Job ID = 2162379 sra ファイルのダウンロード中... Completed: 695709K bytes transferred in 8 seconds (675770K 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 4000 0 4000 0 0 6741 0 --:--:-- --:--:-- --:--:-- 9950 100 35028 0 35028 0 0 44718 0 --:--:-- --:--:-- --:--:-- 59168 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 11397432 spots for /home/okishinya/chipatlas/results/dm3/SRX059817/SRR191859.sra Written 11397432 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: 00:06:46 11397432 reads; of these: 11397432 (100.00%) were unpaired; of these: 185111 (1.62%) aligned 0 times 9348560 (82.02%) aligned exactly 1 time 1863761 (16.35%) aligned >1 times 98.38% overall alignment rate Time searching: 00:06:46 Overall time: 00:06:46 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] 995595 / 11212321 = 0.0888 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 13:49:56: # Command line: callpeak -t SRX059817.bam -f BAM -g dm -n SRX059817.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX059817.10 # format = BAM # ChIP-seq file = ['SRX059817.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 13:49:56: # Command line: callpeak -t SRX059817.bam -f BAM -g dm -n SRX059817.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX059817.05 # format = BAM # ChIP-seq file = ['SRX059817.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 13:49:56: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:49:56: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:49:56: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:49:56: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:49:56: # Command line: callpeak -t SRX059817.bam -f BAM -g dm -n SRX059817.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX059817.20 # format = BAM # ChIP-seq file = ['SRX059817.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 13:49:56: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:49:56: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:50:04: 1000000 INFO @ Tue, 21 Apr 2015 13:50:05: 1000000 INFO @ Tue, 21 Apr 2015 13:50:05: 1000000 INFO @ Tue, 21 Apr 2015 13:50:12: 2000000 INFO @ Tue, 21 Apr 2015 13:50:15: 2000000 INFO @ Tue, 21 Apr 2015 13:50:15: 2000000 INFO @ Tue, 21 Apr 2015 13:50:19: 3000000 INFO @ Tue, 21 Apr 2015 13:50:24: 3000000 INFO @ Tue, 21 Apr 2015 13:50:24: 3000000 INFO @ Tue, 21 Apr 2015 13:50:27: 4000000 INFO @ Tue, 21 Apr 2015 13:50:33: 4000000 INFO @ Tue, 21 Apr 2015 13:50:33: 4000000 INFO @ Tue, 21 Apr 2015 13:50:35: 5000000 INFO @ Tue, 21 Apr 2015 13:50:42: 5000000 INFO @ Tue, 21 Apr 2015 13:50:42: 5000000 INFO @ Tue, 21 Apr 2015 13:50:42: 6000000 INFO @ Tue, 21 Apr 2015 13:50:50: 7000000 INFO @ Tue, 21 Apr 2015 13:50:51: 6000000 INFO @ Tue, 21 Apr 2015 13:50:51: 6000000 INFO @ Tue, 21 Apr 2015 13:50:58: 8000000 INFO @ Tue, 21 Apr 2015 13:51:00: 7000000 INFO @ Tue, 21 Apr 2015 13:51:00: 7000000 INFO @ Tue, 21 Apr 2015 13:51:05: 9000000 INFO @ Tue, 21 Apr 2015 13:51:10: 8000000 INFO @ Tue, 21 Apr 2015 13:51:10: 8000000 INFO @ Tue, 21 Apr 2015 13:51:13: 10000000 INFO @ Tue, 21 Apr 2015 13:51:15: #1 tag size is determined as 100 bps INFO @ Tue, 21 Apr 2015 13:51:15: #1 tag size = 100 INFO @ Tue, 21 Apr 2015 13:51:15: #1 total tags in treatment: 10216726 INFO @ Tue, 21 Apr 2015 13:51:15: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:51:15: #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 13:51:17: #1 tags after filtering in treatment: 10211508 INFO @ Tue, 21 Apr 2015 13:51:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:51:17: #1 finished! INFO @ Tue, 21 Apr 2015 13:51:17: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:51:19: #2 number of paired peaks: 135 WARNING @ Tue, 21 Apr 2015 13:51:19: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Tue, 21 Apr 2015 13:51:19: start model_add_line... INFO @ Tue, 21 Apr 2015 13:51:19: 9000000 INFO @ Tue, 21 Apr 2015 13:51:19: 9000000 INFO @ Tue, 21 Apr 2015 13:51:20: start X-correlation... INFO @ Tue, 21 Apr 2015 13:51:20: end of X-cor INFO @ Tue, 21 Apr 2015 13:51:20: #2 finished! INFO @ Tue, 21 Apr 2015 13:51:20: #2 predicted fragment length is 241 bps INFO @ Tue, 21 Apr 2015 13:51:20: #2 alternative fragment length(s) may be 224,241 bps INFO @ Tue, 21 Apr 2015 13:51:20: #2.2 Generate R script for model : SRX059817.20_model.r INFO @ Tue, 21 Apr 2015 13:51:20: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:51:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:51:28: 10000000 INFO @ Tue, 21 Apr 2015 13:51:28: 10000000 INFO @ Tue, 21 Apr 2015 13:51:30: #1 tag size is determined as 100 bps INFO @ Tue, 21 Apr 2015 13:51:30: #1 tag size = 100 INFO @ Tue, 21 Apr 2015 13:51:30: #1 total tags in treatment: 10216726 INFO @ Tue, 21 Apr 2015 13:51:30: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:51:30: #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 13:51:30: #1 tag size is determined as 100 bps INFO @ Tue, 21 Apr 2015 13:51:30: #1 tag size = 100 INFO @ Tue, 21 Apr 2015 13:51:30: #1 total tags in treatment: 10216726 INFO @ Tue, 21 Apr 2015 13:51:30: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:51:30: #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 13:51:32: #1 tags after filtering in treatment: 10211508 INFO @ Tue, 21 Apr 2015 13:51:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:51:32: #1 finished! INFO @ Tue, 21 Apr 2015 13:51:32: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:51:32: #1 tags after filtering in treatment: 10211508 INFO @ Tue, 21 Apr 2015 13:51:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:51:32: #1 finished! INFO @ Tue, 21 Apr 2015 13:51:32: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:51:34: #2 number of paired peaks: 135 WARNING @ Tue, 21 Apr 2015 13:51:34: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Tue, 21 Apr 2015 13:51:34: start model_add_line... INFO @ Tue, 21 Apr 2015 13:51:34: #2 number of paired peaks: 135 WARNING @ Tue, 21 Apr 2015 13:51:34: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Tue, 21 Apr 2015 13:51:34: start model_add_line... INFO @ Tue, 21 Apr 2015 13:51:35: start X-correlation... INFO @ Tue, 21 Apr 2015 13:51:35: end of X-cor INFO @ Tue, 21 Apr 2015 13:51:35: #2 finished! INFO @ Tue, 21 Apr 2015 13:51:35: #2 predicted fragment length is 241 bps INFO @ Tue, 21 Apr 2015 13:51:35: #2 alternative fragment length(s) may be 224,241 bps INFO @ Tue, 21 Apr 2015 13:51:35: #2.2 Generate R script for model : SRX059817.10_model.r INFO @ Tue, 21 Apr 2015 13:51:35: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:51:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:51:35: start X-correlation... INFO @ Tue, 21 Apr 2015 13:51:35: end of X-cor INFO @ Tue, 21 Apr 2015 13:51:35: #2 finished! INFO @ Tue, 21 Apr 2015 13:51:35: #2 predicted fragment length is 241 bps INFO @ Tue, 21 Apr 2015 13:51:35: #2 alternative fragment length(s) may be 224,241 bps INFO @ Tue, 21 Apr 2015 13:51:35: #2.2 Generate R script for model : SRX059817.05_model.r INFO @ Tue, 21 Apr 2015 13:51:35: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:51:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:52:16: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:52:33: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:52:36: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:52:56: #4 Write output xls file... SRX059817.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:52:56: #4 Write peak in narrowPeak format file... SRX059817.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:52:56: #4 Write summits bed file... SRX059817.20_summits.bed INFO @ Tue, 21 Apr 2015 13:52:56: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (336 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:53:20: #4 Write output xls file... SRX059817.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:53:20: #4 Write peak in narrowPeak format file... SRX059817.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:53:21: #4 Write summits bed file... SRX059817.05_summits.bed INFO @ Tue, 21 Apr 2015 13:53:21: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3810 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:53:22: #4 Write output xls file... SRX059817.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:53:22: #4 Write peak in narrowPeak format file... SRX059817.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:53:22: #4 Write summits bed file... SRX059817.10_summits.bed INFO @ Tue, 21 Apr 2015 13:53:22: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1631 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。