Job ID = 2161353 sra ファイルのダウンロード中... Completed: 371138K bytes transferred in 6 seconds (486111K 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 20044 0 20044 0 0 28094 0 --:--:-- --:--:-- --:--:-- 38325 100 35427 0 35427 0 0 49593 0 --:--:-- --:--:-- --:--:-- 67608 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 25332619 spots for /home/okishinya/chipatlas/results/dm3/SRX022335/SRR058396.sra Written 25332619 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:48 25332619 reads; of these: 25332619 (100.00%) were unpaired; of these: 8857128 (34.96%) aligned 0 times 9132045 (36.05%) aligned exactly 1 time 7343446 (28.99%) aligned >1 times 65.04% overall alignment rate Time searching: 00:06:49 Overall time: 00:06:49 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 8 files... [bam_rmdupse_core] 2948416 / 16475491 = 0.1790 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 12:38:01: # Command line: callpeak -t SRX022335.bam -f BAM -g dm -n SRX022335.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX022335.05 # format = BAM # ChIP-seq file = ['SRX022335.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 12:38:01: # Command line: callpeak -t SRX022335.bam -f BAM -g dm -n SRX022335.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX022335.10 # format = BAM # ChIP-seq file = ['SRX022335.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 12:38:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:38:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:38:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:38:01: # Command line: callpeak -t SRX022335.bam -f BAM -g dm -n SRX022335.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX022335.20 # format = BAM # ChIP-seq file = ['SRX022335.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 12:38:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:38:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:38:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:38:08: 1000000 INFO @ Tue, 21 Apr 2015 12:38:08: 1000000 INFO @ Tue, 21 Apr 2015 12:38:08: 1000000 INFO @ Tue, 21 Apr 2015 12:38:13: 2000000 INFO @ Tue, 21 Apr 2015 12:38:13: 2000000 INFO @ Tue, 21 Apr 2015 12:38:13: 2000000 INFO @ Tue, 21 Apr 2015 12:38:19: 3000000 INFO @ Tue, 21 Apr 2015 12:38:19: 3000000 INFO @ Tue, 21 Apr 2015 12:38:19: 3000000 INFO @ Tue, 21 Apr 2015 12:38:24: 4000000 INFO @ Tue, 21 Apr 2015 12:38:25: 4000000 INFO @ Tue, 21 Apr 2015 12:38:25: 4000000 INFO @ Tue, 21 Apr 2015 12:38:30: 5000000 INFO @ Tue, 21 Apr 2015 12:38:30: 5000000 INFO @ Tue, 21 Apr 2015 12:38:30: 5000000 INFO @ Tue, 21 Apr 2015 12:38:35: 6000000 INFO @ Tue, 21 Apr 2015 12:38:36: 6000000 INFO @ Tue, 21 Apr 2015 12:38:36: 6000000 INFO @ Tue, 21 Apr 2015 12:38:41: 7000000 INFO @ Tue, 21 Apr 2015 12:38:42: 7000000 INFO @ Tue, 21 Apr 2015 12:38:42: 7000000 INFO @ Tue, 21 Apr 2015 12:38:46: 8000000 INFO @ Tue, 21 Apr 2015 12:38:47: 8000000 INFO @ Tue, 21 Apr 2015 12:38:47: 8000000 INFO @ Tue, 21 Apr 2015 12:38:52: 9000000 INFO @ Tue, 21 Apr 2015 12:38:53: 9000000 INFO @ Tue, 21 Apr 2015 12:38:53: 9000000 INFO @ Tue, 21 Apr 2015 12:38:57: 10000000 INFO @ Tue, 21 Apr 2015 12:38:59: 10000000 INFO @ Tue, 21 Apr 2015 12:38:59: 10000000 INFO @ Tue, 21 Apr 2015 12:39:03: 11000000 INFO @ Tue, 21 Apr 2015 12:39:04: 11000000 INFO @ Tue, 21 Apr 2015 12:39:04: 11000000 INFO @ Tue, 21 Apr 2015 12:39:09: 12000000 INFO @ Tue, 21 Apr 2015 12:39:10: 12000000 INFO @ Tue, 21 Apr 2015 12:39:10: 12000000 INFO @ Tue, 21 Apr 2015 12:39:14: 13000000 INFO @ Tue, 21 Apr 2015 12:39:16: 13000000 INFO @ Tue, 21 Apr 2015 12:39:16: 13000000 INFO @ Tue, 21 Apr 2015 12:39:17: #1 tag size is determined as 35 bps INFO @ Tue, 21 Apr 2015 12:39:17: #1 tag size = 35 INFO @ Tue, 21 Apr 2015 12:39:17: #1 total tags in treatment: 13527075 INFO @ Tue, 21 Apr 2015 12:39:17: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:39:17: #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 12:39:19: #1 tag size is determined as 35 bps INFO @ Tue, 21 Apr 2015 12:39:19: #1 tag size = 35 INFO @ Tue, 21 Apr 2015 12:39:19: #1 total tags in treatment: 13527075 INFO @ Tue, 21 Apr 2015 12:39:19: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:39:19: #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 12:39:19: #1 tag size is determined as 35 bps INFO @ Tue, 21 Apr 2015 12:39:19: #1 tag size = 35 INFO @ Tue, 21 Apr 2015 12:39:19: #1 total tags in treatment: 13527075 INFO @ Tue, 21 Apr 2015 12:39:19: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:39:19: #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 12:39:20: #1 tags after filtering in treatment: 13525781 INFO @ Tue, 21 Apr 2015 12:39:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:39:20: #1 finished! INFO @ Tue, 21 Apr 2015 12:39:20: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:39:21: #1 tags after filtering in treatment: 13525781 INFO @ Tue, 21 Apr 2015 12:39:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:39:21: #1 finished! INFO @ Tue, 21 Apr 2015 12:39:21: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:39:21: #1 tags after filtering in treatment: 13525781 INFO @ Tue, 21 Apr 2015 12:39:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:39:21: #1 finished! INFO @ Tue, 21 Apr 2015 12:39:21: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:39:22: #2 number of paired peaks: 522 WARNING @ Tue, 21 Apr 2015 12:39:22: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Tue, 21 Apr 2015 12:39:22: start model_add_line... INFO @ Tue, 21 Apr 2015 12:39:23: #2 number of paired peaks: 522 WARNING @ Tue, 21 Apr 2015 12:39:23: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Tue, 21 Apr 2015 12:39:23: start model_add_line... INFO @ Tue, 21 Apr 2015 12:39:24: #2 number of paired peaks: 522 WARNING @ Tue, 21 Apr 2015 12:39:24: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Tue, 21 Apr 2015 12:39:24: start model_add_line... INFO @ Tue, 21 Apr 2015 12:39:27: start X-correlation... INFO @ Tue, 21 Apr 2015 12:39:27: end of X-cor INFO @ Tue, 21 Apr 2015 12:39:27: #2 finished! INFO @ Tue, 21 Apr 2015 12:39:27: #2 predicted fragment length is 48 bps INFO @ Tue, 21 Apr 2015 12:39:27: #2 alternative fragment length(s) may be 48 bps INFO @ Tue, 21 Apr 2015 12:39:27: #2.2 Generate R script for model : SRX022335.10_model.r WARNING @ Tue, 21 Apr 2015 12:39:27: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:39:27: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Tue, 21 Apr 2015 12:39:27: #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 12:39:27: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:39:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:39:28: start X-correlation... INFO @ Tue, 21 Apr 2015 12:39:28: end of X-cor INFO @ Tue, 21 Apr 2015 12:39:28: #2 finished! INFO @ Tue, 21 Apr 2015 12:39:28: #2 predicted fragment length is 48 bps INFO @ Tue, 21 Apr 2015 12:39:28: #2 alternative fragment length(s) may be 48 bps INFO @ Tue, 21 Apr 2015 12:39:28: #2.2 Generate R script for model : SRX022335.05_model.r WARNING @ Tue, 21 Apr 2015 12:39:28: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:39:28: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Tue, 21 Apr 2015 12:39:28: #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 12:39:28: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:39:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:39:29: start X-correlation... INFO @ Tue, 21 Apr 2015 12:39:29: end of X-cor INFO @ Tue, 21 Apr 2015 12:39:29: #2 finished! INFO @ Tue, 21 Apr 2015 12:39:29: #2 predicted fragment length is 48 bps INFO @ Tue, 21 Apr 2015 12:39:29: #2 alternative fragment length(s) may be 48 bps INFO @ Tue, 21 Apr 2015 12:39:29: #2.2 Generate R script for model : SRX022335.20_model.r WARNING @ Tue, 21 Apr 2015 12:39:29: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:39:29: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Tue, 21 Apr 2015 12:39:29: #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 12:39:29: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:39:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:40:33: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:40:41: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:40:42: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:41:25: #4 Write output xls file... SRX022335.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:41:25: #4 Write peak in narrowPeak format file... SRX022335.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:41:25: #4 Write summits bed file... SRX022335.10_summits.bed INFO @ Tue, 21 Apr 2015 12:41:25: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3928 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:41:34: #4 Write output xls file... SRX022335.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:41:34: #4 Write peak in narrowPeak format file... SRX022335.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:41:34: #4 Write summits bed file... SRX022335.20_summits.bed INFO @ Tue, 21 Apr 2015 12:41:34: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1087 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:41:42: #4 Write output xls file... SRX022335.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:41:42: #4 Write peak in narrowPeak format file... SRX022335.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:41:43: #4 Write summits bed file... SRX022335.05_summits.bed INFO @ Tue, 21 Apr 2015 12:41:43: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11398 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。