Job ID = 9037676 sra ファイルのダウンロード中... Completed: 178585K bytes transferred in 4 seconds (294182K 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 7663 0 7663 0 0 838 0 --:--:-- 0:00:09 --:--:-- 2872 100 38318 0 38318 0 0 3842 0 --:--:-- 0:00:09 --:--:-- 10954 100 43940 0 43940 0 0 4334 0 --:--:-- 0:00:10 --:--:-- 11992 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 7006381 spots for /home/okishinya/chipatlas/results/sacCer3/SRX977467/SRR1951313.sra Written 7006381 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: 00:00:52 7006381 reads; of these: 7006381 (100.00%) were unpaired; of these: 1684403 (24.04%) aligned 0 times 5004212 (71.42%) aligned exactly 1 time 317766 (4.54%) aligned >1 times 75.96% overall alignment rate Time searching: 00:00:52 Overall time: 00:00:52 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] 4849963 / 5321978 = 0.9113 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 05:10:21: # Command line: callpeak -t SRX977467.bam -f BAM -g 12100000 -n SRX977467.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX977467.10 # format = BAM # ChIP-seq file = ['SRX977467.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 05:10:21: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:10:21: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:10:21: # Command line: callpeak -t SRX977467.bam -f BAM -g 12100000 -n SRX977467.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX977467.20 # format = BAM # ChIP-seq file = ['SRX977467.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 05:10:21: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:10:21: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:10:21: # Command line: callpeak -t SRX977467.bam -f BAM -g 12100000 -n SRX977467.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX977467.05 # format = BAM # ChIP-seq file = ['SRX977467.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 05:10:21: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:10:21: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:10:24: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 05:10:24: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 05:10:24: #1 total tags in treatment: 472015 INFO @ Sun, 04 Jun 2017 05:10:24: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:10:24: #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 05:10:24: #1 tags after filtering in treatment: 471096 INFO @ Sun, 04 Jun 2017 05:10:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:10:24: #1 finished! INFO @ Sun, 04 Jun 2017 05:10:24: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:10:24: #2 number of paired peaks: 528 WARNING @ Sun, 04 Jun 2017 05:10:24: Fewer paired peaks (528) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 528 pairs to build model! INFO @ Sun, 04 Jun 2017 05:10:24: start model_add_line... INFO @ Sun, 04 Jun 2017 05:10:24: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 05:10:24: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 05:10:24: #1 total tags in treatment: 472015 INFO @ Sun, 04 Jun 2017 05:10:24: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:10:24: #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 05:10:24: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 05:10:24: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 05:10:24: #1 total tags in treatment: 472015 INFO @ Sun, 04 Jun 2017 05:10:24: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:10:24: #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 05:10:25: #1 tags after filtering in treatment: 471096 INFO @ Sun, 04 Jun 2017 05:10:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:10:25: #1 finished! INFO @ Sun, 04 Jun 2017 05:10:25: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:10:25: #1 tags after filtering in treatment: 471096 INFO @ Sun, 04 Jun 2017 05:10:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:10:25: #1 finished! INFO @ Sun, 04 Jun 2017 05:10:25: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:10:25: #2 number of paired peaks: 528 WARNING @ Sun, 04 Jun 2017 05:10:25: Fewer paired peaks (528) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 528 pairs to build model! INFO @ Sun, 04 Jun 2017 05:10:25: start model_add_line... INFO @ Sun, 04 Jun 2017 05:10:25: #2 number of paired peaks: 528 WARNING @ Sun, 04 Jun 2017 05:10:25: Fewer paired peaks (528) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 528 pairs to build model! INFO @ Sun, 04 Jun 2017 05:10:25: start model_add_line... INFO @ Sun, 04 Jun 2017 05:10:26: start X-correlation... INFO @ Sun, 04 Jun 2017 05:10:26: end of X-cor INFO @ Sun, 04 Jun 2017 05:10:26: #2 finished! INFO @ Sun, 04 Jun 2017 05:10:26: #2 predicted fragment length is 31 bps INFO @ Sun, 04 Jun 2017 05:10:26: #2 alternative fragment length(s) may be 31 bps INFO @ Sun, 04 Jun 2017 05:10:26: #2.2 Generate R script for model : SRX977467.10_model.r WARNING @ Sun, 04 Jun 2017 05:10:26: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:10:26: #2 You may need to consider one of the other alternative d(s): 31 WARNING @ Sun, 04 Jun 2017 05:10:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 05:10:26: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:10:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 05:10:26: start X-correlation... INFO @ Sun, 04 Jun 2017 05:10:26: end of X-cor INFO @ Sun, 04 Jun 2017 05:10:26: #2 finished! INFO @ Sun, 04 Jun 2017 05:10:26: #2 predicted fragment length is 31 bps INFO @ Sun, 04 Jun 2017 05:10:26: #2 alternative fragment length(s) may be 31 bps INFO @ Sun, 04 Jun 2017 05:10:26: #2.2 Generate R script for model : SRX977467.05_model.r WARNING @ Sun, 04 Jun 2017 05:10:26: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:10:26: #2 You may need to consider one of the other alternative d(s): 31 WARNING @ Sun, 04 Jun 2017 05:10:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 05:10:26: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:10:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 05:10:26: start X-correlation... INFO @ Sun, 04 Jun 2017 05:10:26: end of X-cor INFO @ Sun, 04 Jun 2017 05:10:26: #2 finished! INFO @ Sun, 04 Jun 2017 05:10:26: #2 predicted fragment length is 31 bps INFO @ Sun, 04 Jun 2017 05:10:26: #2 alternative fragment length(s) may be 31 bps INFO @ Sun, 04 Jun 2017 05:10:26: #2.2 Generate R script for model : SRX977467.20_model.r WARNING @ Sun, 04 Jun 2017 05:10:26: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:10:26: #2 You may need to consider one of the other alternative d(s): 31 WARNING @ Sun, 04 Jun 2017 05:10:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 05:10:26: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:10:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 05:10:28: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:10:29: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:10:29: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:10:30: #4 Write output xls file... SRX977467.10_peaks.xls INFO @ Sun, 04 Jun 2017 05:10:30: #4 Write peak in narrowPeak format file... SRX977467.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:10:30: #4 Write summits bed file... SRX977467.10_summits.bed INFO @ Sun, 04 Jun 2017 05:10:30: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (1336 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 04 Jun 2017 05:10:31: #4 Write output xls file... SRX977467.20_peaks.xls INFO @ Sun, 04 Jun 2017 05:10:31: #4 Write peak in narrowPeak format file... SRX977467.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:10:31: #4 Write summits bed file... SRX977467.20_summits.bed INFO @ Sun, 04 Jun 2017 05:10:31: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (458 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 05:10:32: #4 Write output xls file... SRX977467.05_peaks.xls INFO @ Sun, 04 Jun 2017 05:10:32: #4 Write peak in narrowPeak format file... SRX977467.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:10:32: #4 Write summits bed file... SRX977467.05_summits.bed INFO @ Sun, 04 Jun 2017 05:10:32: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (2796 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。