Job ID = 2161332 sra ファイルのダウンロード中... Completed: 450191K bytes transferred in 6 seconds (531839K bits/sec), in 3 files, 4 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 35989 0 35989 0 0 41235 0 --:--:-- --:--:-- --:--:-- 53002 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 4598277 spots for /home/okishinya/chipatlas/results/dm3/SRX018628/SRR039092.sra Written 4598277 spots total Written 5082815 spots for /home/okishinya/chipatlas/results/dm3/SRX018628/SRR039091.sra Written 5082815 spots total Written 6849421 spots for /home/okishinya/chipatlas/results/dm3/SRX018628/SRR039090.sra Written 6849421 spots total 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: 00:03:03 16530513 reads; of these: 16530513 (100.00%) were unpaired; of these: 9477978 (57.34%) aligned 0 times 4942002 (29.90%) aligned exactly 1 time 2110533 (12.77%) aligned >1 times 42.66% overall alignment rate Time searching: 00:03:03 Overall time: 00:03:03 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] 519230 / 7052535 = 0.0736 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 12:27:51: # Command line: callpeak -t SRX018628.bam -f BAM -g dm -n SRX018628.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX018628.20 # format = BAM # ChIP-seq file = ['SRX018628.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 12:27:51: # Command line: callpeak -t SRX018628.bam -f BAM -g dm -n SRX018628.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX018628.05 # format = BAM # ChIP-seq file = ['SRX018628.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 12:27:51: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:27:51: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:27:51: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:27:51: # Command line: callpeak -t SRX018628.bam -f BAM -g dm -n SRX018628.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX018628.10 # format = BAM # ChIP-seq file = ['SRX018628.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 12:27:51: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:27:51: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:27:51: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:27:56: 1000000 INFO @ Tue, 21 Apr 2015 12:27:56: 1000000 INFO @ Tue, 21 Apr 2015 12:27:56: 1000000 INFO @ Tue, 21 Apr 2015 12:28:01: 2000000 INFO @ Tue, 21 Apr 2015 12:28:02: 2000000 INFO @ Tue, 21 Apr 2015 12:28:02: 2000000 INFO @ Tue, 21 Apr 2015 12:28:07: 3000000 INFO @ Tue, 21 Apr 2015 12:28:07: 3000000 INFO @ Tue, 21 Apr 2015 12:28:07: 3000000 INFO @ Tue, 21 Apr 2015 12:28:12: 4000000 INFO @ Tue, 21 Apr 2015 12:28:13: 4000000 INFO @ Tue, 21 Apr 2015 12:28:13: 4000000 INFO @ Tue, 21 Apr 2015 12:28:18: 5000000 INFO @ Tue, 21 Apr 2015 12:28:18: 5000000 INFO @ Tue, 21 Apr 2015 12:28:18: 5000000 INFO @ Tue, 21 Apr 2015 12:28:23: 6000000 INFO @ Tue, 21 Apr 2015 12:28:24: 6000000 INFO @ Tue, 21 Apr 2015 12:28:24: 6000000 INFO @ Tue, 21 Apr 2015 12:28:26: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 12:28:26: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 12:28:26: #1 total tags in treatment: 6533305 INFO @ Tue, 21 Apr 2015 12:28:26: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:28:26: #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 12:28:27: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 12:28:27: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 12:28:27: #1 total tags in treatment: 6533305 INFO @ Tue, 21 Apr 2015 12:28:27: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:28:27: #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 12:28:27: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 12:28:27: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 12:28:27: #1 total tags in treatment: 6533305 INFO @ Tue, 21 Apr 2015 12:28:27: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:28:27: #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 12:28:27: #1 tags after filtering in treatment: 6532768 INFO @ Tue, 21 Apr 2015 12:28:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:28:27: #1 finished! INFO @ Tue, 21 Apr 2015 12:28:27: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:28:28: #1 tags after filtering in treatment: 6532768 INFO @ Tue, 21 Apr 2015 12:28:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:28:28: #1 finished! INFO @ Tue, 21 Apr 2015 12:28:28: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:28:28: #1 tags after filtering in treatment: 6532768 INFO @ Tue, 21 Apr 2015 12:28:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:28:28: #1 finished! INFO @ Tue, 21 Apr 2015 12:28:28: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:28:29: #2 number of paired peaks: 601 WARNING @ Tue, 21 Apr 2015 12:28:29: Fewer paired peaks (601) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 601 pairs to build model! INFO @ Tue, 21 Apr 2015 12:28:29: start model_add_line... INFO @ Tue, 21 Apr 2015 12:28:29: #2 number of paired peaks: 601 WARNING @ Tue, 21 Apr 2015 12:28:29: Fewer paired peaks (601) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 601 pairs to build model! INFO @ Tue, 21 Apr 2015 12:28:29: start model_add_line... INFO @ Tue, 21 Apr 2015 12:28:29: #2 number of paired peaks: 601 WARNING @ Tue, 21 Apr 2015 12:28:29: Fewer paired peaks (601) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 601 pairs to build model! INFO @ Tue, 21 Apr 2015 12:28:29: start model_add_line... INFO @ Tue, 21 Apr 2015 12:28:32: start X-correlation... INFO @ Tue, 21 Apr 2015 12:28:32: end of X-cor INFO @ Tue, 21 Apr 2015 12:28:32: #2 finished! INFO @ Tue, 21 Apr 2015 12:28:32: #2 predicted fragment length is 46 bps INFO @ Tue, 21 Apr 2015 12:28:32: #2 alternative fragment length(s) may be 46 bps INFO @ Tue, 21 Apr 2015 12:28:32: #2.2 Generate R script for model : SRX018628.20_model.r WARNING @ Tue, 21 Apr 2015 12:28:32: #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 12:28:32: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Tue, 21 Apr 2015 12:28:32: #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 12:28:32: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:28:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:28:32: start X-correlation... INFO @ Tue, 21 Apr 2015 12:28:32: end of X-cor INFO @ Tue, 21 Apr 2015 12:28:32: #2 finished! INFO @ Tue, 21 Apr 2015 12:28:32: #2 predicted fragment length is 46 bps INFO @ Tue, 21 Apr 2015 12:28:32: #2 alternative fragment length(s) may be 46 bps INFO @ Tue, 21 Apr 2015 12:28:32: #2.2 Generate R script for model : SRX018628.10_model.r WARNING @ Tue, 21 Apr 2015 12:28:32: #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 12:28:32: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Tue, 21 Apr 2015 12:28:32: #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 12:28:32: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:28:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:28:32: start X-correlation... INFO @ Tue, 21 Apr 2015 12:28:32: end of X-cor INFO @ Tue, 21 Apr 2015 12:28:32: #2 finished! INFO @ Tue, 21 Apr 2015 12:28:32: #2 predicted fragment length is 46 bps INFO @ Tue, 21 Apr 2015 12:28:32: #2 alternative fragment length(s) may be 46 bps INFO @ Tue, 21 Apr 2015 12:28:32: #2.2 Generate R script for model : SRX018628.05_model.r WARNING @ Tue, 21 Apr 2015 12:28:32: #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 12:28:32: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Tue, 21 Apr 2015 12:28:32: #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 12:28:32: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:28:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:29:09: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:29:10: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:29:10: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:29:35: #4 Write output xls file... SRX018628.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:29:35: #4 Write peak in narrowPeak format file... SRX018628.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:29:35: #4 Write summits bed file... SRX018628.05_summits.bed INFO @ Tue, 21 Apr 2015 12:29:35: Done! pass1 - making usageList (15 chroms): 22 millis pass2 - checking and writing primary data (2114 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:29:36: #4 Write output xls file... SRX018628.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:29:36: #4 Write peak in narrowPeak format file... SRX018628.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:29:36: #4 Write summits bed file... SRX018628.20_summits.bed INFO @ Tue, 21 Apr 2015 12:29:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (303 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:29:38: #4 Write output xls file... SRX018628.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:29:38: #4 Write peak in narrowPeak format file... SRX018628.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:29:38: #4 Write summits bed file... SRX018628.10_summits.bed INFO @ Tue, 21 Apr 2015 12:29:38: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1004 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。