Job ID = 9029285 sra ファイルのダウンロード中... Completed: 955188K bytes transferred in 10 seconds (749127K 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 1936 0 --:--:-- 0:00:07 --:--:-- 14015 100 38318 0 38318 0 0 4564 0 --:--:-- 0:00:08 --:--:-- 18988 100 70188 0 70188 0 0 7747 0 --:--:-- 0:00:09 --:--:-- 26150 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 28924023 spots for /home/okishinya/chipatlas/results/dm3/SRX1531761/SRR3102819.sra Written 28924023 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: 00:10:17 28924023 reads; of these: 28924023 (100.00%) were unpaired; of these: 13183942 (45.58%) aligned 0 times 9929627 (34.33%) aligned exactly 1 time 5810454 (20.09%) aligned >1 times 54.42% overall alignment rate Time searching: 00:10:17 Overall time: 00:10:17 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 8 files... [bam_rmdupse_core] 4026916 / 15740081 = 0.2558 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 13:16:12: # Command line: callpeak -t SRX1531761.bam -f BAM -g dm -n SRX1531761.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1531761.10 # format = BAM # ChIP-seq file = ['SRX1531761.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 13:16:12: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:16:12: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:16:12: # Command line: callpeak -t SRX1531761.bam -f BAM -g dm -n SRX1531761.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1531761.05 # format = BAM # ChIP-seq file = ['SRX1531761.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 13:16:12: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:16:12: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:16:12: # Command line: callpeak -t SRX1531761.bam -f BAM -g dm -n SRX1531761.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1531761.20 # format = BAM # ChIP-seq file = ['SRX1531761.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 13:16:12: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:16:12: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:16:18: 1000000 INFO @ Sat, 03 Jun 2017 13:16:18: 1000000 INFO @ Sat, 03 Jun 2017 13:16:19: 1000000 INFO @ Sat, 03 Jun 2017 13:16:24: 2000000 INFO @ Sat, 03 Jun 2017 13:16:24: 2000000 INFO @ Sat, 03 Jun 2017 13:16:26: 2000000 INFO @ Sat, 03 Jun 2017 13:16:30: 3000000 INFO @ Sat, 03 Jun 2017 13:16:30: 3000000 INFO @ Sat, 03 Jun 2017 13:16:32: 3000000 INFO @ Sat, 03 Jun 2017 13:16:36: 4000000 INFO @ Sat, 03 Jun 2017 13:16:36: 4000000 INFO @ Sat, 03 Jun 2017 13:16:38: 4000000 INFO @ Sat, 03 Jun 2017 13:16:41: 5000000 INFO @ Sat, 03 Jun 2017 13:16:42: 5000000 INFO @ Sat, 03 Jun 2017 13:16:44: 5000000 INFO @ Sat, 03 Jun 2017 13:16:46: 6000000 INFO @ Sat, 03 Jun 2017 13:16:48: 6000000 INFO @ Sat, 03 Jun 2017 13:16:50: 6000000 INFO @ Sat, 03 Jun 2017 13:16:52: 7000000 INFO @ Sat, 03 Jun 2017 13:16:54: 7000000 INFO @ Sat, 03 Jun 2017 13:16:56: 7000000 INFO @ Sat, 03 Jun 2017 13:16:57: 8000000 INFO @ Sat, 03 Jun 2017 13:17:00: 8000000 INFO @ Sat, 03 Jun 2017 13:17:02: 8000000 INFO @ Sat, 03 Jun 2017 13:17:02: 9000000 INFO @ Sat, 03 Jun 2017 13:17:05: 9000000 INFO @ Sat, 03 Jun 2017 13:17:07: 10000000 INFO @ Sat, 03 Jun 2017 13:17:08: 9000000 INFO @ Sat, 03 Jun 2017 13:17:11: 10000000 INFO @ Sat, 03 Jun 2017 13:17:12: 11000000 INFO @ Sat, 03 Jun 2017 13:17:14: 10000000 INFO @ Sat, 03 Jun 2017 13:17:17: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:17:17: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:17:17: #1 total tags in treatment: 11713165 INFO @ Sat, 03 Jun 2017 13:17:17: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:17:17: #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 13:17:17: 11000000 INFO @ Sat, 03 Jun 2017 13:17:19: #1 tags after filtering in treatment: 11707067 INFO @ Sat, 03 Jun 2017 13:17:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:17:19: #1 finished! INFO @ Sat, 03 Jun 2017 13:17:19: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:17:20: 11000000 INFO @ Sat, 03 Jun 2017 13:17:21: #2 number of paired peaks: 591 WARNING @ Sat, 03 Jun 2017 13:17:21: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Sat, 03 Jun 2017 13:17:21: start model_add_line... INFO @ Sat, 03 Jun 2017 13:17:21: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:17:21: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:17:21: #1 total tags in treatment: 11713165 INFO @ Sat, 03 Jun 2017 13:17:21: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:17:21: #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 13:17:24: #1 tags after filtering in treatment: 11707067 INFO @ Sat, 03 Jun 2017 13:17:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:17:24: #1 finished! INFO @ Sat, 03 Jun 2017 13:17:24: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:17:24: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:17:24: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:17:24: #1 total tags in treatment: 11713165 INFO @ Sat, 03 Jun 2017 13:17:24: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:17:24: #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 13:17:25: start X-correlation... INFO @ Sat, 03 Jun 2017 13:17:25: end of X-cor INFO @ Sat, 03 Jun 2017 13:17:25: #2 finished! INFO @ Sat, 03 Jun 2017 13:17:25: #2 predicted fragment length is 48 bps INFO @ Sat, 03 Jun 2017 13:17:25: #2 alternative fragment length(s) may be 48 bps INFO @ Sat, 03 Jun 2017 13:17:25: #2.2 Generate R script for model : SRX1531761.20_model.r WARNING @ Sat, 03 Jun 2017 13:17:25: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:17:25: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sat, 03 Jun 2017 13:17:25: #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 13:17:25: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:17:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:17:26: #2 number of paired peaks: 591 WARNING @ Sat, 03 Jun 2017 13:17:26: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Sat, 03 Jun 2017 13:17:26: start model_add_line... INFO @ Sat, 03 Jun 2017 13:17:26: #1 tags after filtering in treatment: 11707067 INFO @ Sat, 03 Jun 2017 13:17:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:17:26: #1 finished! INFO @ Sat, 03 Jun 2017 13:17:26: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:17:28: #2 number of paired peaks: 591 WARNING @ Sat, 03 Jun 2017 13:17:28: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Sat, 03 Jun 2017 13:17:28: start model_add_line... INFO @ Sat, 03 Jun 2017 13:17:30: start X-correlation... INFO @ Sat, 03 Jun 2017 13:17:30: end of X-cor INFO @ Sat, 03 Jun 2017 13:17:30: #2 finished! INFO @ Sat, 03 Jun 2017 13:17:30: #2 predicted fragment length is 48 bps INFO @ Sat, 03 Jun 2017 13:17:30: #2 alternative fragment length(s) may be 48 bps INFO @ Sat, 03 Jun 2017 13:17:30: #2.2 Generate R script for model : SRX1531761.10_model.r WARNING @ Sat, 03 Jun 2017 13:17:30: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:17:30: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sat, 03 Jun 2017 13:17:30: #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 13:17:30: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:17:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:17:33: start X-correlation... INFO @ Sat, 03 Jun 2017 13:17:33: end of X-cor INFO @ Sat, 03 Jun 2017 13:17:33: #2 finished! INFO @ Sat, 03 Jun 2017 13:17:33: #2 predicted fragment length is 48 bps INFO @ Sat, 03 Jun 2017 13:17:33: #2 alternative fragment length(s) may be 48 bps INFO @ Sat, 03 Jun 2017 13:17:33: #2.2 Generate R script for model : SRX1531761.05_model.r WARNING @ Sat, 03 Jun 2017 13:17:33: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:17:33: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sat, 03 Jun 2017 13:17:33: #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 13:17:33: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:17:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:18:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:18:32: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:18:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:19:18: #4 Write output xls file... SRX1531761.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:19:18: #4 Write peak in narrowPeak format file... SRX1531761.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:19:18: #4 Write summits bed file... SRX1531761.10_summits.bed INFO @ Sat, 03 Jun 2017 13:19:18: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1664 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:19:20: #4 Write output xls file... SRX1531761.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:19:20: #4 Write peak in narrowPeak format file... SRX1531761.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:19:20: #4 Write summits bed file... SRX1531761.20_summits.bed INFO @ Sat, 03 Jun 2017 13:19:20: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1388 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:19:26: #4 Write output xls file... SRX1531761.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:19:26: #4 Write peak in narrowPeak format file... SRX1531761.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:19:26: #4 Write summits bed file... SRX1531761.05_summits.bed INFO @ Sat, 03 Jun 2017 13:19:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1935 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。