Job ID = 2161395 sra ファイルのダウンロード中... Completed: 440419K bytes transferred in 7 seconds (510583K 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 17110 0 17110 0 0 23675 0 --:--:-- --:--:-- --:--:-- 32161 100 44993 0 44993 0 0 49304 0 --:--:-- --:--:-- --:--:-- 62317 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 27979833 spots for /home/okishinya/chipatlas/results/dm3/SRX025483/SRR063886.sra Written 27979833 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: 00:09:40 27979833 reads; of these: 27979833 (100.00%) were unpaired; of these: 567189 (2.03%) aligned 0 times 19932749 (71.24%) aligned exactly 1 time 7479895 (26.73%) aligned >1 times 97.97% overall alignment rate Time searching: 00:09:40 Overall time: 00:09:40 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] 4339782 / 27412644 = 0.1583 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 12:49:13: # Command line: callpeak -t SRX025483.bam -f BAM -g dm -n SRX025483.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX025483.20 # format = BAM # ChIP-seq file = ['SRX025483.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 12:49:13: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:49:13: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:49:13: # Command line: callpeak -t SRX025483.bam -f BAM -g dm -n SRX025483.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX025483.10 # format = BAM # ChIP-seq file = ['SRX025483.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 12:49:13: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:49:13: # Command line: callpeak -t SRX025483.bam -f BAM -g dm -n SRX025483.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX025483.05 # format = BAM # ChIP-seq file = ['SRX025483.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 12:49:13: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:49:13: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:49:13: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:49:18: 1000000 INFO @ Tue, 21 Apr 2015 12:49:18: 1000000 INFO @ Tue, 21 Apr 2015 12:49:18: 1000000 INFO @ Tue, 21 Apr 2015 12:49:23: 2000000 INFO @ Tue, 21 Apr 2015 12:49:23: 2000000 INFO @ Tue, 21 Apr 2015 12:49:23: 2000000 INFO @ Tue, 21 Apr 2015 12:49:28: 3000000 INFO @ Tue, 21 Apr 2015 12:49:28: 3000000 INFO @ Tue, 21 Apr 2015 12:49:28: 3000000 INFO @ Tue, 21 Apr 2015 12:49:33: 4000000 INFO @ Tue, 21 Apr 2015 12:49:33: 4000000 INFO @ Tue, 21 Apr 2015 12:49:33: 4000000 INFO @ Tue, 21 Apr 2015 12:49:38: 5000000 INFO @ Tue, 21 Apr 2015 12:49:38: 5000000 INFO @ Tue, 21 Apr 2015 12:49:39: 5000000 INFO @ Tue, 21 Apr 2015 12:49:43: 6000000 INFO @ Tue, 21 Apr 2015 12:49:43: 6000000 INFO @ Tue, 21 Apr 2015 12:49:44: 6000000 INFO @ Tue, 21 Apr 2015 12:49:48: 7000000 INFO @ Tue, 21 Apr 2015 12:49:49: 7000000 INFO @ Tue, 21 Apr 2015 12:49:50: 7000000 INFO @ Tue, 21 Apr 2015 12:49:54: 8000000 INFO @ Tue, 21 Apr 2015 12:49:54: 8000000 INFO @ Tue, 21 Apr 2015 12:49:55: 8000000 INFO @ Tue, 21 Apr 2015 12:49:59: 9000000 INFO @ Tue, 21 Apr 2015 12:50:00: 9000000 INFO @ Tue, 21 Apr 2015 12:50:01: 9000000 INFO @ Tue, 21 Apr 2015 12:50:05: 10000000 INFO @ Tue, 21 Apr 2015 12:50:05: 10000000 INFO @ Tue, 21 Apr 2015 12:50:07: 10000000 INFO @ Tue, 21 Apr 2015 12:50:10: 11000000 INFO @ Tue, 21 Apr 2015 12:50:11: 11000000 INFO @ Tue, 21 Apr 2015 12:50:12: 11000000 INFO @ Tue, 21 Apr 2015 12:50:15: 12000000 INFO @ Tue, 21 Apr 2015 12:50:17: 12000000 INFO @ Tue, 21 Apr 2015 12:50:18: 12000000 INFO @ Tue, 21 Apr 2015 12:50:21: 13000000 INFO @ Tue, 21 Apr 2015 12:50:22: 13000000 INFO @ Tue, 21 Apr 2015 12:50:24: 13000000 INFO @ Tue, 21 Apr 2015 12:50:26: 14000000 INFO @ Tue, 21 Apr 2015 12:50:28: 14000000 INFO @ Tue, 21 Apr 2015 12:50:29: 14000000 INFO @ Tue, 21 Apr 2015 12:50:32: 15000000 INFO @ Tue, 21 Apr 2015 12:50:34: 15000000 INFO @ Tue, 21 Apr 2015 12:50:35: 15000000 INFO @ Tue, 21 Apr 2015 12:50:37: 16000000 INFO @ Tue, 21 Apr 2015 12:50:39: 16000000 INFO @ Tue, 21 Apr 2015 12:50:41: 16000000 INFO @ Tue, 21 Apr 2015 12:50:43: 17000000 INFO @ Tue, 21 Apr 2015 12:50:45: 17000000 INFO @ Tue, 21 Apr 2015 12:50:46: 17000000 INFO @ Tue, 21 Apr 2015 12:50:49: 18000000 INFO @ Tue, 21 Apr 2015 12:50:51: 18000000 INFO @ Tue, 21 Apr 2015 12:50:52: 18000000 INFO @ Tue, 21 Apr 2015 12:50:54: 19000000 INFO @ Tue, 21 Apr 2015 12:50:56: 19000000 INFO @ Tue, 21 Apr 2015 12:50:58: 19000000 INFO @ Tue, 21 Apr 2015 12:51:00: 20000000 INFO @ Tue, 21 Apr 2015 12:51:02: 20000000 INFO @ Tue, 21 Apr 2015 12:51:04: 20000000 INFO @ Tue, 21 Apr 2015 12:51:05: 21000000 INFO @ Tue, 21 Apr 2015 12:51:08: 21000000 INFO @ Tue, 21 Apr 2015 12:51:09: 21000000 INFO @ Tue, 21 Apr 2015 12:51:11: 22000000 INFO @ Tue, 21 Apr 2015 12:51:13: 22000000 INFO @ Tue, 21 Apr 2015 12:51:15: 22000000 INFO @ Tue, 21 Apr 2015 12:51:16: 23000000 INFO @ Tue, 21 Apr 2015 12:51:17: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:51:17: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:51:17: #1 total tags in treatment: 23072862 INFO @ Tue, 21 Apr 2015 12:51:17: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:51:17: #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 12:51:19: 23000000 INFO @ Tue, 21 Apr 2015 12:51:20: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:51:20: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:51:20: #1 total tags in treatment: 23072862 INFO @ Tue, 21 Apr 2015 12:51:20: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:51:20: #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 12:51:20: 23000000 INFO @ Tue, 21 Apr 2015 12:51:21: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:51:21: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:51:21: #1 total tags in treatment: 23072862 INFO @ Tue, 21 Apr 2015 12:51:21: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:51:21: #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 12:51:21: #1 tags after filtering in treatment: 23071649 INFO @ Tue, 21 Apr 2015 12:51:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:51:21: #1 finished! INFO @ Tue, 21 Apr 2015 12:51:21: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:51:23: #1 tags after filtering in treatment: 23071649 INFO @ Tue, 21 Apr 2015 12:51:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:51:23: #1 finished! INFO @ Tue, 21 Apr 2015 12:51:23: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:51:25: #2 number of paired peaks: 119 WARNING @ Tue, 21 Apr 2015 12:51:25: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Tue, 21 Apr 2015 12:51:25: start model_add_line... INFO @ Tue, 21 Apr 2015 12:51:25: #1 tags after filtering in treatment: 23071649 INFO @ Tue, 21 Apr 2015 12:51:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:51:25: #1 finished! INFO @ Tue, 21 Apr 2015 12:51:25: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:51:27: start X-correlation... INFO @ Tue, 21 Apr 2015 12:51:27: end of X-cor INFO @ Tue, 21 Apr 2015 12:51:27: #2 finished! INFO @ Tue, 21 Apr 2015 12:51:27: #2 predicted fragment length is 46 bps INFO @ Tue, 21 Apr 2015 12:51:27: #2 alternative fragment length(s) may be 46 bps INFO @ Tue, 21 Apr 2015 12:51:27: #2.2 Generate R script for model : SRX025483.20_model.r WARNING @ Tue, 21 Apr 2015 12:51:27: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:51:27: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Tue, 21 Apr 2015 12:51:27: #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 12:51:27: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:51:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:51:27: #2 number of paired peaks: 119 WARNING @ Tue, 21 Apr 2015 12:51:27: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Tue, 21 Apr 2015 12:51:27: start model_add_line... INFO @ Tue, 21 Apr 2015 12:51:29: start X-correlation... INFO @ Tue, 21 Apr 2015 12:51:29: end of X-cor INFO @ Tue, 21 Apr 2015 12:51:29: #2 finished! INFO @ Tue, 21 Apr 2015 12:51:29: #2 predicted fragment length is 46 bps INFO @ Tue, 21 Apr 2015 12:51:29: #2 alternative fragment length(s) may be 46 bps INFO @ Tue, 21 Apr 2015 12:51:29: #2.2 Generate R script for model : SRX025483.05_model.r WARNING @ Tue, 21 Apr 2015 12:51:29: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:51:29: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Tue, 21 Apr 2015 12:51:29: #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 12:51:29: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:51:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:51:29: #2 number of paired peaks: 119 WARNING @ Tue, 21 Apr 2015 12:51:29: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Tue, 21 Apr 2015 12:51:29: start model_add_line... INFO @ Tue, 21 Apr 2015 12:51:30: start X-correlation... INFO @ Tue, 21 Apr 2015 12:51:30: end of X-cor INFO @ Tue, 21 Apr 2015 12:51:30: #2 finished! INFO @ Tue, 21 Apr 2015 12:51:30: #2 predicted fragment length is 46 bps INFO @ Tue, 21 Apr 2015 12:51:30: #2 alternative fragment length(s) may be 46 bps INFO @ Tue, 21 Apr 2015 12:51:30: #2.2 Generate R script for model : SRX025483.10_model.r WARNING @ Tue, 21 Apr 2015 12:51:30: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:51:30: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Tue, 21 Apr 2015 12:51:30: #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 12:51:30: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:51:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:53:15: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:53:19: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:53:21: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:54:38: #4 Write output xls file... SRX025483.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:54:38: #4 Write peak in narrowPeak format file... SRX025483.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:54:38: #4 Write summits bed file... SRX025483.20_summits.bed INFO @ Tue, 21 Apr 2015 12:54:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1117 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:54:40: #4 Write output xls file... SRX025483.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:54:40: #4 Write peak in narrowPeak format file... SRX025483.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:54:40: #4 Write summits bed file... SRX025483.10_summits.bed INFO @ Tue, 21 Apr 2015 12:54:40: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1573 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:54:43: #4 Write output xls file... SRX025483.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:54:43: #4 Write peak in narrowPeak format file... SRX025483.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:54:43: #4 Write summits bed file... SRX025483.05_summits.bed INFO @ Tue, 21 Apr 2015 12:54:43: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1830 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。