Job ID = 2162273 sra ファイルのダウンロード中... Completed: 406938K bytes transferred in 7 seconds (452667K 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 35235 0 35235 0 0 49501 0 --:--:-- --:--:-- --:--:-- 67759 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 21988686 spots for /home/okishinya/chipatlas/results/dm3/SRX050606/SRR139088.sra Written 21988686 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: 00:04:18 21988686 reads; of these: 21988686 (100.00%) were unpaired; of these: 3217374 (14.63%) aligned 0 times 17444964 (79.34%) aligned exactly 1 time 1326348 (6.03%) aligned >1 times 85.37% overall alignment rate Time searching: 00:04:18 Overall time: 00:04:18 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] 5040887 / 18771312 = 0.2685 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 13:44:53: # Command line: callpeak -t SRX050606.bam -f BAM -g dm -n SRX050606.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX050606.05 # format = BAM # ChIP-seq file = ['SRX050606.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 13:44:53: # Command line: callpeak -t SRX050606.bam -f BAM -g dm -n SRX050606.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX050606.20 # format = BAM # ChIP-seq file = ['SRX050606.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 13:44:53: # Command line: callpeak -t SRX050606.bam -f BAM -g dm -n SRX050606.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX050606.10 # format = BAM # ChIP-seq file = ['SRX050606.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 13:44:53: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:44:53: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:44:53: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:44:53: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:44:53: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:44:53: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:44:58: 1000000 INFO @ Tue, 21 Apr 2015 13:44:59: 1000000 INFO @ Tue, 21 Apr 2015 13:44:59: 1000000 INFO @ Tue, 21 Apr 2015 13:45:04: 2000000 INFO @ Tue, 21 Apr 2015 13:45:04: 2000000 INFO @ Tue, 21 Apr 2015 13:45:04: 2000000 INFO @ Tue, 21 Apr 2015 13:45:09: 3000000 INFO @ Tue, 21 Apr 2015 13:45:10: 3000000 INFO @ Tue, 21 Apr 2015 13:45:10: 3000000 INFO @ Tue, 21 Apr 2015 13:45:14: 4000000 INFO @ Tue, 21 Apr 2015 13:45:15: 4000000 INFO @ Tue, 21 Apr 2015 13:45:15: 4000000 INFO @ Tue, 21 Apr 2015 13:45:19: 5000000 INFO @ Tue, 21 Apr 2015 13:45:21: 5000000 INFO @ Tue, 21 Apr 2015 13:45:21: 5000000 INFO @ Tue, 21 Apr 2015 13:45:24: 6000000 INFO @ Tue, 21 Apr 2015 13:45:26: 6000000 INFO @ Tue, 21 Apr 2015 13:45:26: 6000000 INFO @ Tue, 21 Apr 2015 13:45:30: 7000000 INFO @ Tue, 21 Apr 2015 13:45:32: 7000000 INFO @ Tue, 21 Apr 2015 13:45:32: 7000000 INFO @ Tue, 21 Apr 2015 13:45:35: 8000000 INFO @ Tue, 21 Apr 2015 13:45:38: 8000000 INFO @ Tue, 21 Apr 2015 13:45:38: 8000000 INFO @ Tue, 21 Apr 2015 13:45:40: 9000000 INFO @ Tue, 21 Apr 2015 13:45:43: 9000000 INFO @ Tue, 21 Apr 2015 13:45:43: 9000000 INFO @ Tue, 21 Apr 2015 13:45:45: 10000000 INFO @ Tue, 21 Apr 2015 13:45:49: 10000000 INFO @ Tue, 21 Apr 2015 13:45:49: 10000000 INFO @ Tue, 21 Apr 2015 13:45:50: 11000000 INFO @ Tue, 21 Apr 2015 13:45:54: 11000000 INFO @ Tue, 21 Apr 2015 13:45:54: 11000000 INFO @ Tue, 21 Apr 2015 13:45:56: 12000000 INFO @ Tue, 21 Apr 2015 13:46:00: 12000000 INFO @ Tue, 21 Apr 2015 13:46:00: 12000000 INFO @ Tue, 21 Apr 2015 13:46:01: 13000000 INFO @ Tue, 21 Apr 2015 13:46:05: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:46:05: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:46:05: #1 total tags in treatment: 13730425 INFO @ Tue, 21 Apr 2015 13:46:05: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:46:05: #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 13:46:05: 13000000 INFO @ Tue, 21 Apr 2015 13:46:05: 13000000 INFO @ Tue, 21 Apr 2015 13:46:07: #1 tags after filtering in treatment: 13728538 INFO @ Tue, 21 Apr 2015 13:46:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:46:07: #1 finished! INFO @ Tue, 21 Apr 2015 13:46:07: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:46:10: #2 number of paired peaks: 665 WARNING @ Tue, 21 Apr 2015 13:46:10: Fewer paired peaks (665) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 665 pairs to build model! INFO @ Tue, 21 Apr 2015 13:46:10: start model_add_line... INFO @ Tue, 21 Apr 2015 13:46:10: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:46:10: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:46:10: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:46:10: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:46:10: #1 total tags in treatment: 13730425 INFO @ Tue, 21 Apr 2015 13:46:10: #1 total tags in treatment: 13730425 INFO @ Tue, 21 Apr 2015 13:46:10: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:46:10: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:46:10: #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 13:46:10: #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 13:46:12: #1 tags after filtering in treatment: 13728538 INFO @ Tue, 21 Apr 2015 13:46:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:46:12: #1 finished! INFO @ Tue, 21 Apr 2015 13:46:12: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:46:13: #1 tags after filtering in treatment: 13728538 INFO @ Tue, 21 Apr 2015 13:46:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:46:13: #1 finished! INFO @ Tue, 21 Apr 2015 13:46:13: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:46:14: #2 number of paired peaks: 665 WARNING @ Tue, 21 Apr 2015 13:46:14: Fewer paired peaks (665) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 665 pairs to build model! INFO @ Tue, 21 Apr 2015 13:46:14: start model_add_line... INFO @ Tue, 21 Apr 2015 13:46:15: #2 number of paired peaks: 665 WARNING @ Tue, 21 Apr 2015 13:46:15: Fewer paired peaks (665) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 665 pairs to build model! INFO @ Tue, 21 Apr 2015 13:46:15: start model_add_line... INFO @ Tue, 21 Apr 2015 13:46:15: start X-correlation... INFO @ Tue, 21 Apr 2015 13:46:15: end of X-cor INFO @ Tue, 21 Apr 2015 13:46:15: #2 finished! INFO @ Tue, 21 Apr 2015 13:46:15: #2 predicted fragment length is 137 bps INFO @ Tue, 21 Apr 2015 13:46:15: #2 alternative fragment length(s) may be 137 bps INFO @ Tue, 21 Apr 2015 13:46:15: #2.2 Generate R script for model : SRX050606.05_model.r INFO @ Tue, 21 Apr 2015 13:46:15: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:46:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:46:20: start X-correlation... INFO @ Tue, 21 Apr 2015 13:46:20: end of X-cor INFO @ Tue, 21 Apr 2015 13:46:20: #2 finished! INFO @ Tue, 21 Apr 2015 13:46:20: #2 predicted fragment length is 137 bps INFO @ Tue, 21 Apr 2015 13:46:20: #2 alternative fragment length(s) may be 137 bps INFO @ Tue, 21 Apr 2015 13:46:20: #2.2 Generate R script for model : SRX050606.20_model.r INFO @ Tue, 21 Apr 2015 13:46:20: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:46:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:46:21: start X-correlation... INFO @ Tue, 21 Apr 2015 13:46:21: end of X-cor INFO @ Tue, 21 Apr 2015 13:46:21: #2 finished! INFO @ Tue, 21 Apr 2015 13:46:21: #2 predicted fragment length is 137 bps INFO @ Tue, 21 Apr 2015 13:46:21: #2 alternative fragment length(s) may be 137 bps INFO @ Tue, 21 Apr 2015 13:46:21: #2.2 Generate R script for model : SRX050606.10_model.r INFO @ Tue, 21 Apr 2015 13:46:21: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:46:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:47:28: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:47:32: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:47:34: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:48:26: #4 Write output xls file... SRX050606.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:48:26: #4 Write peak in narrowPeak format file... SRX050606.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:48:26: #4 Write summits bed file... SRX050606.20_summits.bed INFO @ Tue, 21 Apr 2015 13:48:26: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (2066 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:48:27: #4 Write output xls file... SRX050606.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:48:27: #4 Write peak in narrowPeak format file... SRX050606.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:48:27: #4 Write summits bed file... SRX050606.10_summits.bed INFO @ Tue, 21 Apr 2015 13:48:27: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (3977 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:48:28: #4 Write output xls file... SRX050606.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:48:28: #4 Write peak in narrowPeak format file... SRX050606.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:48:28: #4 Write summits bed file... SRX050606.05_summits.bed INFO @ Tue, 21 Apr 2015 13:48:28: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (6279 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。