Job ID = 9029775 sra ファイルのダウンロード中... Completed: 544148K bytes transferred in 8 seconds (518318K 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 22318 0 22318 0 0 2901 0 --:--:-- 0:00:07 --:--:-- 17062 100 30918 0 30918 0 0 3853 0 --:--:-- 0:00:08 --:--:-- 18852 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 23510417 spots for /home/okishinya/chipatlas/results/dm3/SRX2055957/SRR4069189.sra Written 23510417 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: 00:11:36 23510417 reads; of these: 23510417 (100.00%) were unpaired; of these: 549938 (2.34%) aligned 0 times 14361555 (61.09%) aligned exactly 1 time 8598924 (36.57%) aligned >1 times 97.66% overall alignment rate Time searching: 00:11:36 Overall time: 00:11:36 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3135690 / 22960479 = 0.1366 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 15:26:46: # Command line: callpeak -t SRX2055957.bam -f BAM -g dm -n SRX2055957.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2055957.05 # format = BAM # ChIP-seq file = ['SRX2055957.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 15:26:46: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:26:46: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:26:46: # Command line: callpeak -t SRX2055957.bam -f BAM -g dm -n SRX2055957.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2055957.10 # format = BAM # ChIP-seq file = ['SRX2055957.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 15:26:46: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:26:46: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:26:46: # Command line: callpeak -t SRX2055957.bam -f BAM -g dm -n SRX2055957.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2055957.20 # format = BAM # ChIP-seq file = ['SRX2055957.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 15:26:46: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:26:46: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:26:53: 1000000 INFO @ Sat, 03 Jun 2017 15:26:53: 1000000 INFO @ Sat, 03 Jun 2017 15:26:53: 1000000 INFO @ Sat, 03 Jun 2017 15:26:59: 2000000 INFO @ Sat, 03 Jun 2017 15:26:59: 2000000 INFO @ Sat, 03 Jun 2017 15:27:00: 2000000 INFO @ Sat, 03 Jun 2017 15:27:05: 3000000 INFO @ Sat, 03 Jun 2017 15:27:05: 3000000 INFO @ Sat, 03 Jun 2017 15:27:07: 3000000 INFO @ Sat, 03 Jun 2017 15:27:11: 4000000 INFO @ Sat, 03 Jun 2017 15:27:11: 4000000 INFO @ Sat, 03 Jun 2017 15:27:13: 4000000 INFO @ Sat, 03 Jun 2017 15:27:17: 5000000 INFO @ Sat, 03 Jun 2017 15:27:17: 5000000 INFO @ Sat, 03 Jun 2017 15:27:19: 5000000 INFO @ Sat, 03 Jun 2017 15:27:24: 6000000 INFO @ Sat, 03 Jun 2017 15:27:24: 6000000 INFO @ Sat, 03 Jun 2017 15:27:25: 6000000 INFO @ Sat, 03 Jun 2017 15:27:30: 7000000 INFO @ Sat, 03 Jun 2017 15:27:30: 7000000 INFO @ Sat, 03 Jun 2017 15:27:31: 7000000 INFO @ Sat, 03 Jun 2017 15:27:36: 8000000 INFO @ Sat, 03 Jun 2017 15:27:36: 8000000 INFO @ Sat, 03 Jun 2017 15:27:37: 8000000 INFO @ Sat, 03 Jun 2017 15:27:43: 9000000 INFO @ Sat, 03 Jun 2017 15:27:43: 9000000 INFO @ Sat, 03 Jun 2017 15:27:43: 9000000 INFO @ Sat, 03 Jun 2017 15:27:49: 10000000 INFO @ Sat, 03 Jun 2017 15:27:49: 10000000 INFO @ Sat, 03 Jun 2017 15:27:50: 10000000 INFO @ Sat, 03 Jun 2017 15:27:55: 11000000 INFO @ Sat, 03 Jun 2017 15:27:56: 11000000 INFO @ Sat, 03 Jun 2017 15:27:56: 11000000 INFO @ Sat, 03 Jun 2017 15:28:01: 12000000 INFO @ Sat, 03 Jun 2017 15:28:02: 12000000 INFO @ Sat, 03 Jun 2017 15:28:03: 12000000 INFO @ Sat, 03 Jun 2017 15:28:07: 13000000 INFO @ Sat, 03 Jun 2017 15:28:09: 13000000 INFO @ Sat, 03 Jun 2017 15:28:10: 13000000 INFO @ Sat, 03 Jun 2017 15:28:13: 14000000 INFO @ Sat, 03 Jun 2017 15:28:16: 14000000 INFO @ Sat, 03 Jun 2017 15:28:18: 14000000 INFO @ Sat, 03 Jun 2017 15:28:19: 15000000 INFO @ Sat, 03 Jun 2017 15:28:22: 15000000 INFO @ Sat, 03 Jun 2017 15:28:25: 16000000 INFO @ Sat, 03 Jun 2017 15:28:25: 15000000 INFO @ Sat, 03 Jun 2017 15:28:29: 16000000 INFO @ Sat, 03 Jun 2017 15:28:31: 17000000 INFO @ Sat, 03 Jun 2017 15:28:33: 16000000 INFO @ Sat, 03 Jun 2017 15:28:36: 17000000 INFO @ Sat, 03 Jun 2017 15:28:36: 18000000 INFO @ Sat, 03 Jun 2017 15:28:40: 17000000 INFO @ Sat, 03 Jun 2017 15:28:42: 19000000 INFO @ Sat, 03 Jun 2017 15:28:43: 18000000 INFO @ Sat, 03 Jun 2017 15:28:47: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:28:47: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:28:47: #1 total tags in treatment: 19824789 INFO @ Sat, 03 Jun 2017 15:28:47: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:28:47: #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 15:28:48: 18000000 INFO @ Sat, 03 Jun 2017 15:28:50: 19000000 INFO @ Sat, 03 Jun 2017 15:28:51: #1 tags after filtering in treatment: 19820895 INFO @ Sat, 03 Jun 2017 15:28:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:28:51: #1 finished! INFO @ Sat, 03 Jun 2017 15:28:51: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:28:55: 19000000 INFO @ Sat, 03 Jun 2017 15:28:55: #2 number of paired peaks: 906 WARNING @ Sat, 03 Jun 2017 15:28:55: Fewer paired peaks (906) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 906 pairs to build model! INFO @ Sat, 03 Jun 2017 15:28:55: start model_add_line... INFO @ Sat, 03 Jun 2017 15:28:55: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:28:55: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:28:55: #1 total tags in treatment: 19824789 INFO @ Sat, 03 Jun 2017 15:28:55: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:28:55: #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 15:28:59: #1 tags after filtering in treatment: 19820895 INFO @ Sat, 03 Jun 2017 15:28:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:28:59: #1 finished! INFO @ Sat, 03 Jun 2017 15:28:59: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:29:00: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:29:00: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:29:00: #1 total tags in treatment: 19824789 INFO @ Sat, 03 Jun 2017 15:29:00: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:29:00: #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 15:29:03: #2 number of paired peaks: 906 WARNING @ Sat, 03 Jun 2017 15:29:03: Fewer paired peaks (906) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 906 pairs to build model! INFO @ Sat, 03 Jun 2017 15:29:03: start model_add_line... INFO @ Sat, 03 Jun 2017 15:29:04: #1 tags after filtering in treatment: 19820895 INFO @ Sat, 03 Jun 2017 15:29:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:29:04: #1 finished! INFO @ Sat, 03 Jun 2017 15:29:04: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:29:07: #2 number of paired peaks: 906 WARNING @ Sat, 03 Jun 2017 15:29:07: Fewer paired peaks (906) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 906 pairs to build model! INFO @ Sat, 03 Jun 2017 15:29:07: start model_add_line... INFO @ Sat, 03 Jun 2017 15:29:07: start X-correlation... INFO @ Sat, 03 Jun 2017 15:29:07: end of X-cor INFO @ Sat, 03 Jun 2017 15:29:07: #2 finished! INFO @ Sat, 03 Jun 2017 15:29:07: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 15:29:07: #2 alternative fragment length(s) may be 3,49 bps INFO @ Sat, 03 Jun 2017 15:29:07: #2.2 Generate R script for model : SRX2055957.05_model.r WARNING @ Sat, 03 Jun 2017 15:29:07: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:29:07: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Sat, 03 Jun 2017 15:29:07: #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 15:29:07: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:29:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:29:15: start X-correlation... INFO @ Sat, 03 Jun 2017 15:29:15: end of X-cor INFO @ Sat, 03 Jun 2017 15:29:15: #2 finished! INFO @ Sat, 03 Jun 2017 15:29:15: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 15:29:15: #2 alternative fragment length(s) may be 3,49 bps INFO @ Sat, 03 Jun 2017 15:29:15: #2.2 Generate R script for model : SRX2055957.10_model.r WARNING @ Sat, 03 Jun 2017 15:29:15: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:29:15: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Sat, 03 Jun 2017 15:29:15: #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 15:29:15: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:29:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:29:19: start X-correlation... INFO @ Sat, 03 Jun 2017 15:29:19: end of X-cor INFO @ Sat, 03 Jun 2017 15:29:19: #2 finished! INFO @ Sat, 03 Jun 2017 15:29:19: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 15:29:19: #2 alternative fragment length(s) may be 3,49 bps INFO @ Sat, 03 Jun 2017 15:29:19: #2.2 Generate R script for model : SRX2055957.20_model.r WARNING @ Sat, 03 Jun 2017 15:29:19: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:29:19: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Sat, 03 Jun 2017 15:29:19: #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 15:29:19: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:29:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:30:51: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:30:53: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:31:01: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:32:04: #4 Write output xls file... SRX2055957.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:32:04: #4 Write peak in narrowPeak format file... SRX2055957.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:32:04: #4 Write summits bed file... SRX2055957.05_summits.bed INFO @ Sat, 03 Jun 2017 15:32:04: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3951 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:32:10: #4 Write output xls file... SRX2055957.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:32:10: #4 Write peak in narrowPeak format file... SRX2055957.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:32:10: #4 Write summits bed file... SRX2055957.10_summits.bed INFO @ Sat, 03 Jun 2017 15:32:10: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2863 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:32:14: #4 Write output xls file... SRX2055957.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:32:14: #4 Write peak in narrowPeak format file... SRX2055957.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:32:14: #4 Write summits bed file... SRX2055957.20_summits.bed INFO @ Sat, 03 Jun 2017 15:32:14: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1588 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。