Job ID = 9029218 sra ファイルのダウンロード中... Completed: 491823K bytes transferred in 9 seconds (422790K 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 --:--:-- 0 101 5455 0 5455 0 0 767 0 --:--:-- 0:00:07 --:--:-- 8302 100 30318 0 30318 0 0 3739 0 --:--:-- 0:00:08 --:--:-- 18341 100 54437 0 54437 0 0 6206 0 --:--:-- 0:00:08 --:--:-- 23504 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 23075810 spots for /home/okishinya/chipatlas/results/dm3/SRX1433358/SRR2919823.sra Written 23075810 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:27 23075810 reads; of these: 23075810 (100.00%) were unpaired; of these: 523224 (2.27%) aligned 0 times 17077886 (74.01%) aligned exactly 1 time 5474700 (23.72%) aligned >1 times 97.73% overall alignment rate Time searching: 00:10:28 Overall time: 00:10:28 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] 3372267 / 22552586 = 0.1495 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 13:09:04: # Command line: callpeak -t SRX1433358.bam -f BAM -g dm -n SRX1433358.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1433358.05 # format = BAM # ChIP-seq file = ['SRX1433358.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 13:09:04: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:09:04: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:09:04: # Command line: callpeak -t SRX1433358.bam -f BAM -g dm -n SRX1433358.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1433358.20 # format = BAM # ChIP-seq file = ['SRX1433358.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 13:09:04: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:09:04: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:09:04: # Command line: callpeak -t SRX1433358.bam -f BAM -g dm -n SRX1433358.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1433358.10 # format = BAM # ChIP-seq file = ['SRX1433358.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 13:09:04: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:09:04: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:09:11: 1000000 INFO @ Sat, 03 Jun 2017 13:09:11: 1000000 INFO @ Sat, 03 Jun 2017 13:09:11: 1000000 INFO @ Sat, 03 Jun 2017 13:09:18: 2000000 INFO @ Sat, 03 Jun 2017 13:09:18: 2000000 INFO @ Sat, 03 Jun 2017 13:09:18: 2000000 INFO @ Sat, 03 Jun 2017 13:09:24: 3000000 INFO @ Sat, 03 Jun 2017 13:09:26: 3000000 INFO @ Sat, 03 Jun 2017 13:09:26: 3000000 INFO @ Sat, 03 Jun 2017 13:09:32: 4000000 INFO @ Sat, 03 Jun 2017 13:09:33: 4000000 INFO @ Sat, 03 Jun 2017 13:09:33: 4000000 INFO @ Sat, 03 Jun 2017 13:09:38: 5000000 INFO @ Sat, 03 Jun 2017 13:09:40: 5000000 INFO @ Sat, 03 Jun 2017 13:09:40: 5000000 INFO @ Sat, 03 Jun 2017 13:09:45: 6000000 INFO @ Sat, 03 Jun 2017 13:09:47: 6000000 INFO @ Sat, 03 Jun 2017 13:09:47: 6000000 INFO @ Sat, 03 Jun 2017 13:09:51: 7000000 INFO @ Sat, 03 Jun 2017 13:09:53: 7000000 INFO @ Sat, 03 Jun 2017 13:09:53: 7000000 INFO @ Sat, 03 Jun 2017 13:09:57: 8000000 INFO @ Sat, 03 Jun 2017 13:09:59: 8000000 INFO @ Sat, 03 Jun 2017 13:10:00: 8000000 INFO @ Sat, 03 Jun 2017 13:10:03: 9000000 INFO @ Sat, 03 Jun 2017 13:10:06: 9000000 INFO @ Sat, 03 Jun 2017 13:10:06: 9000000 INFO @ Sat, 03 Jun 2017 13:10:09: 10000000 INFO @ Sat, 03 Jun 2017 13:10:12: 10000000 INFO @ Sat, 03 Jun 2017 13:10:13: 10000000 INFO @ Sat, 03 Jun 2017 13:10:15: 11000000 INFO @ Sat, 03 Jun 2017 13:10:19: 11000000 INFO @ Sat, 03 Jun 2017 13:10:19: 11000000 INFO @ Sat, 03 Jun 2017 13:10:22: 12000000 INFO @ Sat, 03 Jun 2017 13:10:25: 12000000 INFO @ Sat, 03 Jun 2017 13:10:26: 12000000 INFO @ Sat, 03 Jun 2017 13:10:29: 13000000 INFO @ Sat, 03 Jun 2017 13:10:32: 13000000 INFO @ Sat, 03 Jun 2017 13:10:33: 13000000 INFO @ Sat, 03 Jun 2017 13:10:36: 14000000 INFO @ Sat, 03 Jun 2017 13:10:38: 14000000 INFO @ Sat, 03 Jun 2017 13:10:40: 14000000 INFO @ Sat, 03 Jun 2017 13:10:42: 15000000 INFO @ Sat, 03 Jun 2017 13:10:45: 15000000 INFO @ Sat, 03 Jun 2017 13:10:46: 15000000 INFO @ Sat, 03 Jun 2017 13:10:48: 16000000 INFO @ Sat, 03 Jun 2017 13:10:51: 16000000 INFO @ Sat, 03 Jun 2017 13:10:52: 16000000 INFO @ Sat, 03 Jun 2017 13:10:54: 17000000 INFO @ Sat, 03 Jun 2017 13:10:58: 17000000 INFO @ Sat, 03 Jun 2017 13:10:58: 17000000 INFO @ Sat, 03 Jun 2017 13:11:01: 18000000 INFO @ Sat, 03 Jun 2017 13:11:05: 18000000 INFO @ Sat, 03 Jun 2017 13:11:05: 18000000 INFO @ Sat, 03 Jun 2017 13:11:09: 19000000 INFO @ Sat, 03 Jun 2017 13:11:10: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:11:10: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:11:10: #1 total tags in treatment: 19180319 INFO @ Sat, 03 Jun 2017 13:11:10: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:11:10: #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 13:11:11: 19000000 INFO @ Sat, 03 Jun 2017 13:11:12: 19000000 INFO @ Sat, 03 Jun 2017 13:11:13: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:11:13: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:11:13: #1 total tags in treatment: 19180319 INFO @ Sat, 03 Jun 2017 13:11:13: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:11:13: #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 13:11:13: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:11:13: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:11:13: #1 total tags in treatment: 19180319 INFO @ Sat, 03 Jun 2017 13:11:13: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:11:13: #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 13:11:14: #1 tags after filtering in treatment: 19175312 INFO @ Sat, 03 Jun 2017 13:11:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:11:14: #1 finished! INFO @ Sat, 03 Jun 2017 13:11:14: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:11:16: #1 tags after filtering in treatment: 19175312 INFO @ Sat, 03 Jun 2017 13:11:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:11:16: #1 finished! INFO @ Sat, 03 Jun 2017 13:11:16: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:11:17: #1 tags after filtering in treatment: 19175312 INFO @ Sat, 03 Jun 2017 13:11:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:11:17: #1 finished! INFO @ Sat, 03 Jun 2017 13:11:17: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:11:17: #2 number of paired peaks: 176 WARNING @ Sat, 03 Jun 2017 13:11:17: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 03 Jun 2017 13:11:17: start model_add_line... INFO @ Sat, 03 Jun 2017 13:11:20: #2 number of paired peaks: 176 WARNING @ Sat, 03 Jun 2017 13:11:20: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 03 Jun 2017 13:11:20: start model_add_line... INFO @ Sat, 03 Jun 2017 13:11:20: start X-correlation... INFO @ Sat, 03 Jun 2017 13:11:20: end of X-cor INFO @ Sat, 03 Jun 2017 13:11:20: #2 finished! INFO @ Sat, 03 Jun 2017 13:11:20: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 13:11:20: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 03 Jun 2017 13:11:20: #2.2 Generate R script for model : SRX1433358.20_model.r WARNING @ Sat, 03 Jun 2017 13:11:20: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:11:20: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 03 Jun 2017 13:11:20: #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 13:11:20: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:11:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:11:21: #2 number of paired peaks: 176 WARNING @ Sat, 03 Jun 2017 13:11:21: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 03 Jun 2017 13:11:21: start model_add_line... INFO @ Sat, 03 Jun 2017 13:11:23: start X-correlation... INFO @ Sat, 03 Jun 2017 13:11:23: end of X-cor INFO @ Sat, 03 Jun 2017 13:11:23: #2 finished! INFO @ Sat, 03 Jun 2017 13:11:23: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 13:11:23: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 03 Jun 2017 13:11:23: #2.2 Generate R script for model : SRX1433358.05_model.r WARNING @ Sat, 03 Jun 2017 13:11:23: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:11:23: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 03 Jun 2017 13:11:23: #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 13:11:23: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:11:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:11:23: start X-correlation... INFO @ Sat, 03 Jun 2017 13:11:23: end of X-cor INFO @ Sat, 03 Jun 2017 13:11:23: #2 finished! INFO @ Sat, 03 Jun 2017 13:11:23: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 13:11:23: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 03 Jun 2017 13:11:23: #2.2 Generate R script for model : SRX1433358.10_model.r WARNING @ Sat, 03 Jun 2017 13:11:24: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:11:24: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 03 Jun 2017 13:11:24: #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 13:11:24: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:11:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:12:55: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:13:00: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:13:03: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:14:09: #4 Write output xls file... SRX1433358.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:14:09: #4 Write peak in narrowPeak format file... SRX1433358.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:14:09: #4 Write summits bed file... SRX1433358.05_summits.bed INFO @ Sat, 03 Jun 2017 13:14:09: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1935 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:14:12: #4 Write output xls file... SRX1433358.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:14:12: #4 Write peak in narrowPeak format file... SRX1433358.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:14:12: #4 Write summits bed file... SRX1433358.20_summits.bed INFO @ Sat, 03 Jun 2017 13:14:12: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (927 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:14:13: #4 Write output xls file... SRX1433358.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:14:13: #4 Write peak in narrowPeak format file... SRX1433358.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:14:13: #4 Write summits bed file... SRX1433358.10_summits.bed INFO @ Sat, 03 Jun 2017 13:14:13: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1306 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。