Job ID = 9029585 sra ファイルのダウンロード中... Completed: 582495K bytes transferred in 9 seconds (512885K 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 --:--:-- 0:00:06 --:--:-- 0 100 14324 0 14324 0 0 1893 0 --:--:-- 0:00:07 --:--:-- 13475 100 62101 0 62101 0 0 7254 0 --:--:-- 0:00:08 --:--:-- 30160 100 81967 0 81967 0 0 9391 0 --:--:-- 0:00:08 --:--:-- 36822 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 10298719 spots for /home/okishinya/chipatlas/results/dm3/SRX1850481/SRR3675038.sra Written 10298719 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: 00:07:26 10298719 reads; of these: 10298719 (100.00%) were unpaired; of these: 1564353 (15.19%) aligned 0 times 7181232 (69.73%) aligned exactly 1 time 1553134 (15.08%) aligned >1 times 84.81% overall alignment rate Time searching: 00:07:26 Overall time: 00:07:26 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 6828184 / 8734366 = 0.7818 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 14:24:03: # Command line: callpeak -t SRX1850481.bam -f BAM -g dm -n SRX1850481.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1850481.10 # format = BAM # ChIP-seq file = ['SRX1850481.bam'] # control file = None # effective genome size = 1.20e+08 # 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 14:24:03: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:24:03: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:24:03: # Command line: callpeak -t SRX1850481.bam -f BAM -g dm -n SRX1850481.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1850481.20 # format = BAM # ChIP-seq file = ['SRX1850481.bam'] # control file = None # effective genome size = 1.20e+08 # 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 14:24:03: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:24:03: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:24:03: # Command line: callpeak -t SRX1850481.bam -f BAM -g dm -n SRX1850481.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1850481.05 # format = BAM # ChIP-seq file = ['SRX1850481.bam'] # control file = None # effective genome size = 1.20e+08 # 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 14:24:03: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:24:03: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:24:10: 1000000 INFO @ Sat, 03 Jun 2017 14:24:11: 1000000 INFO @ Sat, 03 Jun 2017 14:24:11: 1000000 INFO @ Sat, 03 Jun 2017 14:24:17: #1 tag size is determined as 101 bps INFO @ Sat, 03 Jun 2017 14:24:17: #1 tag size = 101 INFO @ Sat, 03 Jun 2017 14:24:17: #1 total tags in treatment: 1906182 INFO @ Sat, 03 Jun 2017 14:24:17: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:24:17: #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 14:24:17: #1 tag size is determined as 101 bps INFO @ Sat, 03 Jun 2017 14:24:17: #1 tag size = 101 INFO @ Sat, 03 Jun 2017 14:24:17: #1 total tags in treatment: 1906182 INFO @ Sat, 03 Jun 2017 14:24:17: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:24:17: #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 14:24:17: #1 tag size is determined as 101 bps INFO @ Sat, 03 Jun 2017 14:24:17: #1 tag size = 101 INFO @ Sat, 03 Jun 2017 14:24:17: #1 total tags in treatment: 1906182 INFO @ Sat, 03 Jun 2017 14:24:17: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:24:17: #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 14:24:17: #1 tags after filtering in treatment: 1902476 INFO @ Sat, 03 Jun 2017 14:24:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:24:17: #1 finished! INFO @ Sat, 03 Jun 2017 14:24:17: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:24:18: #1 tags after filtering in treatment: 1902476 INFO @ Sat, 03 Jun 2017 14:24:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:24:18: #1 finished! INFO @ Sat, 03 Jun 2017 14:24:18: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:24:18: #1 tags after filtering in treatment: 1902476 INFO @ Sat, 03 Jun 2017 14:24:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:24:18: #1 finished! INFO @ Sat, 03 Jun 2017 14:24:18: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:24:18: #2 number of paired peaks: 750 WARNING @ Sat, 03 Jun 2017 14:24:18: Fewer paired peaks (750) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 750 pairs to build model! INFO @ Sat, 03 Jun 2017 14:24:18: start model_add_line... INFO @ Sat, 03 Jun 2017 14:24:18: #2 number of paired peaks: 750 WARNING @ Sat, 03 Jun 2017 14:24:18: Fewer paired peaks (750) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 750 pairs to build model! INFO @ Sat, 03 Jun 2017 14:24:18: start model_add_line... INFO @ Sat, 03 Jun 2017 14:24:18: #2 number of paired peaks: 750 WARNING @ Sat, 03 Jun 2017 14:24:18: Fewer paired peaks (750) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 750 pairs to build model! INFO @ Sat, 03 Jun 2017 14:24:18: start model_add_line... INFO @ Sat, 03 Jun 2017 14:24:19: start X-correlation... INFO @ Sat, 03 Jun 2017 14:24:19: end of X-cor INFO @ Sat, 03 Jun 2017 14:24:19: #2 finished! INFO @ Sat, 03 Jun 2017 14:24:19: #2 predicted fragment length is 94 bps INFO @ Sat, 03 Jun 2017 14:24:19: #2 alternative fragment length(s) may be 94 bps INFO @ Sat, 03 Jun 2017 14:24:19: #2.2 Generate R script for model : SRX1850481.20_model.r WARNING @ Sat, 03 Jun 2017 14:24:19: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:24:19: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sat, 03 Jun 2017 14:24:19: #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 14:24:19: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:24:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:24:19: start X-correlation... INFO @ Sat, 03 Jun 2017 14:24:19: end of X-cor INFO @ Sat, 03 Jun 2017 14:24:19: #2 finished! INFO @ Sat, 03 Jun 2017 14:24:19: #2 predicted fragment length is 94 bps INFO @ Sat, 03 Jun 2017 14:24:19: #2 alternative fragment length(s) may be 94 bps INFO @ Sat, 03 Jun 2017 14:24:19: #2.2 Generate R script for model : SRX1850481.05_model.r WARNING @ Sat, 03 Jun 2017 14:24:19: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:24:19: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sat, 03 Jun 2017 14:24:19: #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 14:24:19: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:24:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:24:19: start X-correlation... INFO @ Sat, 03 Jun 2017 14:24:19: end of X-cor INFO @ Sat, 03 Jun 2017 14:24:19: #2 finished! INFO @ Sat, 03 Jun 2017 14:24:19: #2 predicted fragment length is 94 bps INFO @ Sat, 03 Jun 2017 14:24:19: #2 alternative fragment length(s) may be 94 bps INFO @ Sat, 03 Jun 2017 14:24:19: #2.2 Generate R script for model : SRX1850481.10_model.r WARNING @ Sat, 03 Jun 2017 14:24:19: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:24:19: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sat, 03 Jun 2017 14:24:19: #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 14:24:19: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:24:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:24:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:24:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:24:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:24:39: #4 Write output xls file... SRX1850481.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:24:39: #4 Write peak in narrowPeak format file... SRX1850481.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:24:39: #4 Write summits bed file... SRX1850481.10_summits.bed INFO @ Sat, 03 Jun 2017 14:24:39: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (552 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:24:40: #4 Write output xls file... SRX1850481.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:24:40: #4 Write peak in narrowPeak format file... SRX1850481.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:24:40: #4 Write summits bed file... SRX1850481.20_summits.bed INFO @ Sat, 03 Jun 2017 14:24:40: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (268 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:24:41: #4 Write output xls file... SRX1850481.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:24:41: #4 Write peak in narrowPeak format file... SRX1850481.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:24:41: #4 Write summits bed file... SRX1850481.05_summits.bed INFO @ Sat, 03 Jun 2017 14:24:41: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (947 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。