Job ID = 2161538 sra ファイルのダウンロード中... Completed: 438162K bytes transferred in 6 seconds (534964K 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 --:--:-- --:--:-- --:--:-- 0 101 5460 0 5460 0 0 10141 0 --:--:-- --:--:-- --:--:-- 15689 100 44908 0 44908 0 0 48965 0 --:--:-- --:--:-- --:--:-- 61771 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 22786520 spots for /home/okishinya/chipatlas/results/dm3/SRX026870/SRR065773.sra Written 22786520 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: 00:08:32 22786520 reads; of these: 22786520 (100.00%) were unpaired; of these: 715075 (3.14%) aligned 0 times 15482628 (67.95%) aligned exactly 1 time 6588817 (28.92%) aligned >1 times 96.86% overall alignment rate Time searching: 00:08:32 Overall time: 00:08:32 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] 3084426 / 22071445 = 0.1397 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 12:58:28: # Command line: callpeak -t SRX026870.bam -f BAM -g dm -n SRX026870.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX026870.20 # format = BAM # ChIP-seq file = ['SRX026870.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 12:58:28: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:58:28: # Command line: callpeak -t SRX026870.bam -f BAM -g dm -n SRX026870.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX026870.10 # format = BAM # ChIP-seq file = ['SRX026870.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 12:58:28: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:58:28: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:58:28: # Command line: callpeak -t SRX026870.bam -f BAM -g dm -n SRX026870.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX026870.05 # format = BAM # ChIP-seq file = ['SRX026870.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 12:58:28: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:58:28: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:58:28: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:58:34: 1000000 INFO @ Tue, 21 Apr 2015 12:58:34: 1000000 INFO @ Tue, 21 Apr 2015 12:58:34: 1000000 INFO @ Tue, 21 Apr 2015 12:58:40: 2000000 INFO @ Tue, 21 Apr 2015 12:58:40: 2000000 INFO @ Tue, 21 Apr 2015 12:58:40: 2000000 INFO @ Tue, 21 Apr 2015 12:58:46: 3000000 INFO @ Tue, 21 Apr 2015 12:58:47: 3000000 INFO @ Tue, 21 Apr 2015 12:58:47: 3000000 INFO @ Tue, 21 Apr 2015 12:58:52: 4000000 INFO @ Tue, 21 Apr 2015 12:58:53: 4000000 INFO @ Tue, 21 Apr 2015 12:58:53: 4000000 INFO @ Tue, 21 Apr 2015 12:58:58: 5000000 INFO @ Tue, 21 Apr 2015 12:58:59: 5000000 INFO @ Tue, 21 Apr 2015 12:58:59: 5000000 INFO @ Tue, 21 Apr 2015 12:59:04: 6000000 INFO @ Tue, 21 Apr 2015 12:59:05: 6000000 INFO @ Tue, 21 Apr 2015 12:59:05: 6000000 INFO @ Tue, 21 Apr 2015 12:59:10: 7000000 INFO @ Tue, 21 Apr 2015 12:59:12: 7000000 INFO @ Tue, 21 Apr 2015 12:59:12: 7000000 INFO @ Tue, 21 Apr 2015 12:59:16: 8000000 INFO @ Tue, 21 Apr 2015 12:59:18: 8000000 INFO @ Tue, 21 Apr 2015 12:59:18: 8000000 INFO @ Tue, 21 Apr 2015 12:59:21: 9000000 INFO @ Tue, 21 Apr 2015 12:59:24: 9000000 INFO @ Tue, 21 Apr 2015 12:59:24: 9000000 INFO @ Tue, 21 Apr 2015 12:59:27: 10000000 INFO @ Tue, 21 Apr 2015 12:59:31: 10000000 INFO @ Tue, 21 Apr 2015 12:59:31: 10000000 INFO @ Tue, 21 Apr 2015 12:59:33: 11000000 INFO @ Tue, 21 Apr 2015 12:59:37: 11000000 INFO @ Tue, 21 Apr 2015 12:59:37: 11000000 INFO @ Tue, 21 Apr 2015 12:59:39: 12000000 INFO @ Tue, 21 Apr 2015 12:59:43: 12000000 INFO @ Tue, 21 Apr 2015 12:59:43: 12000000 INFO @ Tue, 21 Apr 2015 12:59:45: 13000000 INFO @ Tue, 21 Apr 2015 12:59:49: 13000000 INFO @ Tue, 21 Apr 2015 12:59:49: 13000000 INFO @ Tue, 21 Apr 2015 12:59:51: 14000000 INFO @ Tue, 21 Apr 2015 12:59:56: 14000000 INFO @ Tue, 21 Apr 2015 12:59:56: 14000000 INFO @ Tue, 21 Apr 2015 12:59:57: 15000000 INFO @ Tue, 21 Apr 2015 13:00:02: 15000000 INFO @ Tue, 21 Apr 2015 13:00:02: 15000000 INFO @ Tue, 21 Apr 2015 13:00:03: 16000000 INFO @ Tue, 21 Apr 2015 13:00:08: 16000000 INFO @ Tue, 21 Apr 2015 13:00:08: 16000000 INFO @ Tue, 21 Apr 2015 13:00:09: 17000000 INFO @ Tue, 21 Apr 2015 13:00:15: 17000000 INFO @ Tue, 21 Apr 2015 13:00:15: 17000000 INFO @ Tue, 21 Apr 2015 13:00:15: 18000000 INFO @ Tue, 21 Apr 2015 13:00:21: 18000000 INFO @ Tue, 21 Apr 2015 13:00:21: 18000000 INFO @ Tue, 21 Apr 2015 13:00:21: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:00:21: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:00:21: #1 total tags in treatment: 18987019 INFO @ Tue, 21 Apr 2015 13:00:21: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:00:21: #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 13:00:25: #1 tags after filtering in treatment: 18985088 INFO @ Tue, 21 Apr 2015 13:00:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:00:25: #1 finished! INFO @ Tue, 21 Apr 2015 13:00:25: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:00:27: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:00:27: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:00:27: #1 total tags in treatment: 18987019 INFO @ Tue, 21 Apr 2015 13:00:27: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:00:27: #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 13:00:27: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:00:27: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:00:27: #1 total tags in treatment: 18987019 INFO @ Tue, 21 Apr 2015 13:00:27: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:00:27: #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 13:00:28: #2 number of paired peaks: 164 WARNING @ Tue, 21 Apr 2015 13:00:28: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Tue, 21 Apr 2015 13:00:28: start model_add_line... INFO @ Tue, 21 Apr 2015 13:00:29: start X-correlation... INFO @ Tue, 21 Apr 2015 13:00:29: end of X-cor INFO @ Tue, 21 Apr 2015 13:00:29: #2 finished! INFO @ Tue, 21 Apr 2015 13:00:29: #2 predicted fragment length is 28 bps INFO @ Tue, 21 Apr 2015 13:00:29: #2 alternative fragment length(s) may be 28 bps INFO @ Tue, 21 Apr 2015 13:00:29: #2.2 Generate R script for model : SRX026870.05_model.r WARNING @ Tue, 21 Apr 2015 13:00:29: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:00:29: #2 You may need to consider one of the other alternative d(s): 28 WARNING @ Tue, 21 Apr 2015 13:00:29: #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 13:00:29: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:00:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:00:31: #1 tags after filtering in treatment: 18985088 INFO @ Tue, 21 Apr 2015 13:00:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:00:31: #1 finished! INFO @ Tue, 21 Apr 2015 13:00:31: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:00:31: #1 tags after filtering in treatment: 18985088 INFO @ Tue, 21 Apr 2015 13:00:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:00:31: #1 finished! INFO @ Tue, 21 Apr 2015 13:00:31: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:00:34: #2 number of paired peaks: 164 WARNING @ Tue, 21 Apr 2015 13:00:34: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Tue, 21 Apr 2015 13:00:34: start model_add_line... INFO @ Tue, 21 Apr 2015 13:00:34: #2 number of paired peaks: 164 WARNING @ Tue, 21 Apr 2015 13:00:34: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Tue, 21 Apr 2015 13:00:34: start model_add_line... INFO @ Tue, 21 Apr 2015 13:00:36: start X-correlation... INFO @ Tue, 21 Apr 2015 13:00:36: end of X-cor INFO @ Tue, 21 Apr 2015 13:00:36: #2 finished! INFO @ Tue, 21 Apr 2015 13:00:36: #2 predicted fragment length is 28 bps INFO @ Tue, 21 Apr 2015 13:00:36: #2 alternative fragment length(s) may be 28 bps INFO @ Tue, 21 Apr 2015 13:00:36: #2.2 Generate R script for model : SRX026870.20_model.r WARNING @ Tue, 21 Apr 2015 13:00:36: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:00:36: #2 You may need to consider one of the other alternative d(s): 28 WARNING @ Tue, 21 Apr 2015 13:00:36: #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 13:00:36: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:00:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:00:36: start X-correlation... INFO @ Tue, 21 Apr 2015 13:00:36: end of X-cor INFO @ Tue, 21 Apr 2015 13:00:36: #2 finished! INFO @ Tue, 21 Apr 2015 13:00:36: #2 predicted fragment length is 28 bps INFO @ Tue, 21 Apr 2015 13:00:36: #2 alternative fragment length(s) may be 28 bps INFO @ Tue, 21 Apr 2015 13:00:36: #2.2 Generate R script for model : SRX026870.10_model.r WARNING @ Tue, 21 Apr 2015 13:00:36: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:00:36: #2 You may need to consider one of the other alternative d(s): 28 WARNING @ Tue, 21 Apr 2015 13:00:36: #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 13:00:36: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:00:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:02:03: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:02:10: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:02:11: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:03:11: #4 Write output xls file... SRX026870.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:03:11: #4 Write peak in narrowPeak format file... SRX026870.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:03:11: #4 Write summits bed file... SRX026870.05_summits.bed INFO @ Tue, 21 Apr 2015 13:03:11: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2073 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:03:19: #4 Write output xls file... SRX026870.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:03:19: #4 Write peak in narrowPeak format file... SRX026870.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:03:19: #4 Write summits bed file... SRX026870.20_summits.bed INFO @ Tue, 21 Apr 2015 13:03:19: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (942 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:03:22: #4 Write output xls file... SRX026870.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:03:22: #4 Write peak in narrowPeak format file... SRX026870.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:03:22: #4 Write summits bed file... SRX026870.10_summits.bed INFO @ Tue, 21 Apr 2015 13:03:22: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (1594 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。