Job ID = 9030310 sra ファイルのダウンロード中... Completed: 566386K bytes transferred in 7 seconds (595089K 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 7663 0 7663 0 0 1069 0 --:--:-- 0:00:07 --:--:-- 10217 100 38317 0 38317 0 0 4693 0 --:--:-- 0:00:08 --:--:-- 21958 100 61889 0 61889 0 0 7284 0 --:--:-- 0:00:08 --:--:-- 29811 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 17667108 spots for /home/okishinya/chipatlas/results/dm3/SRX287968/SRR870157.sra Written 17667108 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: 00:08:14 17667108 reads; of these: 17667108 (100.00%) were unpaired; of these: 720100 (4.08%) aligned 0 times 11489861 (65.04%) aligned exactly 1 time 5457147 (30.89%) aligned >1 times 95.92% overall alignment rate Time searching: 00:08:14 Overall time: 00:08:14 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1984814 / 16947008 = 0.1171 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 17:47:04: # Command line: callpeak -t SRX287968.bam -f BAM -g dm -n SRX287968.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX287968.05 # format = BAM # ChIP-seq file = ['SRX287968.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 17:47:04: #1 read tag files... INFO @ Sat, 03 Jun 2017 17:47:04: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 17:47:04: # Command line: callpeak -t SRX287968.bam -f BAM -g dm -n SRX287968.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX287968.20 # format = BAM # ChIP-seq file = ['SRX287968.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 17:47:04: #1 read tag files... INFO @ Sat, 03 Jun 2017 17:47:04: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 17:47:04: # Command line: callpeak -t SRX287968.bam -f BAM -g dm -n SRX287968.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX287968.10 # format = BAM # ChIP-seq file = ['SRX287968.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 17:47:04: #1 read tag files... INFO @ Sat, 03 Jun 2017 17:47:04: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 17:47:09: 1000000 INFO @ Sat, 03 Jun 2017 17:47:09: 1000000 INFO @ Sat, 03 Jun 2017 17:47:09: 1000000 INFO @ Sat, 03 Jun 2017 17:47:14: 2000000 INFO @ Sat, 03 Jun 2017 17:47:15: 2000000 INFO @ Sat, 03 Jun 2017 17:47:15: 2000000 INFO @ Sat, 03 Jun 2017 17:47:19: 3000000 INFO @ Sat, 03 Jun 2017 17:47:20: 3000000 INFO @ Sat, 03 Jun 2017 17:47:20: 3000000 INFO @ Sat, 03 Jun 2017 17:47:25: 4000000 INFO @ Sat, 03 Jun 2017 17:47:26: 4000000 INFO @ Sat, 03 Jun 2017 17:47:26: 4000000 INFO @ Sat, 03 Jun 2017 17:47:30: 5000000 INFO @ Sat, 03 Jun 2017 17:47:31: 5000000 INFO @ Sat, 03 Jun 2017 17:47:31: 5000000 INFO @ Sat, 03 Jun 2017 17:47:35: 6000000 INFO @ Sat, 03 Jun 2017 17:47:37: 6000000 INFO @ Sat, 03 Jun 2017 17:47:37: 6000000 INFO @ Sat, 03 Jun 2017 17:47:40: 7000000 INFO @ Sat, 03 Jun 2017 17:47:42: 7000000 INFO @ Sat, 03 Jun 2017 17:47:42: 7000000 INFO @ Sat, 03 Jun 2017 17:47:46: 8000000 INFO @ Sat, 03 Jun 2017 17:47:48: 8000000 INFO @ Sat, 03 Jun 2017 17:47:48: 8000000 INFO @ Sat, 03 Jun 2017 17:47:51: 9000000 INFO @ Sat, 03 Jun 2017 17:47:53: 9000000 INFO @ Sat, 03 Jun 2017 17:47:53: 9000000 INFO @ Sat, 03 Jun 2017 17:47:56: 10000000 INFO @ Sat, 03 Jun 2017 17:47:58: 10000000 INFO @ Sat, 03 Jun 2017 17:47:58: 10000000 INFO @ Sat, 03 Jun 2017 17:48:01: 11000000 INFO @ Sat, 03 Jun 2017 17:48:04: 11000000 INFO @ Sat, 03 Jun 2017 17:48:04: 11000000 INFO @ Sat, 03 Jun 2017 17:48:07: 12000000 INFO @ Sat, 03 Jun 2017 17:48:09: 12000000 INFO @ Sat, 03 Jun 2017 17:48:09: 12000000 INFO @ Sat, 03 Jun 2017 17:48:12: 13000000 INFO @ Sat, 03 Jun 2017 17:48:15: 13000000 INFO @ Sat, 03 Jun 2017 17:48:15: 13000000 INFO @ Sat, 03 Jun 2017 17:48:17: 14000000 INFO @ Sat, 03 Jun 2017 17:48:20: 14000000 INFO @ Sat, 03 Jun 2017 17:48:20: 14000000 INFO @ Sat, 03 Jun 2017 17:48:23: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 17:48:23: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 17:48:23: #1 total tags in treatment: 14962194 INFO @ Sat, 03 Jun 2017 17:48:23: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 17:48:23: #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 17:48:25: #1 tags after filtering in treatment: 14958846 INFO @ Sat, 03 Jun 2017 17:48:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 17:48:25: #1 finished! INFO @ Sat, 03 Jun 2017 17:48:25: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 17:48:26: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 17:48:26: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 17:48:26: #1 total tags in treatment: 14962194 INFO @ Sat, 03 Jun 2017 17:48:26: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 17:48:26: #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 17:48:26: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 17:48:26: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 17:48:26: #1 total tags in treatment: 14962194 INFO @ Sat, 03 Jun 2017 17:48:26: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 17:48:26: #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 17:48:28: #2 number of paired peaks: 291 WARNING @ Sat, 03 Jun 2017 17:48:28: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Sat, 03 Jun 2017 17:48:28: start model_add_line... INFO @ Sat, 03 Jun 2017 17:48:28: #1 tags after filtering in treatment: 14958846 INFO @ Sat, 03 Jun 2017 17:48:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 17:48:28: #1 finished! INFO @ Sat, 03 Jun 2017 17:48:28: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 17:48:29: #1 tags after filtering in treatment: 14958846 INFO @ Sat, 03 Jun 2017 17:48:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 17:48:29: #1 finished! INFO @ Sat, 03 Jun 2017 17:48:29: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 17:48:30: start X-correlation... INFO @ Sat, 03 Jun 2017 17:48:30: end of X-cor INFO @ Sat, 03 Jun 2017 17:48:30: #2 finished! INFO @ Sat, 03 Jun 2017 17:48:30: #2 predicted fragment length is 43 bps INFO @ Sat, 03 Jun 2017 17:48:30: #2 alternative fragment length(s) may be 43 bps INFO @ Sat, 03 Jun 2017 17:48:30: #2.2 Generate R script for model : SRX287968.05_model.r WARNING @ Sat, 03 Jun 2017 17:48:30: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 17:48:30: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Sat, 03 Jun 2017 17:48:30: #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 17:48:30: #3 Call peaks... INFO @ Sat, 03 Jun 2017 17:48:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 17:48:31: #2 number of paired peaks: 291 WARNING @ Sat, 03 Jun 2017 17:48:31: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Sat, 03 Jun 2017 17:48:31: start model_add_line... INFO @ Sat, 03 Jun 2017 17:48:31: #2 number of paired peaks: 291 WARNING @ Sat, 03 Jun 2017 17:48:31: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Sat, 03 Jun 2017 17:48:31: start model_add_line... INFO @ Sat, 03 Jun 2017 17:48:33: start X-correlation... INFO @ Sat, 03 Jun 2017 17:48:33: end of X-cor INFO @ Sat, 03 Jun 2017 17:48:33: #2 finished! INFO @ Sat, 03 Jun 2017 17:48:33: #2 predicted fragment length is 43 bps INFO @ Sat, 03 Jun 2017 17:48:33: #2 alternative fragment length(s) may be 43 bps INFO @ Sat, 03 Jun 2017 17:48:33: #2.2 Generate R script for model : SRX287968.20_model.r WARNING @ Sat, 03 Jun 2017 17:48:33: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 17:48:33: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Sat, 03 Jun 2017 17:48:33: #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 17:48:33: #3 Call peaks... INFO @ Sat, 03 Jun 2017 17:48:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 17:48:34: start X-correlation... INFO @ Sat, 03 Jun 2017 17:48:34: end of X-cor INFO @ Sat, 03 Jun 2017 17:48:34: #2 finished! INFO @ Sat, 03 Jun 2017 17:48:34: #2 predicted fragment length is 43 bps INFO @ Sat, 03 Jun 2017 17:48:34: #2 alternative fragment length(s) may be 43 bps INFO @ Sat, 03 Jun 2017 17:48:34: #2.2 Generate R script for model : SRX287968.10_model.r WARNING @ Sat, 03 Jun 2017 17:48:34: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 17:48:34: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Sat, 03 Jun 2017 17:48:34: #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 17:48:34: #3 Call peaks... INFO @ Sat, 03 Jun 2017 17:48:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 17:49:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 17:49:55: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 17:49:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 17:50:51: #4 Write output xls file... SRX287968.05_peaks.xls INFO @ Sat, 03 Jun 2017 17:50:51: #4 Write peak in narrowPeak format file... SRX287968.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 17:50:51: #4 Write summits bed file... SRX287968.05_summits.bed INFO @ Sat, 03 Jun 2017 17:50:51: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2138 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 17:50:53: #4 Write output xls file... SRX287968.20_peaks.xls INFO @ Sat, 03 Jun 2017 17:50:53: #4 Write peak in narrowPeak format file... SRX287968.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 17:50:53: #4 Write summits bed file... SRX287968.20_summits.bed INFO @ Sat, 03 Jun 2017 17:50:53: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1464 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 17:50:57: #4 Write output xls file... SRX287968.10_peaks.xls INFO @ Sat, 03 Jun 2017 17:50:57: #4 Write peak in narrowPeak format file... SRX287968.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 17:50:57: #4 Write summits bed file... SRX287968.10_summits.bed INFO @ Sat, 03 Jun 2017 17:50:57: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1888 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。