Job ID = 9031878 sra ファイルのダウンロード中... Completed: 924711K bytes transferred in 8 seconds (896173K 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 6903 0 6903 0 0 957 0 --:--:-- 0:00:07 --:--:-- 9932 100 30318 0 30318 0 0 3771 0 --:--:-- 0:00:08 --:--:-- 19880 100 70344 0 70344 0 0 8082 0 --:--:-- 0:00:08 --:--:-- 32149 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 31914569 spots for /home/okishinya/chipatlas/results/dm3/SRX529168/SRR1265774.sra Written 31914569 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: 00:13:34 31914569 reads; of these: 31914569 (100.00%) were unpaired; of these: 2248397 (7.05%) aligned 0 times 20790440 (65.14%) aligned exactly 1 time 8875732 (27.81%) aligned >1 times 92.95% overall alignment rate Time searching: 00:13:34 Overall time: 00:13:34 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 16 files... [bam_rmdupse_core] 5874702 / 29666172 = 0.1980 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 22:10:48: # Command line: callpeak -t SRX529168.bam -f BAM -g dm -n SRX529168.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX529168.20 # format = BAM # ChIP-seq file = ['SRX529168.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 22:10:48: #1 read tag files... INFO @ Sat, 03 Jun 2017 22:10:48: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 22:10:48: # Command line: callpeak -t SRX529168.bam -f BAM -g dm -n SRX529168.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX529168.10 # format = BAM # ChIP-seq file = ['SRX529168.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 22:10:48: #1 read tag files... INFO @ Sat, 03 Jun 2017 22:10:48: # Command line: callpeak -t SRX529168.bam -f BAM -g dm -n SRX529168.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX529168.05 # format = BAM # ChIP-seq file = ['SRX529168.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 22:10:48: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 22:10:48: #1 read tag files... INFO @ Sat, 03 Jun 2017 22:10:48: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 22:10:55: 1000000 INFO @ Sat, 03 Jun 2017 22:10:55: 1000000 INFO @ Sat, 03 Jun 2017 22:10:55: 1000000 INFO @ Sat, 03 Jun 2017 22:11:02: 2000000 INFO @ Sat, 03 Jun 2017 22:11:02: 2000000 INFO @ Sat, 03 Jun 2017 22:11:02: 2000000 INFO @ Sat, 03 Jun 2017 22:11:09: 3000000 INFO @ Sat, 03 Jun 2017 22:11:09: 3000000 INFO @ Sat, 03 Jun 2017 22:11:09: 3000000 INFO @ Sat, 03 Jun 2017 22:11:16: 4000000 INFO @ Sat, 03 Jun 2017 22:11:16: 4000000 INFO @ Sat, 03 Jun 2017 22:11:16: 4000000 INFO @ Sat, 03 Jun 2017 22:11:24: 5000000 INFO @ Sat, 03 Jun 2017 22:11:24: 5000000 INFO @ Sat, 03 Jun 2017 22:11:24: 5000000 INFO @ Sat, 03 Jun 2017 22:11:31: 6000000 INFO @ Sat, 03 Jun 2017 22:11:31: 6000000 INFO @ Sat, 03 Jun 2017 22:11:31: 6000000 INFO @ Sat, 03 Jun 2017 22:11:38: 7000000 INFO @ Sat, 03 Jun 2017 22:11:38: 7000000 INFO @ Sat, 03 Jun 2017 22:11:38: 7000000 INFO @ Sat, 03 Jun 2017 22:11:45: 8000000 INFO @ Sat, 03 Jun 2017 22:11:45: 8000000 INFO @ Sat, 03 Jun 2017 22:11:45: 8000000 INFO @ Sat, 03 Jun 2017 22:11:52: 9000000 INFO @ Sat, 03 Jun 2017 22:11:52: 9000000 INFO @ Sat, 03 Jun 2017 22:11:52: 9000000 INFO @ Sat, 03 Jun 2017 22:11:59: 10000000 INFO @ Sat, 03 Jun 2017 22:11:59: 10000000 INFO @ Sat, 03 Jun 2017 22:12:00: 10000000 INFO @ Sat, 03 Jun 2017 22:12:07: 11000000 INFO @ Sat, 03 Jun 2017 22:12:07: 11000000 INFO @ Sat, 03 Jun 2017 22:12:07: 11000000 INFO @ Sat, 03 Jun 2017 22:12:14: 12000000 INFO @ Sat, 03 Jun 2017 22:12:14: 12000000 INFO @ Sat, 03 Jun 2017 22:12:14: 12000000 INFO @ Sat, 03 Jun 2017 22:12:21: 13000000 INFO @ Sat, 03 Jun 2017 22:12:21: 13000000 INFO @ Sat, 03 Jun 2017 22:12:21: 13000000 INFO @ Sat, 03 Jun 2017 22:12:28: 14000000 INFO @ Sat, 03 Jun 2017 22:12:28: 14000000 INFO @ Sat, 03 Jun 2017 22:12:28: 14000000 INFO @ Sat, 03 Jun 2017 22:12:35: 15000000 INFO @ Sat, 03 Jun 2017 22:12:35: 15000000 INFO @ Sat, 03 Jun 2017 22:12:35: 15000000 INFO @ Sat, 03 Jun 2017 22:12:42: 16000000 INFO @ Sat, 03 Jun 2017 22:12:42: 16000000 INFO @ Sat, 03 Jun 2017 22:12:43: 16000000 INFO @ Sat, 03 Jun 2017 22:12:50: 17000000 INFO @ Sat, 03 Jun 2017 22:12:50: 17000000 INFO @ Sat, 03 Jun 2017 22:12:50: 17000000 INFO @ Sat, 03 Jun 2017 22:12:57: 18000000 INFO @ Sat, 03 Jun 2017 22:12:57: 18000000 INFO @ Sat, 03 Jun 2017 22:12:57: 18000000 INFO @ Sat, 03 Jun 2017 22:13:04: 19000000 INFO @ Sat, 03 Jun 2017 22:13:04: 19000000 INFO @ Sat, 03 Jun 2017 22:13:04: 19000000 INFO @ Sat, 03 Jun 2017 22:13:11: 20000000 INFO @ Sat, 03 Jun 2017 22:13:11: 20000000 INFO @ Sat, 03 Jun 2017 22:13:11: 20000000 INFO @ Sat, 03 Jun 2017 22:13:18: 21000000 INFO @ Sat, 03 Jun 2017 22:13:18: 21000000 INFO @ Sat, 03 Jun 2017 22:13:18: 21000000 INFO @ Sat, 03 Jun 2017 22:13:25: 22000000 INFO @ Sat, 03 Jun 2017 22:13:25: 22000000 INFO @ Sat, 03 Jun 2017 22:13:25: 22000000 INFO @ Sat, 03 Jun 2017 22:13:32: 23000000 INFO @ Sat, 03 Jun 2017 22:13:32: 23000000 INFO @ Sat, 03 Jun 2017 22:13:32: 23000000 INFO @ Sat, 03 Jun 2017 22:13:38: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 22:13:38: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 22:13:38: #1 total tags in treatment: 23791470 INFO @ Sat, 03 Jun 2017 22:13:38: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 22:13:38: #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 22:13:38: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 22:13:38: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 22:13:38: #1 total tags in treatment: 23791470 INFO @ Sat, 03 Jun 2017 22:13:38: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 22:13:38: #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 22:13:38: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 22:13:38: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 22:13:38: #1 total tags in treatment: 23791470 INFO @ Sat, 03 Jun 2017 22:13:38: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 22:13:38: #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 22:13:42: #1 tags after filtering in treatment: 23786066 INFO @ Sat, 03 Jun 2017 22:13:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 22:13:42: #1 finished! INFO @ Sat, 03 Jun 2017 22:13:42: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 22:13:42: #1 tags after filtering in treatment: 23786066 INFO @ Sat, 03 Jun 2017 22:13:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 22:13:42: #1 finished! INFO @ Sat, 03 Jun 2017 22:13:42: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 22:13:43: #1 tags after filtering in treatment: 23786066 INFO @ Sat, 03 Jun 2017 22:13:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 22:13:43: #1 finished! INFO @ Sat, 03 Jun 2017 22:13:43: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 22:13:46: #2 number of paired peaks: 102 WARNING @ Sat, 03 Jun 2017 22:13:46: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Sat, 03 Jun 2017 22:13:46: start model_add_line... INFO @ Sat, 03 Jun 2017 22:13:47: #2 number of paired peaks: 102 WARNING @ Sat, 03 Jun 2017 22:13:47: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Sat, 03 Jun 2017 22:13:47: start model_add_line... INFO @ Sat, 03 Jun 2017 22:13:47: #2 number of paired peaks: 102 WARNING @ Sat, 03 Jun 2017 22:13:47: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Sat, 03 Jun 2017 22:13:47: start model_add_line... INFO @ Sat, 03 Jun 2017 22:13:49: start X-correlation... INFO @ Sat, 03 Jun 2017 22:13:49: end of X-cor INFO @ Sat, 03 Jun 2017 22:13:49: #2 finished! INFO @ Sat, 03 Jun 2017 22:13:49: #2 predicted fragment length is 48 bps INFO @ Sat, 03 Jun 2017 22:13:49: #2 alternative fragment length(s) may be 4,48,535,559 bps INFO @ Sat, 03 Jun 2017 22:13:49: #2.2 Generate R script for model : SRX529168.10_model.r WARNING @ Sat, 03 Jun 2017 22:13:49: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 22:13:49: #2 You may need to consider one of the other alternative d(s): 4,48,535,559 WARNING @ Sat, 03 Jun 2017 22:13:49: #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 22:13:49: #3 Call peaks... INFO @ Sat, 03 Jun 2017 22:13:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 22:13:49: start X-correlation... INFO @ Sat, 03 Jun 2017 22:13:50: end of X-cor INFO @ Sat, 03 Jun 2017 22:13:50: #2 finished! INFO @ Sat, 03 Jun 2017 22:13:50: #2 predicted fragment length is 48 bps INFO @ Sat, 03 Jun 2017 22:13:50: #2 alternative fragment length(s) may be 4,48,535,559 bps INFO @ Sat, 03 Jun 2017 22:13:50: #2.2 Generate R script for model : SRX529168.20_model.r WARNING @ Sat, 03 Jun 2017 22:13:50: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 22:13:50: #2 You may need to consider one of the other alternative d(s): 4,48,535,559 WARNING @ Sat, 03 Jun 2017 22:13:50: #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 22:13:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 22:13:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 22:13:50: start X-correlation... INFO @ Sat, 03 Jun 2017 22:13:50: end of X-cor INFO @ Sat, 03 Jun 2017 22:13:50: #2 finished! INFO @ Sat, 03 Jun 2017 22:13:50: #2 predicted fragment length is 48 bps INFO @ Sat, 03 Jun 2017 22:13:50: #2 alternative fragment length(s) may be 4,48,535,559 bps INFO @ Sat, 03 Jun 2017 22:13:50: #2.2 Generate R script for model : SRX529168.05_model.r WARNING @ Sat, 03 Jun 2017 22:13:50: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 22:13:50: #2 You may need to consider one of the other alternative d(s): 4,48,535,559 WARNING @ Sat, 03 Jun 2017 22:13:50: #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 22:13:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 22:13:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 22:15:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 22:15:40: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 22:15:44: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 22:17:02: #4 Write output xls file... SRX529168.05_peaks.xls INFO @ Sat, 03 Jun 2017 22:17:02: #4 Write peak in narrowPeak format file... SRX529168.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 22:17:02: #4 Write summits bed file... SRX529168.05_summits.bed INFO @ Sat, 03 Jun 2017 22:17:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3901 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 22:17:04: #4 Write output xls file... SRX529168.20_peaks.xls INFO @ Sat, 03 Jun 2017 22:17:04: #4 Write peak in narrowPeak format file... SRX529168.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 22:17:04: #4 Write summits bed file... SRX529168.20_summits.bed INFO @ Sat, 03 Jun 2017 22:17:04: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (1032 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 22:17:10: #4 Write output xls file... SRX529168.10_peaks.xls INFO @ Sat, 03 Jun 2017 22:17:10: #4 Write peak in narrowPeak format file... SRX529168.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 22:17:10: #4 Write summits bed file... SRX529168.10_summits.bed INFO @ Sat, 03 Jun 2017 22:17:10: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2055 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。