Job ID = 2161556 sra ファイルのダウンロード中... Completed: 7664269K bytes transferred in 103 seconds (605146K 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 36314 0 36314 0 0 50611 0 --:--:-- --:--:-- --:--:-- 69038 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 19594741 spots for /home/okishinya/chipatlas/results/dm3/SRX027831/SRR067914.sra Written 19594741 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: 00:05:28 19594741 reads; of these: 19594741 (100.00%) were unpaired; of these: 5681441 (28.99%) aligned 0 times 9306158 (47.49%) aligned exactly 1 time 4607142 (23.51%) aligned >1 times 71.01% overall alignment rate Time searching: 00:05:29 Overall time: 00:05:29 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] 1165669 / 13913300 = 0.0838 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 12:58:17: # Command line: callpeak -t SRX027831.bam -f BAM -g dm -n SRX027831.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX027831.05 # format = BAM # ChIP-seq file = ['SRX027831.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 12:58:17: # Command line: callpeak -t SRX027831.bam -f BAM -g dm -n SRX027831.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX027831.20 # format = BAM # ChIP-seq file = ['SRX027831.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 12:58:17: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:58:17: # Command line: callpeak -t SRX027831.bam -f BAM -g dm -n SRX027831.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX027831.10 # format = BAM # ChIP-seq file = ['SRX027831.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 12:58:17: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:58:17: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:58:17: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:58:17: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:58:17: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:58:22: 1000000 INFO @ Tue, 21 Apr 2015 12:58:23: 1000000 INFO @ Tue, 21 Apr 2015 12:58:23: 1000000 INFO @ Tue, 21 Apr 2015 12:58:28: 2000000 INFO @ Tue, 21 Apr 2015 12:58:28: 2000000 INFO @ Tue, 21 Apr 2015 12:58:28: 2000000 INFO @ Tue, 21 Apr 2015 12:58:33: 3000000 INFO @ Tue, 21 Apr 2015 12:58:34: 3000000 INFO @ Tue, 21 Apr 2015 12:58:34: 3000000 INFO @ Tue, 21 Apr 2015 12:58:39: 4000000 INFO @ Tue, 21 Apr 2015 12:58:40: 4000000 INFO @ Tue, 21 Apr 2015 12:58:40: 4000000 INFO @ Tue, 21 Apr 2015 12:58:44: 5000000 INFO @ Tue, 21 Apr 2015 12:58:46: 5000000 INFO @ Tue, 21 Apr 2015 12:58:46: 5000000 INFO @ Tue, 21 Apr 2015 12:58:49: 6000000 INFO @ Tue, 21 Apr 2015 12:58:52: 6000000 INFO @ Tue, 21 Apr 2015 12:58:52: 6000000 INFO @ Tue, 21 Apr 2015 12:58:55: 7000000 INFO @ Tue, 21 Apr 2015 12:58:58: 7000000 INFO @ Tue, 21 Apr 2015 12:58:58: 7000000 INFO @ Tue, 21 Apr 2015 12:59:00: 8000000 INFO @ Tue, 21 Apr 2015 12:59:04: 8000000 INFO @ Tue, 21 Apr 2015 12:59:04: 8000000 INFO @ Tue, 21 Apr 2015 12:59:06: 9000000 INFO @ Tue, 21 Apr 2015 12:59:09: 9000000 INFO @ Tue, 21 Apr 2015 12:59:09: 9000000 INFO @ Tue, 21 Apr 2015 12:59:11: 10000000 INFO @ Tue, 21 Apr 2015 12:59:15: 10000000 INFO @ Tue, 21 Apr 2015 12:59:15: 10000000 INFO @ Tue, 21 Apr 2015 12:59:17: 11000000 INFO @ Tue, 21 Apr 2015 12:59:21: 11000000 INFO @ Tue, 21 Apr 2015 12:59:21: 11000000 INFO @ Tue, 21 Apr 2015 12:59:22: 12000000 INFO @ Tue, 21 Apr 2015 12:59:26: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:59:26: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:59:26: #1 total tags in treatment: 12747631 INFO @ Tue, 21 Apr 2015 12:59:26: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:59:26: #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 12:59:27: 12000000 INFO @ Tue, 21 Apr 2015 12:59:27: 12000000 INFO @ Tue, 21 Apr 2015 12:59:29: #1 tags after filtering in treatment: 12746707 INFO @ Tue, 21 Apr 2015 12:59:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:59:29: #1 finished! INFO @ Tue, 21 Apr 2015 12:59:29: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:59:31: #2 number of paired peaks: 751 WARNING @ Tue, 21 Apr 2015 12:59:31: Fewer paired peaks (751) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 751 pairs to build model! INFO @ Tue, 21 Apr 2015 12:59:31: start model_add_line... INFO @ Tue, 21 Apr 2015 12:59:32: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:59:32: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:59:32: #1 total tags in treatment: 12747631 INFO @ Tue, 21 Apr 2015 12:59:32: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:59:32: #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 12:59:32: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:59:32: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:59:32: #1 total tags in treatment: 12747631 INFO @ Tue, 21 Apr 2015 12:59:32: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:59:32: #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 12:59:34: #1 tags after filtering in treatment: 12746707 INFO @ Tue, 21 Apr 2015 12:59:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:59:34: #1 finished! INFO @ Tue, 21 Apr 2015 12:59:34: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:59:34: #1 tags after filtering in treatment: 12746707 INFO @ Tue, 21 Apr 2015 12:59:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:59:34: #1 finished! INFO @ Tue, 21 Apr 2015 12:59:34: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:59:36: #2 number of paired peaks: 751 WARNING @ Tue, 21 Apr 2015 12:59:36: Fewer paired peaks (751) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 751 pairs to build model! INFO @ Tue, 21 Apr 2015 12:59:36: start model_add_line... INFO @ Tue, 21 Apr 2015 12:59:36: #2 number of paired peaks: 751 WARNING @ Tue, 21 Apr 2015 12:59:36: Fewer paired peaks (751) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 751 pairs to build model! INFO @ Tue, 21 Apr 2015 12:59:36: start model_add_line... INFO @ Tue, 21 Apr 2015 12:59:38: start X-correlation... INFO @ Tue, 21 Apr 2015 12:59:38: end of X-cor INFO @ Tue, 21 Apr 2015 12:59:38: #2 finished! INFO @ Tue, 21 Apr 2015 12:59:38: #2 predicted fragment length is 62 bps INFO @ Tue, 21 Apr 2015 12:59:38: #2 alternative fragment length(s) may be 4,43,62 bps INFO @ Tue, 21 Apr 2015 12:59:38: #2.2 Generate R script for model : SRX027831.05_model.r WARNING @ Tue, 21 Apr 2015 12:59:38: #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 12:59:38: #2 You may need to consider one of the other alternative d(s): 4,43,62 WARNING @ Tue, 21 Apr 2015 12:59:38: #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 12:59:38: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:59:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:59:43: start X-correlation... INFO @ Tue, 21 Apr 2015 12:59:43: end of X-cor INFO @ Tue, 21 Apr 2015 12:59:43: #2 finished! INFO @ Tue, 21 Apr 2015 12:59:43: #2 predicted fragment length is 62 bps INFO @ Tue, 21 Apr 2015 12:59:43: #2 alternative fragment length(s) may be 4,43,62 bps INFO @ Tue, 21 Apr 2015 12:59:43: #2.2 Generate R script for model : SRX027831.20_model.r WARNING @ Tue, 21 Apr 2015 12:59:43: #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 12:59:43: #2 You may need to consider one of the other alternative d(s): 4,43,62 WARNING @ Tue, 21 Apr 2015 12:59:43: #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 12:59:43: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:59:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:59:43: start X-correlation... INFO @ Tue, 21 Apr 2015 12:59:43: end of X-cor INFO @ Tue, 21 Apr 2015 12:59:43: #2 finished! INFO @ Tue, 21 Apr 2015 12:59:43: #2 predicted fragment length is 62 bps INFO @ Tue, 21 Apr 2015 12:59:43: #2 alternative fragment length(s) may be 4,43,62 bps INFO @ Tue, 21 Apr 2015 12:59:43: #2.2 Generate R script for model : SRX027831.10_model.r WARNING @ Tue, 21 Apr 2015 12:59:43: #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 12:59:43: #2 You may need to consider one of the other alternative d(s): 4,43,62 WARNING @ Tue, 21 Apr 2015 12:59:43: #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 12:59:43: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:59:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:00:45: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:00:49: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:00:51: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:01:33: #4 Write output xls file... SRX027831.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:01:33: #4 Write peak in narrowPeak format file... SRX027831.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:01:33: #4 Write summits bed file... SRX027831.05_summits.bed INFO @ Tue, 21 Apr 2015 13:01:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3598 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:01:38: #4 Write output xls file... SRX027831.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:01:38: #4 Write peak in narrowPeak format file... SRX027831.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:01:38: #4 Write summits bed file... SRX027831.20_summits.bed INFO @ Tue, 21 Apr 2015 13:01:38: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1021 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:01:40: #4 Write output xls file... SRX027831.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:01:40: #4 Write peak in narrowPeak format file... SRX027831.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:01:40: #4 Write summits bed file... SRX027831.10_summits.bed INFO @ Tue, 21 Apr 2015 13:01:40: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2261 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。