Job ID = 9029540 sra ファイルのダウンロード中... Completed: 1084229K bytes transferred in 16 seconds (550596K 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 7663 0 7663 0 0 1077 0 --:--:-- 0:00:07 --:--:-- 11041 100 30317 0 30317 0 0 3588 0 --:--:-- 0:00:08 --:--:-- 14949 100 46317 0 46317 0 0 4991 0 --:--:-- 0:00:09 --:--:-- 16194 100 70317 0 70317 0 0 6952 0 --:--:-- 0:00:10 --:--:-- 19035 100 84223 0 84223 0 0 7936 0 --:--:-- 0:00:10 --:--:-- 20096 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 17562043 spots for /home/okishinya/chipatlas/results/dm3/SRX1837980/SRR3658921.sra Written 17562043 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: 00:00:01 Multiseed full-index search: 00:21:48 17562043 reads; of these: 17562043 (100.00%) were unpaired; of these: 445878 (2.54%) aligned 0 times 13701489 (78.02%) aligned exactly 1 time 3414676 (19.44%) aligned >1 times 97.46% overall alignment rate Time searching: 00:21:49 Overall time: 00:21:49 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] 2305492 / 17116165 = 0.1347 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 14:35:34: # Command line: callpeak -t SRX1837980.bam -f BAM -g dm -n SRX1837980.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1837980.10 # format = BAM # ChIP-seq file = ['SRX1837980.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 14:35:34: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:35:34: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:35:34: # Command line: callpeak -t SRX1837980.bam -f BAM -g dm -n SRX1837980.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1837980.20 # format = BAM # ChIP-seq file = ['SRX1837980.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 14:35:34: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:35:34: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:35:34: # Command line: callpeak -t SRX1837980.bam -f BAM -g dm -n SRX1837980.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1837980.05 # format = BAM # ChIP-seq file = ['SRX1837980.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 14:35:34: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:35:34: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:35:42: 1000000 INFO @ Sat, 03 Jun 2017 14:35:42: 1000000 INFO @ Sat, 03 Jun 2017 14:35:42: 1000000 INFO @ Sat, 03 Jun 2017 14:35:49: 2000000 INFO @ Sat, 03 Jun 2017 14:35:50: 2000000 INFO @ Sat, 03 Jun 2017 14:35:50: 2000000 INFO @ Sat, 03 Jun 2017 14:35:58: 3000000 INFO @ Sat, 03 Jun 2017 14:35:58: 3000000 INFO @ Sat, 03 Jun 2017 14:35:58: 3000000 INFO @ Sat, 03 Jun 2017 14:36:05: 4000000 INFO @ Sat, 03 Jun 2017 14:36:06: 4000000 INFO @ Sat, 03 Jun 2017 14:36:06: 4000000 INFO @ Sat, 03 Jun 2017 14:36:13: 5000000 INFO @ Sat, 03 Jun 2017 14:36:15: 5000000 INFO @ Sat, 03 Jun 2017 14:36:15: 5000000 INFO @ Sat, 03 Jun 2017 14:36:21: 6000000 INFO @ Sat, 03 Jun 2017 14:36:23: 6000000 INFO @ Sat, 03 Jun 2017 14:36:24: 6000000 INFO @ Sat, 03 Jun 2017 14:36:28: 7000000 INFO @ Sat, 03 Jun 2017 14:36:32: 7000000 INFO @ Sat, 03 Jun 2017 14:36:33: 7000000 INFO @ Sat, 03 Jun 2017 14:36:36: 8000000 INFO @ Sat, 03 Jun 2017 14:36:40: 8000000 INFO @ Sat, 03 Jun 2017 14:36:41: 8000000 INFO @ Sat, 03 Jun 2017 14:36:44: 9000000 INFO @ Sat, 03 Jun 2017 14:36:48: 9000000 INFO @ Sat, 03 Jun 2017 14:36:50: 9000000 INFO @ Sat, 03 Jun 2017 14:36:52: 10000000 INFO @ Sat, 03 Jun 2017 14:36:58: 10000000 INFO @ Sat, 03 Jun 2017 14:36:59: 10000000 INFO @ Sat, 03 Jun 2017 14:37:00: 11000000 INFO @ Sat, 03 Jun 2017 14:37:08: 11000000 INFO @ Sat, 03 Jun 2017 14:37:09: 12000000 INFO @ Sat, 03 Jun 2017 14:37:09: 11000000 INFO @ Sat, 03 Jun 2017 14:37:18: 12000000 INFO @ Sat, 03 Jun 2017 14:37:18: 13000000 INFO @ Sat, 03 Jun 2017 14:37:19: 12000000 INFO @ Sat, 03 Jun 2017 14:37:27: 14000000 INFO @ Sat, 03 Jun 2017 14:37:28: 13000000 INFO @ Sat, 03 Jun 2017 14:37:30: 13000000 INFO @ Sat, 03 Jun 2017 14:37:34: #1 tag size is determined as 148 bps INFO @ Sat, 03 Jun 2017 14:37:34: #1 tag size = 148 INFO @ Sat, 03 Jun 2017 14:37:34: #1 total tags in treatment: 14810673 INFO @ Sat, 03 Jun 2017 14:37:34: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:37:34: #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 14:37:36: #1 tags after filtering in treatment: 14783655 INFO @ Sat, 03 Jun 2017 14:37:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:37:36: #1 finished! INFO @ Sat, 03 Jun 2017 14:37:36: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:37:37: 14000000 INFO @ Sat, 03 Jun 2017 14:37:39: #2 number of paired peaks: 227 WARNING @ Sat, 03 Jun 2017 14:37:39: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Sat, 03 Jun 2017 14:37:39: start model_add_line... INFO @ Sat, 03 Jun 2017 14:37:40: 14000000 INFO @ Sat, 03 Jun 2017 14:37:42: start X-correlation... INFO @ Sat, 03 Jun 2017 14:37:42: end of X-cor INFO @ Sat, 03 Jun 2017 14:37:42: #2 finished! INFO @ Sat, 03 Jun 2017 14:37:42: #2 predicted fragment length is 140 bps INFO @ Sat, 03 Jun 2017 14:37:42: #2 alternative fragment length(s) may be 140 bps INFO @ Sat, 03 Jun 2017 14:37:42: #2.2 Generate R script for model : SRX1837980.05_model.r WARNING @ Sat, 03 Jun 2017 14:37:42: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:37:42: #2 You may need to consider one of the other alternative d(s): 140 WARNING @ Sat, 03 Jun 2017 14:37:42: #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 14:37:42: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:37:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:37:46: #1 tag size is determined as 148 bps INFO @ Sat, 03 Jun 2017 14:37:46: #1 tag size = 148 INFO @ Sat, 03 Jun 2017 14:37:46: #1 total tags in treatment: 14810673 INFO @ Sat, 03 Jun 2017 14:37:46: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:37:46: #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 14:37:48: #1 tag size is determined as 148 bps INFO @ Sat, 03 Jun 2017 14:37:48: #1 tag size = 148 INFO @ Sat, 03 Jun 2017 14:37:48: #1 total tags in treatment: 14810673 INFO @ Sat, 03 Jun 2017 14:37:48: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:37:48: #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 14:37:48: #1 tags after filtering in treatment: 14783655 INFO @ Sat, 03 Jun 2017 14:37:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:37:48: #1 finished! INFO @ Sat, 03 Jun 2017 14:37:48: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:37:50: #1 tags after filtering in treatment: 14783655 INFO @ Sat, 03 Jun 2017 14:37:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:37:50: #1 finished! INFO @ Sat, 03 Jun 2017 14:37:50: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:37:51: #2 number of paired peaks: 227 WARNING @ Sat, 03 Jun 2017 14:37:51: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Sat, 03 Jun 2017 14:37:51: start model_add_line... INFO @ Sat, 03 Jun 2017 14:37:53: #2 number of paired peaks: 227 WARNING @ Sat, 03 Jun 2017 14:37:53: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Sat, 03 Jun 2017 14:37:53: start model_add_line... INFO @ Sat, 03 Jun 2017 14:37:54: start X-correlation... INFO @ Sat, 03 Jun 2017 14:37:54: end of X-cor INFO @ Sat, 03 Jun 2017 14:37:54: #2 finished! INFO @ Sat, 03 Jun 2017 14:37:54: #2 predicted fragment length is 140 bps INFO @ Sat, 03 Jun 2017 14:37:54: #2 alternative fragment length(s) may be 140 bps INFO @ Sat, 03 Jun 2017 14:37:54: #2.2 Generate R script for model : SRX1837980.10_model.r WARNING @ Sat, 03 Jun 2017 14:37:54: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:37:54: #2 You may need to consider one of the other alternative d(s): 140 WARNING @ Sat, 03 Jun 2017 14:37:54: #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 14:37:54: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:37:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:37:56: start X-correlation... INFO @ Sat, 03 Jun 2017 14:37:56: end of X-cor INFO @ Sat, 03 Jun 2017 14:37:56: #2 finished! INFO @ Sat, 03 Jun 2017 14:37:56: #2 predicted fragment length is 140 bps INFO @ Sat, 03 Jun 2017 14:37:56: #2 alternative fragment length(s) may be 140 bps INFO @ Sat, 03 Jun 2017 14:37:56: #2.2 Generate R script for model : SRX1837980.20_model.r WARNING @ Sat, 03 Jun 2017 14:37:56: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:37:56: #2 You may need to consider one of the other alternative d(s): 140 WARNING @ Sat, 03 Jun 2017 14:37:56: #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 14:37:56: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:37:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:39:05: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:39:11: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:39:22: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:40:12: #4 Write output xls file... SRX1837980.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:40:12: #4 Write peak in narrowPeak format file... SRX1837980.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:40:12: #4 Write summits bed file... SRX1837980.10_summits.bed INFO @ Sat, 03 Jun 2017 14:40:12: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6266 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:40:23: #4 Write output xls file... SRX1837980.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:40:23: #4 Write peak in narrowPeak format file... SRX1837980.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:40:23: #4 Write summits bed file... SRX1837980.20_summits.bed INFO @ Sat, 03 Jun 2017 14:40:23: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1542 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:40:26: #4 Write output xls file... SRX1837980.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:40:26: #4 Write peak in narrowPeak format file... SRX1837980.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:40:26: #4 Write summits bed file... SRX1837980.05_summits.bed INFO @ Sat, 03 Jun 2017 14:40:26: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (18769 records, 4 fields): 22 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。