Job ID = 9037681 sra ファイルのダウンロード中... Completed: 110057K bytes transferred in 4 seconds (207359K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:08 --:--:-- 0 100 14324 0 14324 0 0 1616 0 --:--:-- 0:00:08 --:--:-- 5818 100 36798 0 36798 0 0 3798 0 --:--:-- 0:00:09 --:--:-- 11178 100 45257 0 45257 0 0 4516 0 --:--:-- 0:00:10 --:--:-- 12491 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 5314849 spots for /home/okishinya/chipatlas/results/sacCer3/SRX977472/SRR1951318.sra Written 5314849 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: 00:00:39 5314849 reads; of these: 5314849 (100.00%) were unpaired; of these: 1032247 (19.42%) aligned 0 times 3403721 (64.04%) aligned exactly 1 time 878881 (16.54%) aligned >1 times 80.58% overall alignment rate Time searching: 00:00:39 Overall time: 00:00:39 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 4242533 / 4282602 = 0.9906 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 @ Sun, 04 Jun 2017 05:09:56: # Command line: callpeak -t SRX977472.bam -f BAM -g 12100000 -n SRX977472.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX977472.05 # format = BAM # ChIP-seq file = ['SRX977472.bam'] # control file = None # effective genome size = 1.21e+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 @ Sun, 04 Jun 2017 05:09:56: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:09:56: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:09:56: # Command line: callpeak -t SRX977472.bam -f BAM -g 12100000 -n SRX977472.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX977472.20 # format = BAM # ChIP-seq file = ['SRX977472.bam'] # control file = None # effective genome size = 1.21e+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 @ Sun, 04 Jun 2017 05:09:56: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:09:56: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:09:56: # Command line: callpeak -t SRX977472.bam -f BAM -g 12100000 -n SRX977472.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX977472.10 # format = BAM # ChIP-seq file = ['SRX977472.bam'] # control file = None # effective genome size = 1.21e+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 @ Sun, 04 Jun 2017 05:09:56: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:09:56: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:09:57: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 05:09:57: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 05:09:57: #1 total tags in treatment: 40069 INFO @ Sun, 04 Jun 2017 05:09:57: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:09:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 05:09:57: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 05:09:57: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 05:09:57: #1 total tags in treatment: 40069 INFO @ Sun, 04 Jun 2017 05:09:57: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 05:09:57: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:09:57: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 05:09:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 05:09:57: #1 total tags in treatment: 40069 INFO @ Sun, 04 Jun 2017 05:09:57: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:09:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 05:09:57: #1 tags after filtering in treatment: 39947 INFO @ Sun, 04 Jun 2017 05:09:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:09:57: #1 finished! INFO @ Sun, 04 Jun 2017 05:09:57: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:09:57: #1 tags after filtering in treatment: 39947 INFO @ Sun, 04 Jun 2017 05:09:57: #1 tags after filtering in treatment: 39947 INFO @ Sun, 04 Jun 2017 05:09:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:09:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:09:57: #1 finished! INFO @ Sun, 04 Jun 2017 05:09:57: #1 finished! INFO @ Sun, 04 Jun 2017 05:09:57: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:09:57: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:09:57: #2 number of paired peaks: 323 WARNING @ Sun, 04 Jun 2017 05:09:57: Fewer paired peaks (323) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 323 pairs to build model! INFO @ Sun, 04 Jun 2017 05:09:57: start model_add_line... INFO @ Sun, 04 Jun 2017 05:09:57: #2 number of paired peaks: 323 WARNING @ Sun, 04 Jun 2017 05:09:57: Fewer paired peaks (323) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 323 pairs to build model! INFO @ Sun, 04 Jun 2017 05:09:57: start model_add_line... INFO @ Sun, 04 Jun 2017 05:09:57: #2 number of paired peaks: 323 WARNING @ Sun, 04 Jun 2017 05:09:57: Fewer paired peaks (323) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 323 pairs to build model! INFO @ Sun, 04 Jun 2017 05:09:57: start model_add_line... INFO @ Sun, 04 Jun 2017 05:09:57: start X-correlation... INFO @ Sun, 04 Jun 2017 05:09:57: end of X-cor INFO @ Sun, 04 Jun 2017 05:09:57: #2 finished! INFO @ Sun, 04 Jun 2017 05:09:57: #2 predicted fragment length is 275 bps INFO @ Sun, 04 Jun 2017 05:09:57: #2 alternative fragment length(s) may be 30,45,72,112,137,178,275,316,343,359,383,412,455,482,521,548,562,591 bps INFO @ Sun, 04 Jun 2017 05:09:57: #2.2 Generate R script for model : SRX977472.05_model.r INFO @ Sun, 04 Jun 2017 05:09:57: start X-correlation... INFO @ Sun, 04 Jun 2017 05:09:57: start X-correlation... INFO @ Sun, 04 Jun 2017 05:09:57: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:09:57: end of X-cor INFO @ Sun, 04 Jun 2017 05:09:57: #2 finished! INFO @ Sun, 04 Jun 2017 05:09:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 05:09:57: #2 predicted fragment length is 275 bps INFO @ Sun, 04 Jun 2017 05:09:57: #2 alternative fragment length(s) may be 30,45,72,112,137,178,275,316,343,359,383,412,455,482,521,548,562,591 bps INFO @ Sun, 04 Jun 2017 05:09:57: #2.2 Generate R script for model : SRX977472.20_model.r INFO @ Sun, 04 Jun 2017 05:09:57: end of X-cor INFO @ Sun, 04 Jun 2017 05:09:57: #2 finished! INFO @ Sun, 04 Jun 2017 05:09:57: #2 predicted fragment length is 275 bps INFO @ Sun, 04 Jun 2017 05:09:57: #2 alternative fragment length(s) may be 30,45,72,112,137,178,275,316,343,359,383,412,455,482,521,548,562,591 bps INFO @ Sun, 04 Jun 2017 05:09:57: #2.2 Generate R script for model : SRX977472.10_model.r INFO @ Sun, 04 Jun 2017 05:09:57: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:09:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 05:09:57: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:09:57: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sun, 04 Jun 2017 05:09:57: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:09:57: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:09:57: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:09:57: #4 Write output xls file... SRX977472.05_peaks.xls INFO @ Sun, 04 Jun 2017 05:09:57: #4 Write peak in narrowPeak format file... SRX977472.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:09:57: #4 Write summits bed file... SRX977472.05_summits.bed INFO @ Sun, 04 Jun 2017 05:09:57: Done! INFO @ Sun, 04 Jun 2017 05:09:57: #4 Write output xls file... SRX977472.20_peaks.xls INFO @ Sun, 04 Jun 2017 05:09:57: #4 Write peak in narrowPeak format file... SRX977472.20_peaks.narrowPeak pass1 - making usageList (13 chroms): 0 millis INFO @ Sun, 04 Jun 2017 05:09:57: #4 Write summits bed file... SRX977472.20_summits.bed INFO @ Sun, 04 Jun 2017 05:09:57: Done! pass2 - checking and writing primary data (29 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 05:09:57: #4 Write output xls file... SRX977472.10_peaks.xls INFO @ Sun, 04 Jun 2017 05:09:57: #4 Write peak in narrowPeak format file... SRX977472.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:09:57: #4 Write summits bed file... SRX977472.10_summits.bed INFO @ Sun, 04 Jun 2017 05:09:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (9 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (19 records, 4 fields): 2 millis CompletedMACS2peakCalling