Job ID = 9040851 sra ファイルのダウンロード中... Completed: 247687K bytes transferred in 5 seconds (374224K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 100 28110 0 28110 0 0 3272 0 --:--:-- 0:00:08 --:--:-- 15599 100 46521 0 46521 0 0 5212 0 --:--:-- 0:00:08 --:--:-- 21789 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 24349796 spots for /home/okishinya/chipatlas/results/dm3/SRX1151230/SRR2189054.sra Written 24349796 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: 00:03:35 24349796 reads; of these: 24349796 (100.00%) were unpaired; of these: 504887 (2.07%) aligned 0 times 19261252 (79.10%) aligned exactly 1 time 4583657 (18.82%) aligned >1 times 97.93% overall alignment rate Time searching: 00:03:35 Overall time: 00:03:35 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] 7292957 / 23844909 = 0.3058 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 @ Mon, 05 Jun 2017 00:24:17: # Command line: callpeak -t SRX1151230.bam -f BAM -g dm -n SRX1151230.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1151230.05 # format = BAM # ChIP-seq file = ['SRX1151230.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 @ Mon, 05 Jun 2017 00:24:17: #1 read tag files... INFO @ Mon, 05 Jun 2017 00:24:17: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 00:24:17: # Command line: callpeak -t SRX1151230.bam -f BAM -g dm -n SRX1151230.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1151230.20 # format = BAM # ChIP-seq file = ['SRX1151230.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 @ Mon, 05 Jun 2017 00:24:17: #1 read tag files... INFO @ Mon, 05 Jun 2017 00:24:17: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 00:24:17: # Command line: callpeak -t SRX1151230.bam -f BAM -g dm -n SRX1151230.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1151230.10 # format = BAM # ChIP-seq file = ['SRX1151230.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 @ Mon, 05 Jun 2017 00:24:17: #1 read tag files... INFO @ Mon, 05 Jun 2017 00:24:17: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 00:24:23: 1000000 INFO @ Mon, 05 Jun 2017 00:24:23: 1000000 INFO @ Mon, 05 Jun 2017 00:24:23: 1000000 INFO @ Mon, 05 Jun 2017 00:24:30: 2000000 INFO @ Mon, 05 Jun 2017 00:24:30: 2000000 INFO @ Mon, 05 Jun 2017 00:24:30: 2000000 INFO @ Mon, 05 Jun 2017 00:24:36: 3000000 INFO @ Mon, 05 Jun 2017 00:24:36: 3000000 INFO @ Mon, 05 Jun 2017 00:24:36: 3000000 INFO @ Mon, 05 Jun 2017 00:24:43: 4000000 INFO @ Mon, 05 Jun 2017 00:24:43: 4000000 INFO @ Mon, 05 Jun 2017 00:24:43: 4000000 INFO @ Mon, 05 Jun 2017 00:24:49: 5000000 INFO @ Mon, 05 Jun 2017 00:24:49: 5000000 INFO @ Mon, 05 Jun 2017 00:24:49: 5000000 INFO @ Mon, 05 Jun 2017 00:24:56: 6000000 INFO @ Mon, 05 Jun 2017 00:24:56: 6000000 INFO @ Mon, 05 Jun 2017 00:24:56: 6000000 INFO @ Mon, 05 Jun 2017 00:25:02: 7000000 INFO @ Mon, 05 Jun 2017 00:25:02: 7000000 INFO @ Mon, 05 Jun 2017 00:25:02: 7000000 INFO @ Mon, 05 Jun 2017 00:25:09: 8000000 INFO @ Mon, 05 Jun 2017 00:25:09: 8000000 INFO @ Mon, 05 Jun 2017 00:25:09: 8000000 INFO @ Mon, 05 Jun 2017 00:25:16: 9000000 INFO @ Mon, 05 Jun 2017 00:25:16: 9000000 INFO @ Mon, 05 Jun 2017 00:25:16: 9000000 INFO @ Mon, 05 Jun 2017 00:25:23: 10000000 INFO @ Mon, 05 Jun 2017 00:25:23: 10000000 INFO @ Mon, 05 Jun 2017 00:25:23: 10000000 INFO @ Mon, 05 Jun 2017 00:25:31: 11000000 INFO @ Mon, 05 Jun 2017 00:25:31: 11000000 INFO @ Mon, 05 Jun 2017 00:25:31: 11000000 INFO @ Mon, 05 Jun 2017 00:25:38: 12000000 INFO @ Mon, 05 Jun 2017 00:25:38: 12000000 INFO @ Mon, 05 Jun 2017 00:25:38: 12000000 INFO @ Mon, 05 Jun 2017 00:25:46: 13000000 INFO @ Mon, 05 Jun 2017 00:25:46: 13000000 INFO @ Mon, 05 Jun 2017 00:25:46: 13000000 INFO @ Mon, 05 Jun 2017 00:25:53: 14000000 INFO @ Mon, 05 Jun 2017 00:25:53: 14000000 INFO @ Mon, 05 Jun 2017 00:25:53: 14000000 INFO @ Mon, 05 Jun 2017 00:26:01: 15000000 INFO @ Mon, 05 Jun 2017 00:26:01: 15000000 INFO @ Mon, 05 Jun 2017 00:26:01: 15000000 INFO @ Mon, 05 Jun 2017 00:26:08: 16000000 INFO @ Mon, 05 Jun 2017 00:26:08: 16000000 INFO @ Mon, 05 Jun 2017 00:26:08: 16000000 INFO @ Mon, 05 Jun 2017 00:26:12: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 00:26:12: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 00:26:12: #1 total tags in treatment: 16551952 INFO @ Mon, 05 Jun 2017 00:26:12: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 00:26:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 00:26:12: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 00:26:12: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 00:26:12: #1 total tags in treatment: 16551952 INFO @ Mon, 05 Jun 2017 00:26:12: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 00:26:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 00:26:12: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 00:26:12: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 00:26:12: #1 total tags in treatment: 16551952 INFO @ Mon, 05 Jun 2017 00:26:12: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 00:26:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 00:26:15: #1 tags after filtering in treatment: 16548259 INFO @ Mon, 05 Jun 2017 00:26:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 00:26:15: #1 finished! INFO @ Mon, 05 Jun 2017 00:26:15: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 00:26:15: #1 tags after filtering in treatment: 16548259 INFO @ Mon, 05 Jun 2017 00:26:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 00:26:15: #1 finished! INFO @ Mon, 05 Jun 2017 00:26:15: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 00:26:15: #1 tags after filtering in treatment: 16548259 INFO @ Mon, 05 Jun 2017 00:26:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 00:26:15: #1 finished! INFO @ Mon, 05 Jun 2017 00:26:15: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 00:26:17: #2 number of paired peaks: 126 WARNING @ Mon, 05 Jun 2017 00:26:17: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Mon, 05 Jun 2017 00:26:17: start model_add_line... INFO @ Mon, 05 Jun 2017 00:26:18: #2 number of paired peaks: 126 WARNING @ Mon, 05 Jun 2017 00:26:18: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Mon, 05 Jun 2017 00:26:18: start model_add_line... INFO @ Mon, 05 Jun 2017 00:26:18: #2 number of paired peaks: 126 WARNING @ Mon, 05 Jun 2017 00:26:18: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Mon, 05 Jun 2017 00:26:18: start model_add_line... INFO @ Mon, 05 Jun 2017 00:26:20: start X-correlation... INFO @ Mon, 05 Jun 2017 00:26:20: end of X-cor INFO @ Mon, 05 Jun 2017 00:26:20: #2 finished! INFO @ Mon, 05 Jun 2017 00:26:20: #2 predicted fragment length is 51 bps INFO @ Mon, 05 Jun 2017 00:26:20: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 05 Jun 2017 00:26:20: #2.2 Generate R script for model : SRX1151230.05_model.r WARNING @ Mon, 05 Jun 2017 00:26:20: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 00:26:20: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 05 Jun 2017 00:26:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 05 Jun 2017 00:26:20: #3 Call peaks... INFO @ Mon, 05 Jun 2017 00:26:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 00:26:20: start X-correlation... INFO @ Mon, 05 Jun 2017 00:26:20: end of X-cor INFO @ Mon, 05 Jun 2017 00:26:20: #2 finished! INFO @ Mon, 05 Jun 2017 00:26:20: #2 predicted fragment length is 51 bps INFO @ Mon, 05 Jun 2017 00:26:20: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 05 Jun 2017 00:26:20: #2.2 Generate R script for model : SRX1151230.20_model.r WARNING @ Mon, 05 Jun 2017 00:26:20: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 00:26:20: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 05 Jun 2017 00:26:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 05 Jun 2017 00:26:20: #3 Call peaks... INFO @ Mon, 05 Jun 2017 00:26:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 00:26:20: start X-correlation... INFO @ Mon, 05 Jun 2017 00:26:20: end of X-cor INFO @ Mon, 05 Jun 2017 00:26:20: #2 finished! INFO @ Mon, 05 Jun 2017 00:26:20: #2 predicted fragment length is 51 bps INFO @ Mon, 05 Jun 2017 00:26:20: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 05 Jun 2017 00:26:20: #2.2 Generate R script for model : SRX1151230.10_model.r WARNING @ Mon, 05 Jun 2017 00:26:20: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 00:26:20: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 05 Jun 2017 00:26:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 05 Jun 2017 00:26:20: #3 Call peaks... INFO @ Mon, 05 Jun 2017 00:26:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 00:27:40: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 00:27:44: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 00:27:46: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 00:28:40: #4 Write output xls file... SRX1151230.10_peaks.xls INFO @ Mon, 05 Jun 2017 00:28:40: #4 Write peak in narrowPeak format file... SRX1151230.10_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 00:28:40: #4 Write summits bed file... SRX1151230.10_summits.bed INFO @ Mon, 05 Jun 2017 00:28:40: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1213 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 00:28:48: #4 Write output xls file... SRX1151230.20_peaks.xls INFO @ Mon, 05 Jun 2017 00:28:48: #4 Write peak in narrowPeak format file... SRX1151230.20_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 00:28:48: #4 Write summits bed file... SRX1151230.20_summits.bed INFO @ Mon, 05 Jun 2017 00:28:48: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (613 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 00:28:51: #4 Write output xls file... SRX1151230.05_peaks.xls INFO @ Mon, 05 Jun 2017 00:28:51: #4 Write peak in narrowPeak format file... SRX1151230.05_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 00:28:51: #4 Write summits bed file... SRX1151230.05_summits.bed INFO @ Mon, 05 Jun 2017 00:28:51: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1830 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。