Job ID = 2236852 sra ファイルのダウンロード中... Completed: 564591K bytes transferred in 12 seconds (363220K 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 --:--:-- --:--:-- --:--:-- 0 108 1087 0 1087 0 0 1948 0 --:--:-- --:--:-- --:--:-- 2961 100 34659 0 34659 0 0 46337 0 --:--:-- --:--:-- --:--:-- 62112 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 19141045 spots for /home/okishinya/chipatlas/results/ce10/SRX059228/SRR190668.sra Written 19141045 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: 00:04:08 19141045 reads; of these: 19141045 (100.00%) were unpaired; of these: 248297 (1.30%) aligned 0 times 15163818 (79.22%) aligned exactly 1 time 3728930 (19.48%) aligned >1 times 98.70% overall alignment rate Time searching: 00:04:08 Overall time: 00:04:08 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2762634 / 18892748 = 0.1462 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 @ Thu, 30 Apr 2015 11:20:13: # Command line: callpeak -t SRX059228.bam -f BAM -g ce -n SRX059228.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX059228.05 # format = BAM # ChIP-seq file = ['SRX059228.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 30 Apr 2015 11:20:13: # Command line: callpeak -t SRX059228.bam -f BAM -g ce -n SRX059228.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX059228.20 # format = BAM # ChIP-seq file = ['SRX059228.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 30 Apr 2015 11:20:13: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:20:13: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:20:13: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:20:13: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:20:13: # Command line: callpeak -t SRX059228.bam -f BAM -g ce -n SRX059228.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX059228.10 # format = BAM # ChIP-seq file = ['SRX059228.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 30 Apr 2015 11:20:13: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:20:13: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:20:18: 1000000 INFO @ Thu, 30 Apr 2015 11:20:18: 1000000 INFO @ Thu, 30 Apr 2015 11:20:18: 1000000 INFO @ Thu, 30 Apr 2015 11:20:24: 2000000 INFO @ Thu, 30 Apr 2015 11:20:24: 2000000 INFO @ Thu, 30 Apr 2015 11:20:24: 2000000 INFO @ Thu, 30 Apr 2015 11:20:29: 3000000 INFO @ Thu, 30 Apr 2015 11:20:30: 3000000 INFO @ Thu, 30 Apr 2015 11:20:30: 3000000 INFO @ Thu, 30 Apr 2015 11:20:34: 4000000 INFO @ Thu, 30 Apr 2015 11:20:35: 4000000 INFO @ Thu, 30 Apr 2015 11:20:35: 4000000 INFO @ Thu, 30 Apr 2015 11:20:40: 5000000 INFO @ Thu, 30 Apr 2015 11:20:41: 5000000 INFO @ Thu, 30 Apr 2015 11:20:41: 5000000 INFO @ Thu, 30 Apr 2015 11:20:45: 6000000 INFO @ Thu, 30 Apr 2015 11:20:46: 6000000 INFO @ Thu, 30 Apr 2015 11:20:47: 6000000 INFO @ Thu, 30 Apr 2015 11:20:51: 7000000 INFO @ Thu, 30 Apr 2015 11:20:52: 7000000 INFO @ Thu, 30 Apr 2015 11:20:53: 7000000 INFO @ Thu, 30 Apr 2015 11:20:57: 8000000 INFO @ Thu, 30 Apr 2015 11:20:59: 8000000 INFO @ Thu, 30 Apr 2015 11:20:59: 8000000 INFO @ Thu, 30 Apr 2015 11:21:02: 9000000 INFO @ Thu, 30 Apr 2015 11:21:04: 9000000 INFO @ Thu, 30 Apr 2015 11:21:06: 9000000 INFO @ Thu, 30 Apr 2015 11:21:08: 10000000 INFO @ Thu, 30 Apr 2015 11:21:10: 10000000 INFO @ Thu, 30 Apr 2015 11:21:13: 11000000 INFO @ Thu, 30 Apr 2015 11:21:13: 10000000 INFO @ Thu, 30 Apr 2015 11:21:16: 11000000 INFO @ Thu, 30 Apr 2015 11:21:19: 12000000 INFO @ Thu, 30 Apr 2015 11:21:21: 11000000 INFO @ Thu, 30 Apr 2015 11:21:21: 12000000 INFO @ Thu, 30 Apr 2015 11:21:24: 13000000 INFO @ Thu, 30 Apr 2015 11:21:27: 13000000 INFO @ Thu, 30 Apr 2015 11:21:28: 12000000 INFO @ Thu, 30 Apr 2015 11:21:30: 14000000 INFO @ Thu, 30 Apr 2015 11:21:32: 14000000 INFO @ Thu, 30 Apr 2015 11:21:35: 13000000 INFO @ Thu, 30 Apr 2015 11:21:35: 15000000 INFO @ Thu, 30 Apr 2015 11:21:38: 15000000 INFO @ Thu, 30 Apr 2015 11:21:41: 16000000 INFO @ Thu, 30 Apr 2015 11:21:42: #1 tag size is determined as 42 bps INFO @ Thu, 30 Apr 2015 11:21:42: #1 tag size = 42 INFO @ Thu, 30 Apr 2015 11:21:42: #1 total tags in treatment: 16130114 INFO @ Thu, 30 Apr 2015 11:21:42: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:21:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:21:42: 14000000 INFO @ Thu, 30 Apr 2015 11:21:43: 16000000 INFO @ Thu, 30 Apr 2015 11:21:44: #1 tags after filtering in treatment: 16126061 INFO @ Thu, 30 Apr 2015 11:21:44: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:21:44: #1 finished! INFO @ Thu, 30 Apr 2015 11:21:44: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:21:44: #1 tag size is determined as 42 bps INFO @ Thu, 30 Apr 2015 11:21:44: #1 tag size = 42 INFO @ Thu, 30 Apr 2015 11:21:44: #1 total tags in treatment: 16130114 INFO @ Thu, 30 Apr 2015 11:21:44: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:21:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:21:47: #1 tags after filtering in treatment: 16126061 INFO @ Thu, 30 Apr 2015 11:21:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:21:47: #1 finished! INFO @ Thu, 30 Apr 2015 11:21:47: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:21:47: #2 number of paired peaks: 259 WARNING @ Thu, 30 Apr 2015 11:21:47: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Thu, 30 Apr 2015 11:21:47: start model_add_line... INFO @ Thu, 30 Apr 2015 11:21:49: 15000000 INFO @ Thu, 30 Apr 2015 11:21:50: #2 number of paired peaks: 259 WARNING @ Thu, 30 Apr 2015 11:21:50: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Thu, 30 Apr 2015 11:21:50: start model_add_line... INFO @ Thu, 30 Apr 2015 11:21:53: start X-correlation... INFO @ Thu, 30 Apr 2015 11:21:53: end of X-cor INFO @ Thu, 30 Apr 2015 11:21:53: #2 finished! INFO @ Thu, 30 Apr 2015 11:21:53: #2 predicted fragment length is 32 bps INFO @ Thu, 30 Apr 2015 11:21:53: #2 alternative fragment length(s) may be 2,32 bps INFO @ Thu, 30 Apr 2015 11:21:53: #2.2 Generate R script for model : SRX059228.05_model.r WARNING @ Thu, 30 Apr 2015 11:21:53: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:21:53: #2 You may need to consider one of the other alternative d(s): 2,32 WARNING @ Thu, 30 Apr 2015 11:21:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 11:21:53: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:21:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:21:55: start X-correlation... INFO @ Thu, 30 Apr 2015 11:21:55: end of X-cor INFO @ Thu, 30 Apr 2015 11:21:55: #2 finished! INFO @ Thu, 30 Apr 2015 11:21:55: #2 predicted fragment length is 32 bps INFO @ Thu, 30 Apr 2015 11:21:55: #2 alternative fragment length(s) may be 2,32 bps INFO @ Thu, 30 Apr 2015 11:21:55: #2.2 Generate R script for model : SRX059228.20_model.r WARNING @ Thu, 30 Apr 2015 11:21:55: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:21:55: #2 You may need to consider one of the other alternative d(s): 2,32 WARNING @ Thu, 30 Apr 2015 11:21:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 11:21:55: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:21:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:21:56: 16000000 INFO @ Thu, 30 Apr 2015 11:21:58: #1 tag size is determined as 42 bps INFO @ Thu, 30 Apr 2015 11:21:58: #1 tag size = 42 INFO @ Thu, 30 Apr 2015 11:21:58: #1 total tags in treatment: 16130114 INFO @ Thu, 30 Apr 2015 11:21:58: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:21:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:22:00: #1 tags after filtering in treatment: 16126061 INFO @ Thu, 30 Apr 2015 11:22:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:22:00: #1 finished! INFO @ Thu, 30 Apr 2015 11:22:00: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:22:03: #2 number of paired peaks: 259 WARNING @ Thu, 30 Apr 2015 11:22:03: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Thu, 30 Apr 2015 11:22:03: start model_add_line... INFO @ Thu, 30 Apr 2015 11:22:09: start X-correlation... INFO @ Thu, 30 Apr 2015 11:22:09: end of X-cor INFO @ Thu, 30 Apr 2015 11:22:09: #2 finished! INFO @ Thu, 30 Apr 2015 11:22:09: #2 predicted fragment length is 32 bps INFO @ Thu, 30 Apr 2015 11:22:09: #2 alternative fragment length(s) may be 2,32 bps INFO @ Thu, 30 Apr 2015 11:22:09: #2.2 Generate R script for model : SRX059228.10_model.r WARNING @ Thu, 30 Apr 2015 11:22:09: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:22:09: #2 You may need to consider one of the other alternative d(s): 2,32 WARNING @ Thu, 30 Apr 2015 11:22:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 11:22:09: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:22:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:23:09: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:23:11: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:23:28: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:23:59: #4 Write output xls file... SRX059228.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:23:59: #4 Write peak in narrowPeak format file... SRX059228.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:23:59: #4 Write summits bed file... SRX059228.20_summits.bed INFO @ Thu, 30 Apr 2015 11:23:59: Done! pass1 - making usageList (6 chroms): 5 millis pass2 - checking and writing primary data (104 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:24:09: #4 Write output xls file... SRX059228.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:24:09: #4 Write peak in narrowPeak format file... SRX059228.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:24:09: #4 Write summits bed file... SRX059228.05_summits.bed INFO @ Thu, 30 Apr 2015 11:24:09: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (8280 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:24:23: #4 Write output xls file... SRX059228.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:24:23: #4 Write peak in narrowPeak format file... SRX059228.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:24:23: #4 Write summits bed file... SRX059228.10_summits.bed INFO @ Thu, 30 Apr 2015 11:24:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1007 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。