Job ID = 2161275 sra ファイルのダウンロード中... Completed: 403163K bytes transferred in 6 seconds (513928K 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 --:--:-- --:--:-- --:--:-- 0 100 34356 0 34356 0 0 46561 0 --:--:-- --:--:-- --:--:-- 62923 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 16502467 spots for /home/okishinya/chipatlas/results/dm3/SRX016141/SRR034692.sra Written 16502467 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: 00:03:20 16502467 reads; of these: 16502467 (100.00%) were unpaired; of these: 3461364 (20.97%) aligned 0 times 11277897 (68.34%) aligned exactly 1 time 1763206 (10.68%) aligned >1 times 79.03% overall alignment rate Time searching: 00:03:20 Overall time: 00:03:20 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_rmdupse_core] 1862623 / 13041103 = 0.1428 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 @ Tue, 21 Apr 2015 12:18:12: # Command line: callpeak -t SRX016141.bam -f BAM -g dm -n SRX016141.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX016141.10 # format = BAM # ChIP-seq file = ['SRX016141.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 @ Tue, 21 Apr 2015 12:18:12: # Command line: callpeak -t SRX016141.bam -f BAM -g dm -n SRX016141.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX016141.20 # format = BAM # ChIP-seq file = ['SRX016141.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 @ Tue, 21 Apr 2015 12:18:12: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:18:12: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:18:12: # Command line: callpeak -t SRX016141.bam -f BAM -g dm -n SRX016141.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX016141.05 # format = BAM # ChIP-seq file = ['SRX016141.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 @ Tue, 21 Apr 2015 12:18:12: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:18:12: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:18:12: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:18:12: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:18:18: 1000000 INFO @ Tue, 21 Apr 2015 12:18:18: 1000000 INFO @ Tue, 21 Apr 2015 12:18:18: 1000000 INFO @ Tue, 21 Apr 2015 12:18:23: 2000000 INFO @ Tue, 21 Apr 2015 12:18:23: 2000000 INFO @ Tue, 21 Apr 2015 12:18:24: 2000000 INFO @ Tue, 21 Apr 2015 12:18:28: 3000000 INFO @ Tue, 21 Apr 2015 12:18:29: 3000000 INFO @ Tue, 21 Apr 2015 12:18:29: 3000000 INFO @ Tue, 21 Apr 2015 12:18:33: 4000000 INFO @ Tue, 21 Apr 2015 12:18:34: 4000000 INFO @ Tue, 21 Apr 2015 12:18:35: 4000000 INFO @ Tue, 21 Apr 2015 12:18:38: 5000000 INFO @ Tue, 21 Apr 2015 12:18:40: 5000000 INFO @ Tue, 21 Apr 2015 12:18:40: 5000000 INFO @ Tue, 21 Apr 2015 12:18:44: 6000000 INFO @ Tue, 21 Apr 2015 12:18:45: 6000000 INFO @ Tue, 21 Apr 2015 12:18:46: 6000000 INFO @ Tue, 21 Apr 2015 12:18:49: 7000000 INFO @ Tue, 21 Apr 2015 12:18:52: 7000000 INFO @ Tue, 21 Apr 2015 12:18:52: 7000000 INFO @ Tue, 21 Apr 2015 12:18:55: 8000000 INFO @ Tue, 21 Apr 2015 12:18:58: 8000000 INFO @ Tue, 21 Apr 2015 12:18:58: 8000000 INFO @ Tue, 21 Apr 2015 12:19:01: 9000000 INFO @ Tue, 21 Apr 2015 12:19:04: 9000000 INFO @ Tue, 21 Apr 2015 12:19:05: 9000000 INFO @ Tue, 21 Apr 2015 12:19:06: 10000000 INFO @ Tue, 21 Apr 2015 12:19:10: 10000000 INFO @ Tue, 21 Apr 2015 12:19:11: 10000000 INFO @ Tue, 21 Apr 2015 12:19:12: 11000000 INFO @ Tue, 21 Apr 2015 12:19:13: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:19:13: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:19:13: #1 total tags in treatment: 11178480 INFO @ Tue, 21 Apr 2015 12:19:13: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:19:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:19:15: #1 tags after filtering in treatment: 11173136 INFO @ Tue, 21 Apr 2015 12:19:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:19:15: #1 finished! INFO @ Tue, 21 Apr 2015 12:19:15: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:19:16: 11000000 INFO @ Tue, 21 Apr 2015 12:19:17: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:19:17: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:19:17: #1 total tags in treatment: 11178480 INFO @ Tue, 21 Apr 2015 12:19:17: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:19:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:19:17: #2 number of paired peaks: 113 WARNING @ Tue, 21 Apr 2015 12:19:17: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Tue, 21 Apr 2015 12:19:17: start model_add_line... INFO @ Tue, 21 Apr 2015 12:19:17: 11000000 INFO @ Tue, 21 Apr 2015 12:19:18: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:19:18: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:19:18: #1 total tags in treatment: 11178480 INFO @ Tue, 21 Apr 2015 12:19:18: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:19:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:19:19: start X-correlation... INFO @ Tue, 21 Apr 2015 12:19:19: end of X-cor INFO @ Tue, 21 Apr 2015 12:19:19: #2 finished! INFO @ Tue, 21 Apr 2015 12:19:19: #2 predicted fragment length is 62 bps INFO @ Tue, 21 Apr 2015 12:19:19: #2 alternative fragment length(s) may be 4,49,62,540,558 bps INFO @ Tue, 21 Apr 2015 12:19:19: #2.2 Generate R script for model : SRX016141.20_model.r WARNING @ Tue, 21 Apr 2015 12:19:19: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:19:19: #2 You may need to consider one of the other alternative d(s): 4,49,62,540,558 WARNING @ Tue, 21 Apr 2015 12:19:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 12:19:19: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:19:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:19:19: #1 tags after filtering in treatment: 11173136 INFO @ Tue, 21 Apr 2015 12:19:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:19:19: #1 finished! INFO @ Tue, 21 Apr 2015 12:19:19: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:19:20: #1 tags after filtering in treatment: 11173136 INFO @ Tue, 21 Apr 2015 12:19:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:19:20: #1 finished! INFO @ Tue, 21 Apr 2015 12:19:20: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:19:21: #2 number of paired peaks: 113 WARNING @ Tue, 21 Apr 2015 12:19:21: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Tue, 21 Apr 2015 12:19:21: start model_add_line... INFO @ Tue, 21 Apr 2015 12:19:22: #2 number of paired peaks: 113 WARNING @ Tue, 21 Apr 2015 12:19:22: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Tue, 21 Apr 2015 12:19:22: start model_add_line... INFO @ Tue, 21 Apr 2015 12:19:23: start X-correlation... INFO @ Tue, 21 Apr 2015 12:19:23: end of X-cor INFO @ Tue, 21 Apr 2015 12:19:23: #2 finished! INFO @ Tue, 21 Apr 2015 12:19:23: #2 predicted fragment length is 62 bps INFO @ Tue, 21 Apr 2015 12:19:23: #2 alternative fragment length(s) may be 4,49,62,540,558 bps INFO @ Tue, 21 Apr 2015 12:19:23: #2.2 Generate R script for model : SRX016141.10_model.r WARNING @ Tue, 21 Apr 2015 12:19:23: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:19:23: #2 You may need to consider one of the other alternative d(s): 4,49,62,540,558 WARNING @ Tue, 21 Apr 2015 12:19:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 12:19:23: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:19:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:19:24: start X-correlation... INFO @ Tue, 21 Apr 2015 12:19:24: end of X-cor INFO @ Tue, 21 Apr 2015 12:19:24: #2 finished! INFO @ Tue, 21 Apr 2015 12:19:24: #2 predicted fragment length is 62 bps INFO @ Tue, 21 Apr 2015 12:19:24: #2 alternative fragment length(s) may be 4,49,62,540,558 bps INFO @ Tue, 21 Apr 2015 12:19:24: #2.2 Generate R script for model : SRX016141.05_model.r WARNING @ Tue, 21 Apr 2015 12:19:24: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:19:24: #2 You may need to consider one of the other alternative d(s): 4,49,62,540,558 WARNING @ Tue, 21 Apr 2015 12:19:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 12:19:24: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:19:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:20:18: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:20:21: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:20:23: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:20:59: #4 Write output xls file... SRX016141.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:20:59: #4 Write peak in narrowPeak format file... SRX016141.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:20:59: #4 Write summits bed file... SRX016141.20_summits.bed INFO @ Tue, 21 Apr 2015 12:20:59: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (144 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:21:04: #4 Write output xls file... SRX016141.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:21:04: #4 Write peak in narrowPeak format file... SRX016141.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:21:04: #4 Write summits bed file... SRX016141.05_summits.bed INFO @ Tue, 21 Apr 2015 12:21:04: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (746 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:21:07: #4 Write output xls file... SRX016141.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:21:07: #4 Write peak in narrowPeak format file... SRX016141.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:21:07: #4 Write summits bed file... SRX016141.10_summits.bed INFO @ Tue, 21 Apr 2015 12:21:07: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (277 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。