Job ID = 9029703 sra ファイルのダウンロード中... Completed: 829174K bytes transferred in 11 seconds (603719K 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 1075 0 --:--:-- 0:00:07 --:--:-- 11073 100 30318 0 30318 0 0 3811 0 --:--:-- 0:00:07 --:--:-- 19906 100 69712 0 69712 0 0 8087 0 --:--:-- 0:00:08 --:--:-- 31890 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 17793839 spots for /home/okishinya/chipatlas/results/dm3/SRX2011092/SRR4017245.sra Written 17793839 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: 00:14:18 17793839 reads; of these: 17793839 (100.00%) were unpaired; of these: 630462 (3.54%) aligned 0 times 11649042 (65.47%) aligned exactly 1 time 5514335 (30.99%) aligned >1 times 96.46% overall alignment rate Time searching: 00:14:18 Overall time: 00:14:18 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] 1555411 / 17163377 = 0.0906 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 15:10:21: # Command line: callpeak -t SRX2011092.bam -f BAM -g dm -n SRX2011092.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2011092.05 # format = BAM # ChIP-seq file = ['SRX2011092.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 15:10:21: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:10:21: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:10:21: # Command line: callpeak -t SRX2011092.bam -f BAM -g dm -n SRX2011092.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2011092.20 # format = BAM # ChIP-seq file = ['SRX2011092.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 15:10:21: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:10:21: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:10:21: # Command line: callpeak -t SRX2011092.bam -f BAM -g dm -n SRX2011092.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2011092.10 # format = BAM # ChIP-seq file = ['SRX2011092.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 15:10:21: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:10:21: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:10:30: 1000000 INFO @ Sat, 03 Jun 2017 15:10:30: 1000000 INFO @ Sat, 03 Jun 2017 15:10:30: 1000000 INFO @ Sat, 03 Jun 2017 15:10:39: 2000000 INFO @ Sat, 03 Jun 2017 15:10:39: 2000000 INFO @ Sat, 03 Jun 2017 15:10:39: 2000000 INFO @ Sat, 03 Jun 2017 15:10:47: 3000000 INFO @ Sat, 03 Jun 2017 15:10:48: 3000000 INFO @ Sat, 03 Jun 2017 15:10:48: 3000000 INFO @ Sat, 03 Jun 2017 15:10:56: 4000000 INFO @ Sat, 03 Jun 2017 15:10:57: 4000000 INFO @ Sat, 03 Jun 2017 15:10:58: 4000000 INFO @ Sat, 03 Jun 2017 15:11:05: 5000000 INFO @ Sat, 03 Jun 2017 15:11:07: 5000000 INFO @ Sat, 03 Jun 2017 15:11:07: 5000000 INFO @ Sat, 03 Jun 2017 15:11:14: 6000000 INFO @ Sat, 03 Jun 2017 15:11:15: 6000000 INFO @ Sat, 03 Jun 2017 15:11:16: 6000000 INFO @ Sat, 03 Jun 2017 15:11:23: 7000000 INFO @ Sat, 03 Jun 2017 15:11:24: 7000000 INFO @ Sat, 03 Jun 2017 15:11:24: 7000000 INFO @ Sat, 03 Jun 2017 15:11:31: 8000000 INFO @ Sat, 03 Jun 2017 15:11:33: 8000000 INFO @ Sat, 03 Jun 2017 15:11:33: 8000000 INFO @ Sat, 03 Jun 2017 15:11:40: 9000000 INFO @ Sat, 03 Jun 2017 15:11:42: 9000000 INFO @ Sat, 03 Jun 2017 15:11:42: 9000000 INFO @ Sat, 03 Jun 2017 15:11:49: 10000000 INFO @ Sat, 03 Jun 2017 15:11:51: 10000000 INFO @ Sat, 03 Jun 2017 15:11:51: 10000000 INFO @ Sat, 03 Jun 2017 15:11:58: 11000000 INFO @ Sat, 03 Jun 2017 15:12:00: 11000000 INFO @ Sat, 03 Jun 2017 15:12:01: 11000000 INFO @ Sat, 03 Jun 2017 15:12:06: 12000000 INFO @ Sat, 03 Jun 2017 15:12:10: 12000000 INFO @ Sat, 03 Jun 2017 15:12:10: 12000000 INFO @ Sat, 03 Jun 2017 15:12:15: 13000000 INFO @ Sat, 03 Jun 2017 15:12:19: 13000000 INFO @ Sat, 03 Jun 2017 15:12:19: 13000000 INFO @ Sat, 03 Jun 2017 15:12:24: 14000000 INFO @ Sat, 03 Jun 2017 15:12:28: 14000000 INFO @ Sat, 03 Jun 2017 15:12:28: 14000000 INFO @ Sat, 03 Jun 2017 15:12:33: 15000000 INFO @ Sat, 03 Jun 2017 15:12:37: 15000000 INFO @ Sat, 03 Jun 2017 15:12:37: 15000000 INFO @ Sat, 03 Jun 2017 15:12:38: #1 tag size is determined as 100 bps INFO @ Sat, 03 Jun 2017 15:12:38: #1 tag size = 100 INFO @ Sat, 03 Jun 2017 15:12:38: #1 total tags in treatment: 15607966 INFO @ Sat, 03 Jun 2017 15:12:38: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:12:38: #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 15:12:41: #1 tags after filtering in treatment: 15592209 INFO @ Sat, 03 Jun 2017 15:12:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:12:41: #1 finished! INFO @ Sat, 03 Jun 2017 15:12:41: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:12:43: #1 tag size is determined as 100 bps INFO @ Sat, 03 Jun 2017 15:12:43: #1 tag size = 100 INFO @ Sat, 03 Jun 2017 15:12:43: #1 total tags in treatment: 15607966 INFO @ Sat, 03 Jun 2017 15:12:43: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:12:43: #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 15:12:43: #1 tag size is determined as 100 bps INFO @ Sat, 03 Jun 2017 15:12:43: #1 tag size = 100 INFO @ Sat, 03 Jun 2017 15:12:43: #1 total tags in treatment: 15607966 INFO @ Sat, 03 Jun 2017 15:12:43: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:12:43: #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 15:12:44: #2 number of paired peaks: 110 WARNING @ Sat, 03 Jun 2017 15:12:44: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Sat, 03 Jun 2017 15:12:44: start model_add_line... INFO @ Sat, 03 Jun 2017 15:12:45: start X-correlation... INFO @ Sat, 03 Jun 2017 15:12:45: end of X-cor INFO @ Sat, 03 Jun 2017 15:12:45: #2 finished! INFO @ Sat, 03 Jun 2017 15:12:45: #2 predicted fragment length is 94 bps INFO @ Sat, 03 Jun 2017 15:12:45: #2 alternative fragment length(s) may be 94 bps INFO @ Sat, 03 Jun 2017 15:12:45: #2.2 Generate R script for model : SRX2011092.20_model.r WARNING @ Sat, 03 Jun 2017 15:12:45: #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 15:12:45: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sat, 03 Jun 2017 15:12:45: #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 15:12:45: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:12:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:12:46: #1 tags after filtering in treatment: 15592209 INFO @ Sat, 03 Jun 2017 15:12:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:12:46: #1 finished! INFO @ Sat, 03 Jun 2017 15:12:46: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:12:46: #1 tags after filtering in treatment: 15592209 INFO @ Sat, 03 Jun 2017 15:12:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:12:46: #1 finished! INFO @ Sat, 03 Jun 2017 15:12:46: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:12:48: #2 number of paired peaks: 110 WARNING @ Sat, 03 Jun 2017 15:12:48: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Sat, 03 Jun 2017 15:12:48: start model_add_line... INFO @ Sat, 03 Jun 2017 15:12:49: #2 number of paired peaks: 110 WARNING @ Sat, 03 Jun 2017 15:12:49: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Sat, 03 Jun 2017 15:12:49: start model_add_line... INFO @ Sat, 03 Jun 2017 15:12:50: start X-correlation... INFO @ Sat, 03 Jun 2017 15:12:50: end of X-cor INFO @ Sat, 03 Jun 2017 15:12:50: #2 finished! INFO @ Sat, 03 Jun 2017 15:12:50: #2 predicted fragment length is 94 bps INFO @ Sat, 03 Jun 2017 15:12:50: #2 alternative fragment length(s) may be 94 bps INFO @ Sat, 03 Jun 2017 15:12:50: #2.2 Generate R script for model : SRX2011092.10_model.r WARNING @ Sat, 03 Jun 2017 15:12:50: #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 15:12:50: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sat, 03 Jun 2017 15:12:50: #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 15:12:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:12:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:12:50: start X-correlation... INFO @ Sat, 03 Jun 2017 15:12:50: end of X-cor INFO @ Sat, 03 Jun 2017 15:12:50: #2 finished! INFO @ Sat, 03 Jun 2017 15:12:50: #2 predicted fragment length is 94 bps INFO @ Sat, 03 Jun 2017 15:12:50: #2 alternative fragment length(s) may be 94 bps INFO @ Sat, 03 Jun 2017 15:12:50: #2.2 Generate R script for model : SRX2011092.05_model.r WARNING @ Sat, 03 Jun 2017 15:12:50: #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 15:12:50: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sat, 03 Jun 2017 15:12:50: #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 15:12:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:12:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:14:08: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:14:09: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:14:17: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:15:07: #4 Write output xls file... SRX2011092.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:15:07: #4 Write peak in narrowPeak format file... SRX2011092.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:15:07: #4 Write summits bed file... SRX2011092.20_summits.bed INFO @ Sat, 03 Jun 2017 15:15:07: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (697 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:15:08: #4 Write output xls file... SRX2011092.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:15:08: #4 Write peak in narrowPeak format file... SRX2011092.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:15:08: #4 Write summits bed file... SRX2011092.10_summits.bed INFO @ Sat, 03 Jun 2017 15:15:08: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1119 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:15:16: #4 Write output xls file... SRX2011092.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:15:16: #4 Write peak in narrowPeak format file... SRX2011092.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:15:16: #4 Write summits bed file... SRX2011092.05_summits.bed INFO @ Sat, 03 Jun 2017 15:15:16: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1781 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。