Job ID = 9040890 sra ファイルのダウンロード中... Completed: 114942K bytes transferred in 4 seconds (213298K 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 --:--:-- 0 100 14324 0 14324 0 0 1872 0 --:--:-- 0:00:07 --:--:-- 13069 100 45615 0 45615 0 0 5380 0 --:--:-- 0:00:08 --:--:-- 23683 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 5357900 spots for /home/okishinya/chipatlas/results/dm3/SRX1151231/SRR2163807.sra Written 5357900 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: 00:01:12 5357900 reads; of these: 5357900 (100.00%) were unpaired; of these: 82966 (1.55%) aligned 0 times 3012225 (56.22%) aligned exactly 1 time 2262709 (42.23%) aligned >1 times 98.45% overall alignment rate Time searching: 00:01:12 Overall time: 00:01:12 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] 367770 / 5274934 = 0.0697 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 @ Mon, 05 Jun 2017 00:24:17: # Command line: callpeak -t SRX1151231.bam -f BAM -g dm -n SRX1151231.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1151231.20 # format = BAM # ChIP-seq file = ['SRX1151231.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 @ Mon, 05 Jun 2017 00:24:17: #1 read tag files... INFO @ Mon, 05 Jun 2017 00:24:17: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 00:24:17: # Command line: callpeak -t SRX1151231.bam -f BAM -g dm -n SRX1151231.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1151231.05 # format = BAM # ChIP-seq file = ['SRX1151231.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 @ Mon, 05 Jun 2017 00:24:17: #1 read tag files... INFO @ Mon, 05 Jun 2017 00:24:17: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 00:24:17: # Command line: callpeak -t SRX1151231.bam -f BAM -g dm -n SRX1151231.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1151231.10 # format = BAM # ChIP-seq file = ['SRX1151231.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 @ Mon, 05 Jun 2017 00:24:17: #1 read tag files... INFO @ Mon, 05 Jun 2017 00:24:17: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 00:24:22: 1000000 INFO @ Mon, 05 Jun 2017 00:24:22: 1000000 INFO @ Mon, 05 Jun 2017 00:24:22: 1000000 INFO @ Mon, 05 Jun 2017 00:24:27: 2000000 INFO @ Mon, 05 Jun 2017 00:24:27: 2000000 INFO @ Mon, 05 Jun 2017 00:24:27: 2000000 INFO @ Mon, 05 Jun 2017 00:24:32: 3000000 INFO @ Mon, 05 Jun 2017 00:24:32: 3000000 INFO @ Mon, 05 Jun 2017 00:24:32: 3000000 INFO @ Mon, 05 Jun 2017 00:24:37: 4000000 INFO @ Mon, 05 Jun 2017 00:24:37: 4000000 INFO @ Mon, 05 Jun 2017 00:24:38: 4000000 INFO @ Mon, 05 Jun 2017 00:24:42: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 00:24:42: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 00:24:42: #1 total tags in treatment: 4907164 INFO @ Mon, 05 Jun 2017 00:24:42: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 00:24:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 00:24:42: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 00:24:42: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 00:24:42: #1 total tags in treatment: 4907164 INFO @ Mon, 05 Jun 2017 00:24:42: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 00:24:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 00:24:42: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 00:24:42: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 00:24:42: #1 total tags in treatment: 4907164 INFO @ Mon, 05 Jun 2017 00:24:42: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 00:24:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 00:24:42: #1 tags after filtering in treatment: 4906710 INFO @ Mon, 05 Jun 2017 00:24:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 00:24:42: #1 finished! INFO @ Mon, 05 Jun 2017 00:24:42: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 00:24:43: #1 tags after filtering in treatment: 4906710 INFO @ Mon, 05 Jun 2017 00:24:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 00:24:43: #1 finished! INFO @ Mon, 05 Jun 2017 00:24:43: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 00:24:43: #1 tags after filtering in treatment: 4906710 INFO @ Mon, 05 Jun 2017 00:24:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 00:24:43: #1 finished! INFO @ Mon, 05 Jun 2017 00:24:43: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 00:24:43: #2 number of paired peaks: 374 WARNING @ Mon, 05 Jun 2017 00:24:43: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Mon, 05 Jun 2017 00:24:43: start model_add_line... INFO @ Mon, 05 Jun 2017 00:24:44: #2 number of paired peaks: 374 WARNING @ Mon, 05 Jun 2017 00:24:44: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Mon, 05 Jun 2017 00:24:44: start model_add_line... INFO @ Mon, 05 Jun 2017 00:24:44: #2 number of paired peaks: 374 WARNING @ Mon, 05 Jun 2017 00:24:44: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Mon, 05 Jun 2017 00:24:44: start model_add_line... INFO @ Mon, 05 Jun 2017 00:24:45: start X-correlation... INFO @ Mon, 05 Jun 2017 00:24:45: end of X-cor INFO @ Mon, 05 Jun 2017 00:24:45: #2 finished! INFO @ Mon, 05 Jun 2017 00:24:45: #2 predicted fragment length is 51 bps INFO @ Mon, 05 Jun 2017 00:24:45: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 05 Jun 2017 00:24:45: #2.2 Generate R script for model : SRX1151231.10_model.r WARNING @ Mon, 05 Jun 2017 00:24:45: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 00:24:45: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 05 Jun 2017 00:24:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 05 Jun 2017 00:24:45: #3 Call peaks... INFO @ Mon, 05 Jun 2017 00:24:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 00:24:45: start X-correlation... INFO @ Mon, 05 Jun 2017 00:24:45: end of X-cor INFO @ Mon, 05 Jun 2017 00:24:45: #2 finished! INFO @ Mon, 05 Jun 2017 00:24:45: #2 predicted fragment length is 51 bps INFO @ Mon, 05 Jun 2017 00:24:45: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 05 Jun 2017 00:24:45: #2.2 Generate R script for model : SRX1151231.05_model.r WARNING @ Mon, 05 Jun 2017 00:24:45: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 00:24:45: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 05 Jun 2017 00:24:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 05 Jun 2017 00:24:45: #3 Call peaks... INFO @ Mon, 05 Jun 2017 00:24:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 00:24:45: start X-correlation... INFO @ Mon, 05 Jun 2017 00:24:45: end of X-cor INFO @ Mon, 05 Jun 2017 00:24:45: #2 finished! INFO @ Mon, 05 Jun 2017 00:24:45: #2 predicted fragment length is 51 bps INFO @ Mon, 05 Jun 2017 00:24:45: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 05 Jun 2017 00:24:45: #2.2 Generate R script for model : SRX1151231.20_model.r WARNING @ Mon, 05 Jun 2017 00:24:45: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 00:24:45: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 05 Jun 2017 00:24:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 05 Jun 2017 00:24:45: #3 Call peaks... INFO @ Mon, 05 Jun 2017 00:24:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 00:25:11: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 00:25:16: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 00:25:17: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 00:25:32: #4 Write output xls file... SRX1151231.10_peaks.xls INFO @ Mon, 05 Jun 2017 00:25:32: #4 Write peak in narrowPeak format file... SRX1151231.10_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 00:25:32: #4 Write summits bed file... SRX1151231.10_summits.bed INFO @ Mon, 05 Jun 2017 00:25:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (741 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 00:25:36: #4 Write output xls file... SRX1151231.20_peaks.xls INFO @ Mon, 05 Jun 2017 00:25:36: #4 Write peak in narrowPeak format file... SRX1151231.20_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 00:25:36: #4 Write summits bed file... SRX1151231.20_summits.bed INFO @ Mon, 05 Jun 2017 00:25:36: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (307 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 00:25:40: #4 Write output xls file... SRX1151231.05_peaks.xls INFO @ Mon, 05 Jun 2017 00:25:40: #4 Write peak in narrowPeak format file... SRX1151231.05_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 00:25:40: #4 Write summits bed file... SRX1151231.05_summits.bed INFO @ Mon, 05 Jun 2017 00:25:40: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1516 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。