaks: 1157 INFO @ Sat, 03 Jun 2017 04:08:49: start model_add_line... INFO @ Sat, 03 Jun 2017 04:08:49: #2 number of paired peaks: 1157 INFO @ Sat, 03 Jun 2017 04:08:49: start model_add_line... INFO @ Sat, 03 Jun 2017 04:08:49: start X-correlation... INFO @ Sat, 03 Jun 2017 04:08:49: end of X-cor INFO @ Sat, 03 Jun 2017 04:08:49: #2 finished! INFO @ Sat, 03 Jun 2017 04:08:49: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Jun 2017 04:08:49: #2 alternative fragment length(s) may be 47,107,196,474,543 bps INFO @ Sat, 03 Jun 2017 04:08:49: #2.2 Generate R script for model : SRX1388751.20_model.r WARNING @ Sat, 03 Jun 2017 04:08:49: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:08:49: #2 You may need to consider one of the other alternative d(s): 47,107,196,474,543 WARNING @ Sat, 03 Jun 2017 04:08:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 04:08:49: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:08:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:08:49: start X-correlation... INFO @ Sat, 03 Jun 2017 04:08:49: end of X-cor INFO @ Sat, 03 Jun 2017 04:08:49: #2 finished! INFO @ Sat, 03 Jun 2017 04:08:49: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Jun 2017 04:08:49: #2 alternative fragment length(s) may be 47,107,196,474,543 bps INFO @ Sat, 03 Jun 2017 04:08:49: #2.2 Generate R script for model : SRX1388751.05_model.r INFO @ Sat, 03 Jun 2017 04:08:49: start X-correlation... WARNING @ Sat, 03 Jun 2017 04:08:49: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:08:49: #2 You may need to consider one of the other alternative d(s): 47,107,196,474,543 WARNING @ Sat, 03 Jun 2017 04:08:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 04:08:49: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:08:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:08:49: end of X-cor INFO @ Sat, 03 Jun 2017 04:08:49: #2 finished! INFO @ Sat, 03 Jun 2017 04:08:49: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Jun 2017 04:08:49: #2 alternative fragment length(s) may be 47,107,196,474,543 bps INFO @ Sat, 03 Jun 2017 04:08:49: #2.2 Generate R script for model : SRX1388751.10_model.r WARNING @ Sat, 03 Jun 2017 04:08:49: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:08:49: #2 You may need to consider one of the other alternative d(s): 47,107,196,474,543 WARNING @ Sat, 03 Jun 2017 04:08:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 04:08:49: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:08:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:08:50: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:08:50: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:08:50: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 04:08:51: #4 Write output xls file... SRX1388751.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:08:51: #4 Write peak in narrowPeak format file... SRX1388751.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:08:51: #4 Write summits bed file... SRX1388751.20_summits.bed INFO @ Sat, 03 Jun 2017 04:08:51: Done! BigWig に変換しました。 pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (46 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:08:51: #4 Write output xls file... SRX1388751.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:08:51: #4 Write peak in narrowPeak format file... SRX1388751.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:08:51: #4 Write summits bed file... SRX1388751.05_summits.bed INFO @ Sat, 03 Jun 2017 04:08:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (94 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:08:51: #4 Write output xls file... SRX1388751.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:08:51: #4 Write peak in narrowPeak format file... SRX1388751.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:08:51: #4 Write summits bed file... SRX1388751.10_summits.bed INFO @ Sat, 03 Jun 2017 04:08:51: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (71 records, 4 fields): 2 millis CompletedMACS2peakCalling