Job ID = 9029247 sra ファイルのダウンロード中... Completed: 721454K bytes transferred in 12 seconds (480449K 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 1951 0 --:--:-- 0:00:07 --:--:-- 13590 100 49069 0 49069 0 0 6006 0 --:--:-- 0:00:08 --:--:-- 26031 100 109k 0 109k 0 0 12354 0 --:--:-- 0:00:09 --:--:-- 40151 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 34677956 spots for /home/okishinya/chipatlas/results/dm3/SRX1433396/SRR2919812.sra Written 34677956 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: 00:12:52 34677956 reads; of these: 34677956 (100.00%) were unpaired; of these: 4119533 (11.88%) aligned 0 times 22592669 (65.15%) aligned exactly 1 time 7965754 (22.97%) aligned >1 times 88.12% overall alignment rate Time searching: 00:12:52 Overall time: 00:12:52 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] 11390612 / 30558423 = 0.3727 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 13:14:10: # Command line: callpeak -t SRX1433396.bam -f BAM -g dm -n SRX1433396.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1433396.10 # format = BAM # ChIP-seq file = ['SRX1433396.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 13:14:10: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:14:10: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:14:10: # Command line: callpeak -t SRX1433396.bam -f BAM -g dm -n SRX1433396.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1433396.05 # format = BAM # ChIP-seq file = ['SRX1433396.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 13:14:10: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:14:10: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:14:10: # Command line: callpeak -t SRX1433396.bam -f BAM -g dm -n SRX1433396.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1433396.20 # format = BAM # ChIP-seq file = ['SRX1433396.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 13:14:10: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:14:10: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:14:16: 1000000 INFO @ Sat, 03 Jun 2017 13:14:16: 1000000 INFO @ Sat, 03 Jun 2017 13:14:16: 1000000 INFO @ Sat, 03 Jun 2017 13:14:22: 2000000 INFO @ Sat, 03 Jun 2017 13:14:22: 2000000 INFO @ Sat, 03 Jun 2017 13:14:22: 2000000 INFO @ Sat, 03 Jun 2017 13:14:28: 3000000 INFO @ Sat, 03 Jun 2017 13:14:28: 3000000 INFO @ Sat, 03 Jun 2017 13:14:28: 3000000 INFO @ Sat, 03 Jun 2017 13:14:34: 4000000 INFO @ Sat, 03 Jun 2017 13:14:34: 4000000 INFO @ Sat, 03 Jun 2017 13:14:34: 4000000 INFO @ Sat, 03 Jun 2017 13:14:40: 5000000 INFO @ Sat, 03 Jun 2017 13:14:40: 5000000 INFO @ Sat, 03 Jun 2017 13:14:40: 5000000 INFO @ Sat, 03 Jun 2017 13:14:46: 6000000 INFO @ Sat, 03 Jun 2017 13:14:46: 6000000 INFO @ Sat, 03 Jun 2017 13:14:46: 6000000 INFO @ Sat, 03 Jun 2017 13:14:52: 7000000 INFO @ Sat, 03 Jun 2017 13:14:52: 7000000 INFO @ Sat, 03 Jun 2017 13:14:52: 7000000 INFO @ Sat, 03 Jun 2017 13:14:57: 8000000 INFO @ Sat, 03 Jun 2017 13:14:57: 8000000 INFO @ Sat, 03 Jun 2017 13:14:58: 8000000 INFO @ Sat, 03 Jun 2017 13:15:03: 9000000 INFO @ Sat, 03 Jun 2017 13:15:03: 9000000 INFO @ Sat, 03 Jun 2017 13:15:04: 9000000 INFO @ Sat, 03 Jun 2017 13:15:09: 10000000 INFO @ Sat, 03 Jun 2017 13:15:09: 10000000 INFO @ Sat, 03 Jun 2017 13:15:10: 10000000 INFO @ Sat, 03 Jun 2017 13:15:16: 11000000 INFO @ Sat, 03 Jun 2017 13:15:16: 11000000 INFO @ Sat, 03 Jun 2017 13:15:16: 11000000 INFO @ Sat, 03 Jun 2017 13:15:22: 12000000 INFO @ Sat, 03 Jun 2017 13:15:22: 12000000 INFO @ Sat, 03 Jun 2017 13:15:23: 12000000 INFO @ Sat, 03 Jun 2017 13:15:28: 13000000 INFO @ Sat, 03 Jun 2017 13:15:28: 13000000 INFO @ Sat, 03 Jun 2017 13:15:29: 13000000 INFO @ Sat, 03 Jun 2017 13:15:34: 14000000 INFO @ Sat, 03 Jun 2017 13:15:34: 14000000 INFO @ Sat, 03 Jun 2017 13:15:35: 14000000 INFO @ Sat, 03 Jun 2017 13:15:41: 15000000 INFO @ Sat, 03 Jun 2017 13:15:41: 15000000 INFO @ Sat, 03 Jun 2017 13:15:42: 15000000 INFO @ Sat, 03 Jun 2017 13:15:47: 16000000 INFO @ Sat, 03 Jun 2017 13:15:47: 16000000 INFO @ Sat, 03 Jun 2017 13:15:49: 16000000 INFO @ Sat, 03 Jun 2017 13:15:54: 17000000 INFO @ Sat, 03 Jun 2017 13:15:54: 17000000 INFO @ Sat, 03 Jun 2017 13:15:56: 17000000 INFO @ Sat, 03 Jun 2017 13:16:00: 18000000 INFO @ Sat, 03 Jun 2017 13:16:00: 18000000 INFO @ Sat, 03 Jun 2017 13:16:02: 18000000 INFO @ Sat, 03 Jun 2017 13:16:06: 19000000 INFO @ Sat, 03 Jun 2017 13:16:06: 19000000 INFO @ Sat, 03 Jun 2017 13:16:08: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 13:16:08: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 13:16:08: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 13:16:08: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 13:16:08: #1 total tags in treatment: 19167811 INFO @ Sat, 03 Jun 2017 13:16:08: #1 total tags in treatment: 19167811 INFO @ Sat, 03 Jun 2017 13:16:08: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:16:08: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:16:08: #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 13:16:08: #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 13:16:09: 19000000 INFO @ Sat, 03 Jun 2017 13:16:10: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 13:16:10: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 13:16:10: #1 total tags in treatment: 19167811 INFO @ Sat, 03 Jun 2017 13:16:10: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:16:10: #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 13:16:12: #1 tags after filtering in treatment: 19161813 INFO @ Sat, 03 Jun 2017 13:16:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:16:12: #1 finished! INFO @ Sat, 03 Jun 2017 13:16:12: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:16:12: #1 tags after filtering in treatment: 19161813 INFO @ Sat, 03 Jun 2017 13:16:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:16:12: #1 finished! INFO @ Sat, 03 Jun 2017 13:16:12: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:16:13: #1 tags after filtering in treatment: 19161813 INFO @ Sat, 03 Jun 2017 13:16:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:16:13: #1 finished! INFO @ Sat, 03 Jun 2017 13:16:13: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:16:15: #2 number of paired peaks: 514 WARNING @ Sat, 03 Jun 2017 13:16:15: Fewer paired peaks (514) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 514 pairs to build model! INFO @ Sat, 03 Jun 2017 13:16:15: start model_add_line... INFO @ Sat, 03 Jun 2017 13:16:16: #2 number of paired peaks: 514 WARNING @ Sat, 03 Jun 2017 13:16:16: Fewer paired peaks (514) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 514 pairs to build model! INFO @ Sat, 03 Jun 2017 13:16:16: start model_add_line... INFO @ Sat, 03 Jun 2017 13:16:17: #2 number of paired peaks: 514 WARNING @ Sat, 03 Jun 2017 13:16:17: Fewer paired peaks (514) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 514 pairs to build model! INFO @ Sat, 03 Jun 2017 13:16:17: start model_add_line... INFO @ Sat, 03 Jun 2017 13:16:22: start X-correlation... INFO @ Sat, 03 Jun 2017 13:16:22: end of X-cor INFO @ Sat, 03 Jun 2017 13:16:22: #2 finished! INFO @ Sat, 03 Jun 2017 13:16:22: #2 predicted fragment length is 86 bps INFO @ Sat, 03 Jun 2017 13:16:22: #2 alternative fragment length(s) may be 86 bps INFO @ Sat, 03 Jun 2017 13:16:22: #2.2 Generate R script for model : SRX1433396.20_model.r WARNING @ Sat, 03 Jun 2017 13:16:22: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:16:22: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Sat, 03 Jun 2017 13:16:22: #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 13:16:22: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:16:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:16:23: start X-correlation... INFO @ Sat, 03 Jun 2017 13:16:23: end of X-cor INFO @ Sat, 03 Jun 2017 13:16:23: #2 finished! INFO @ Sat, 03 Jun 2017 13:16:23: #2 predicted fragment length is 86 bps INFO @ Sat, 03 Jun 2017 13:16:23: #2 alternative fragment length(s) may be 86 bps INFO @ Sat, 03 Jun 2017 13:16:23: #2.2 Generate R script for model : SRX1433396.10_model.r WARNING @ Sat, 03 Jun 2017 13:16:23: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:16:23: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Sat, 03 Jun 2017 13:16:23: #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 13:16:23: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:16:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:16:25: start X-correlation... INFO @ Sat, 03 Jun 2017 13:16:25: end of X-cor INFO @ Sat, 03 Jun 2017 13:16:25: #2 finished! INFO @ Sat, 03 Jun 2017 13:16:25: #2 predicted fragment length is 86 bps INFO @ Sat, 03 Jun 2017 13:16:25: #2 alternative fragment length(s) may be 86 bps INFO @ Sat, 03 Jun 2017 13:16:25: #2.2 Generate R script for model : SRX1433396.05_model.r WARNING @ Sat, 03 Jun 2017 13:16:25: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:16:25: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Sat, 03 Jun 2017 13:16:25: #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 13:16:25: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:16:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:18:03: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:18:04: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:18:12: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:19:15: #4 Write output xls file... SRX1433396.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:19:15: #4 Write peak in narrowPeak format file... SRX1433396.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:19:15: #4 Write summits bed file... SRX1433396.20_summits.bed INFO @ Sat, 03 Jun 2017 13:19:15: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2067 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:19:20: #4 Write output xls file... SRX1433396.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:19:20: #4 Write peak in narrowPeak format file... SRX1433396.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:19:20: #4 Write summits bed file... SRX1433396.10_summits.bed INFO @ Sat, 03 Jun 2017 13:19:20: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3877 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:19:32: #4 Write output xls file... SRX1433396.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:19:32: #4 Write peak in narrowPeak format file... SRX1433396.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:19:32: #4 Write summits bed file... SRX1433396.05_summits.bed INFO @ Sat, 03 Jun 2017 13:19:32: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6022 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。