Job ID = 2161796 sra ファイルのダウンロード中... Completed: 328575K bytes transferred in 5 seconds (471933K 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 38282 0 38282 0 0 33544 0 --:--:-- 0:00:01 --:--:-- 40296 100 44454 0 44454 0 0 38924 0 --:--:-- 0:00:01 --:--:-- 46744 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 14017947 spots for /home/okishinya/chipatlas/results/dm3/SRX033317/SRR080711.sra Written 14017947 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: 00:03:56 14017947 reads; of these: 14017947 (100.00%) were unpaired; of these: 2373571 (16.93%) aligned 0 times 8675617 (61.89%) aligned exactly 1 time 2968759 (21.18%) aligned >1 times 83.07% overall alignment rate Time searching: 00:03:56 Overall time: 00:03:56 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] 3498337 / 11644376 = 0.3004 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 13:10:51: # Command line: callpeak -t SRX033317.bam -f BAM -g dm -n SRX033317.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX033317.05 # format = BAM # ChIP-seq file = ['SRX033317.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 13:10:51: # Command line: callpeak -t SRX033317.bam -f BAM -g dm -n SRX033317.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX033317.10 # format = BAM # ChIP-seq file = ['SRX033317.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 13:10:51: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:10:51: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:10:51: # Command line: callpeak -t SRX033317.bam -f BAM -g dm -n SRX033317.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX033317.20 # format = BAM # ChIP-seq file = ['SRX033317.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 13:10:51: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:10:51: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:10:51: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:10:51: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:10:57: 1000000 INFO @ Tue, 21 Apr 2015 13:10:57: 1000000 INFO @ Tue, 21 Apr 2015 13:10:57: 1000000 INFO @ Tue, 21 Apr 2015 13:11:03: 2000000 INFO @ Tue, 21 Apr 2015 13:11:03: 2000000 INFO @ Tue, 21 Apr 2015 13:11:03: 2000000 INFO @ Tue, 21 Apr 2015 13:11:08: 3000000 INFO @ Tue, 21 Apr 2015 13:11:10: 3000000 INFO @ Tue, 21 Apr 2015 13:11:10: 3000000 INFO @ Tue, 21 Apr 2015 13:11:14: 4000000 INFO @ Tue, 21 Apr 2015 13:11:16: 4000000 INFO @ Tue, 21 Apr 2015 13:11:16: 4000000 INFO @ Tue, 21 Apr 2015 13:11:20: 5000000 INFO @ Tue, 21 Apr 2015 13:11:22: 5000000 INFO @ Tue, 21 Apr 2015 13:11:22: 5000000 INFO @ Tue, 21 Apr 2015 13:11:26: 6000000 INFO @ Tue, 21 Apr 2015 13:11:28: 6000000 INFO @ Tue, 21 Apr 2015 13:11:28: 6000000 INFO @ Tue, 21 Apr 2015 13:11:32: 7000000 INFO @ Tue, 21 Apr 2015 13:11:34: 7000000 INFO @ Tue, 21 Apr 2015 13:11:34: 7000000 INFO @ Tue, 21 Apr 2015 13:11:38: 8000000 INFO @ Tue, 21 Apr 2015 13:11:39: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:11:39: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:11:39: #1 total tags in treatment: 8146039 INFO @ Tue, 21 Apr 2015 13:11:39: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:11:39: #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 13:11:40: 8000000 INFO @ Tue, 21 Apr 2015 13:11:41: #1 tags after filtering in treatment: 8145249 INFO @ Tue, 21 Apr 2015 13:11:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:11:41: #1 finished! INFO @ Tue, 21 Apr 2015 13:11:41: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:11:41: 8000000 INFO @ Tue, 21 Apr 2015 13:11:41: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:11:41: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:11:41: #1 total tags in treatment: 8146039 INFO @ Tue, 21 Apr 2015 13:11:41: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:11:41: #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 13:11:42: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:11:42: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:11:42: #1 total tags in treatment: 8146039 INFO @ Tue, 21 Apr 2015 13:11:42: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:11:42: #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 13:11:42: #2 number of paired peaks: 234 WARNING @ Tue, 21 Apr 2015 13:11:42: Fewer paired peaks (234) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 234 pairs to build model! INFO @ Tue, 21 Apr 2015 13:11:42: start model_add_line... INFO @ Tue, 21 Apr 2015 13:11:43: #1 tags after filtering in treatment: 8145249 INFO @ Tue, 21 Apr 2015 13:11:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:11:43: #1 finished! INFO @ Tue, 21 Apr 2015 13:11:43: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:11:43: #1 tags after filtering in treatment: 8145249 INFO @ Tue, 21 Apr 2015 13:11:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:11:43: #1 finished! INFO @ Tue, 21 Apr 2015 13:11:43: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:11:44: start X-correlation... INFO @ Tue, 21 Apr 2015 13:11:44: end of X-cor INFO @ Tue, 21 Apr 2015 13:11:44: #2 finished! INFO @ Tue, 21 Apr 2015 13:11:44: #2 predicted fragment length is 37 bps INFO @ Tue, 21 Apr 2015 13:11:44: #2 alternative fragment length(s) may be 37 bps INFO @ Tue, 21 Apr 2015 13:11:44: #2.2 Generate R script for model : SRX033317.20_model.r WARNING @ Tue, 21 Apr 2015 13:11:44: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:11:44: #2 You may need to consider one of the other alternative d(s): 37 WARNING @ Tue, 21 Apr 2015 13:11:44: #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 13:11:44: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:11:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:11:44: #2 number of paired peaks: 234 WARNING @ Tue, 21 Apr 2015 13:11:44: Fewer paired peaks (234) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 234 pairs to build model! INFO @ Tue, 21 Apr 2015 13:11:44: start model_add_line... INFO @ Tue, 21 Apr 2015 13:11:45: #2 number of paired peaks: 234 WARNING @ Tue, 21 Apr 2015 13:11:45: Fewer paired peaks (234) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 234 pairs to build model! INFO @ Tue, 21 Apr 2015 13:11:45: start model_add_line... INFO @ Tue, 21 Apr 2015 13:11:46: start X-correlation... INFO @ Tue, 21 Apr 2015 13:11:46: end of X-cor INFO @ Tue, 21 Apr 2015 13:11:46: #2 finished! INFO @ Tue, 21 Apr 2015 13:11:46: #2 predicted fragment length is 37 bps INFO @ Tue, 21 Apr 2015 13:11:46: #2 alternative fragment length(s) may be 37 bps INFO @ Tue, 21 Apr 2015 13:11:46: #2.2 Generate R script for model : SRX033317.05_model.r WARNING @ Tue, 21 Apr 2015 13:11:46: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:11:46: #2 You may need to consider one of the other alternative d(s): 37 WARNING @ Tue, 21 Apr 2015 13:11:46: #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 13:11:46: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:11:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:11:46: start X-correlation... INFO @ Tue, 21 Apr 2015 13:11:46: end of X-cor INFO @ Tue, 21 Apr 2015 13:11:46: #2 finished! INFO @ Tue, 21 Apr 2015 13:11:46: #2 predicted fragment length is 37 bps INFO @ Tue, 21 Apr 2015 13:11:46: #2 alternative fragment length(s) may be 37 bps INFO @ Tue, 21 Apr 2015 13:11:46: #2.2 Generate R script for model : SRX033317.10_model.r WARNING @ Tue, 21 Apr 2015 13:11:46: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:11:46: #2 You may need to consider one of the other alternative d(s): 37 WARNING @ Tue, 21 Apr 2015 13:11:46: #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 13:11:46: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:11:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:12:27: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:12:29: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:12:31: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:13:01: #4 Write output xls file... SRX033317.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:13:01: #4 Write peak in narrowPeak format file... SRX033317.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:13:01: #4 Write summits bed file... SRX033317.05_summits.bed INFO @ Tue, 21 Apr 2015 13:13:01: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (750 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:13:01: #4 Write output xls file... SRX033317.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:13:01: #4 Write peak in narrowPeak format file... SRX033317.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:13:01: #4 Write summits bed file... SRX033317.20_summits.bed INFO @ Tue, 21 Apr 2015 13:13:01: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (423 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:13:04: #4 Write output xls file... SRX033317.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:13:04: #4 Write peak in narrowPeak format file... SRX033317.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:13:04: #4 Write summits bed file... SRX033317.10_summits.bed INFO @ Tue, 21 Apr 2015 13:13:04: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (548 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。