Job ID = 9037661 sra ファイルのダウンロード中... Completed: 467897K bytes transferred in 7 seconds (534219K 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 30246 0 30246 0 0 3545 0 --:--:-- 0:00:08 --:--:-- 16148 100 65375 0 65375 0 0 7240 0 --:--:-- 0:00:09 --:--:-- 27584 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 16719804 spots for /home/okishinya/chipatlas/results/sacCer3/SRX977452/SRR1951298.sra Written 16719804 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: 00:02:36 16719804 reads; of these: 16719804 (100.00%) were unpaired; of these: 5167799 (30.91%) aligned 0 times 4117702 (24.63%) aligned exactly 1 time 7434303 (44.46%) aligned >1 times 69.09% overall alignment rate Time searching: 00:02:36 Overall time: 00:02:36 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_sort_core] merging from 8 files... [bam_rmdupse_core] 11032721 / 11552005 = 0.9550 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 05:11:13: # Command line: callpeak -t SRX977452.bam -f BAM -g 12100000 -n SRX977452.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX977452.05 # format = BAM # ChIP-seq file = ['SRX977452.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 05:11:13: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:11:13: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:11:13: # Command line: callpeak -t SRX977452.bam -f BAM -g 12100000 -n SRX977452.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX977452.20 # format = BAM # ChIP-seq file = ['SRX977452.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 05:11:13: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:11:13: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:11:13: # Command line: callpeak -t SRX977452.bam -f BAM -g 12100000 -n SRX977452.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX977452.10 # format = BAM # ChIP-seq file = ['SRX977452.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 05:11:13: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:11:13: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:11:16: #1 tag size is determined as 45 bps INFO @ Sun, 04 Jun 2017 05:11:16: #1 tag size = 45 INFO @ Sun, 04 Jun 2017 05:11:16: #1 total tags in treatment: 519284 INFO @ Sun, 04 Jun 2017 05:11:16: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:11:16: #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 05:11:16: #1 tag size is determined as 45 bps INFO @ Sun, 04 Jun 2017 05:11:16: #1 tag size = 45 INFO @ Sun, 04 Jun 2017 05:11:16: #1 total tags in treatment: 519284 INFO @ Sun, 04 Jun 2017 05:11:16: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:11:16: #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 05:11:16: #1 tags after filtering in treatment: 517426 INFO @ Sun, 04 Jun 2017 05:11:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:11:16: #1 finished! INFO @ Sun, 04 Jun 2017 05:11:16: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:11:16: #1 tag size is determined as 45 bps INFO @ Sun, 04 Jun 2017 05:11:16: #1 tag size = 45 INFO @ Sun, 04 Jun 2017 05:11:16: #1 total tags in treatment: 519284 INFO @ Sun, 04 Jun 2017 05:11:16: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:11:16: #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 05:11:16: #1 tags after filtering in treatment: 517426 INFO @ Sun, 04 Jun 2017 05:11:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:11:16: #1 finished! INFO @ Sun, 04 Jun 2017 05:11:16: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:11:16: #2 number of paired peaks: 169 WARNING @ Sun, 04 Jun 2017 05:11:16: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sun, 04 Jun 2017 05:11:16: start model_add_line... INFO @ Sun, 04 Jun 2017 05:11:16: #1 tags after filtering in treatment: 517426 INFO @ Sun, 04 Jun 2017 05:11:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:11:16: #1 finished! INFO @ Sun, 04 Jun 2017 05:11:16: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:11:16: #2 number of paired peaks: 169 WARNING @ Sun, 04 Jun 2017 05:11:16: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sun, 04 Jun 2017 05:11:16: start model_add_line... INFO @ Sun, 04 Jun 2017 05:11:16: #2 number of paired peaks: 169 WARNING @ Sun, 04 Jun 2017 05:11:16: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sun, 04 Jun 2017 05:11:16: start model_add_line... INFO @ Sun, 04 Jun 2017 05:11:17: start X-correlation... INFO @ Sun, 04 Jun 2017 05:11:17: end of X-cor INFO @ Sun, 04 Jun 2017 05:11:17: #2 finished! INFO @ Sun, 04 Jun 2017 05:11:17: #2 predicted fragment length is 29 bps INFO @ Sun, 04 Jun 2017 05:11:17: #2 alternative fragment length(s) may be 29 bps INFO @ Sun, 04 Jun 2017 05:11:17: #2.2 Generate R script for model : SRX977452.05_model.r WARNING @ Sun, 04 Jun 2017 05:11:17: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:11:17: #2 You may need to consider one of the other alternative d(s): 29 WARNING @ Sun, 04 Jun 2017 05:11:17: #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 05:11:17: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:11:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 05:11:17: start X-correlation... INFO @ Sun, 04 Jun 2017 05:11:17: end of X-cor INFO @ Sun, 04 Jun 2017 05:11:17: #2 finished! INFO @ Sun, 04 Jun 2017 05:11:17: #2 predicted fragment length is 29 bps INFO @ Sun, 04 Jun 2017 05:11:17: #2 alternative fragment length(s) may be 29 bps INFO @ Sun, 04 Jun 2017 05:11:17: #2.2 Generate R script for model : SRX977452.10_model.r WARNING @ Sun, 04 Jun 2017 05:11:17: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:11:17: #2 You may need to consider one of the other alternative d(s): 29 WARNING @ Sun, 04 Jun 2017 05:11:17: #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 05:11:17: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:11:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 05:11:17: start X-correlation... INFO @ Sun, 04 Jun 2017 05:11:17: end of X-cor INFO @ Sun, 04 Jun 2017 05:11:17: #2 finished! INFO @ Sun, 04 Jun 2017 05:11:17: #2 predicted fragment length is 29 bps INFO @ Sun, 04 Jun 2017 05:11:17: #2 alternative fragment length(s) may be 29 bps INFO @ Sun, 04 Jun 2017 05:11:17: #2.2 Generate R script for model : SRX977452.20_model.r WARNING @ Sun, 04 Jun 2017 05:11:17: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:11:17: #2 You may need to consider one of the other alternative d(s): 29 WARNING @ Sun, 04 Jun 2017 05:11:17: #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 05:11:17: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:11:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 05:11:20: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:11:20: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:11:20: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:11:22: #4 Write output xls file... SRX977452.10_peaks.xls INFO @ Sun, 04 Jun 2017 05:11:22: #4 Write peak in narrowPeak format file... SRX977452.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:11:22: #4 Write summits bed file... SRX977452.10_summits.bed INFO @ Sun, 04 Jun 2017 05:11:22: Done! INFO @ Sun, 04 Jun 2017 05:11:22: #4 Write output xls file... SRX977452.05_peaks.xls INFO @ Sun, 04 Jun 2017 05:11:22: #4 Write peak in narrowPeak format file... SRX977452.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:11:22: #4 Write summits bed file... SRX977452.05_summits.bed INFO @ Sun, 04 Jun 2017 05:11:22: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (176 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (459 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 05:11:23: #4 Write output xls file... SRX977452.20_peaks.xls INFO @ Sun, 04 Jun 2017 05:11:23: #4 Write peak in narrowPeak format file... SRX977452.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:11:23: #4 Write summits bed file... SRX977452.20_summits.bed INFO @ Sun, 04 Jun 2017 05:11:23: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (110 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。