Job ID = 2161336 sra ファイルのダウンロード中... Completed: 333441K bytes transferred in 6 seconds (419942K bits/sec), in 2 files, 3 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 35997 0 35997 0 0 50150 0 --:--:-- --:--:-- --:--:-- 68305 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 5703341 spots for /home/okishinya/chipatlas/results/dm3/SRX018632/SRR039103.sra Written 5703341 spots total Written 6070585 spots for /home/okishinya/chipatlas/results/dm3/SRX018632/SRR039104.sra Written 6070585 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: 00:03:09 11773926 reads; of these: 11773926 (100.00%) were unpaired; of these: 3240152 (27.52%) aligned 0 times 6067787 (51.54%) aligned exactly 1 time 2465987 (20.94%) aligned >1 times 72.48% overall alignment rate Time searching: 00:03:09 Overall time: 00:03:09 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] 530641 / 8533774 = 0.0622 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 12:28:45: # Command line: callpeak -t SRX018632.bam -f BAM -g dm -n SRX018632.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX018632.05 # format = BAM # ChIP-seq file = ['SRX018632.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 12:28:45: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:28:45: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:28:45: # Command line: callpeak -t SRX018632.bam -f BAM -g dm -n SRX018632.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX018632.20 # format = BAM # ChIP-seq file = ['SRX018632.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 12:28:45: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:28:45: # Command line: callpeak -t SRX018632.bam -f BAM -g dm -n SRX018632.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX018632.10 # format = BAM # ChIP-seq file = ['SRX018632.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 12:28:45: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:28:45: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:28:45: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:28:50: 1000000 INFO @ Tue, 21 Apr 2015 12:28:50: 1000000 INFO @ Tue, 21 Apr 2015 12:28:51: 1000000 INFO @ Tue, 21 Apr 2015 12:28:55: 2000000 INFO @ Tue, 21 Apr 2015 12:28:56: 2000000 INFO @ Tue, 21 Apr 2015 12:28:56: 2000000 INFO @ Tue, 21 Apr 2015 12:29:00: 3000000 INFO @ Tue, 21 Apr 2015 12:29:01: 3000000 INFO @ Tue, 21 Apr 2015 12:29:02: 3000000 INFO @ Tue, 21 Apr 2015 12:29:05: 4000000 INFO @ Tue, 21 Apr 2015 12:29:07: 4000000 INFO @ Tue, 21 Apr 2015 12:29:08: 4000000 INFO @ Tue, 21 Apr 2015 12:29:10: 5000000 INFO @ Tue, 21 Apr 2015 12:29:13: 5000000 INFO @ Tue, 21 Apr 2015 12:29:14: 5000000 INFO @ Tue, 21 Apr 2015 12:29:15: 6000000 INFO @ Tue, 21 Apr 2015 12:29:18: 6000000 INFO @ Tue, 21 Apr 2015 12:29:20: 6000000 INFO @ Tue, 21 Apr 2015 12:29:20: 7000000 INFO @ Tue, 21 Apr 2015 12:29:24: 7000000 INFO @ Tue, 21 Apr 2015 12:29:25: 8000000 INFO @ Tue, 21 Apr 2015 12:29:25: #1 tag size is determined as 39 bps INFO @ Tue, 21 Apr 2015 12:29:25: #1 tag size = 39 INFO @ Tue, 21 Apr 2015 12:29:25: #1 total tags in treatment: 8003133 INFO @ Tue, 21 Apr 2015 12:29:25: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:29:25: #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 12:29:26: 7000000 INFO @ Tue, 21 Apr 2015 12:29:26: #1 tags after filtering in treatment: 8002518 INFO @ Tue, 21 Apr 2015 12:29:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:29:26: #1 finished! INFO @ Tue, 21 Apr 2015 12:29:26: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:29:28: #2 number of paired peaks: 694 WARNING @ Tue, 21 Apr 2015 12:29:28: Fewer paired peaks (694) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 694 pairs to build model! INFO @ Tue, 21 Apr 2015 12:29:28: start model_add_line... INFO @ Tue, 21 Apr 2015 12:29:30: 8000000 INFO @ Tue, 21 Apr 2015 12:29:30: #1 tag size is determined as 39 bps INFO @ Tue, 21 Apr 2015 12:29:30: #1 tag size = 39 INFO @ Tue, 21 Apr 2015 12:29:30: #1 total tags in treatment: 8003133 INFO @ Tue, 21 Apr 2015 12:29:30: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:29:30: #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 12:29:31: 8000000 INFO @ Tue, 21 Apr 2015 12:29:31: #1 tags after filtering in treatment: 8002518 INFO @ Tue, 21 Apr 2015 12:29:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:29:31: #1 finished! INFO @ Tue, 21 Apr 2015 12:29:31: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:29:31: #1 tag size is determined as 39 bps INFO @ Tue, 21 Apr 2015 12:29:31: #1 tag size = 39 INFO @ Tue, 21 Apr 2015 12:29:31: #1 total tags in treatment: 8003133 INFO @ Tue, 21 Apr 2015 12:29:31: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:29:31: #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 12:29:32: start X-correlation... INFO @ Tue, 21 Apr 2015 12:29:32: end of X-cor INFO @ Tue, 21 Apr 2015 12:29:32: #2 finished! INFO @ Tue, 21 Apr 2015 12:29:32: #2 predicted fragment length is 55 bps INFO @ Tue, 21 Apr 2015 12:29:32: #2 alternative fragment length(s) may be 55 bps INFO @ Tue, 21 Apr 2015 12:29:32: #2.2 Generate R script for model : SRX018632.05_model.r WARNING @ Tue, 21 Apr 2015 12:29:32: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:29:32: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Tue, 21 Apr 2015 12:29:32: #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 12:29:32: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:29:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:29:33: #1 tags after filtering in treatment: 8002518 INFO @ Tue, 21 Apr 2015 12:29:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:29:33: #1 finished! INFO @ Tue, 21 Apr 2015 12:29:33: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:29:33: #2 number of paired peaks: 694 WARNING @ Tue, 21 Apr 2015 12:29:33: Fewer paired peaks (694) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 694 pairs to build model! INFO @ Tue, 21 Apr 2015 12:29:33: start model_add_line... INFO @ Tue, 21 Apr 2015 12:29:34: #2 number of paired peaks: 694 WARNING @ Tue, 21 Apr 2015 12:29:34: Fewer paired peaks (694) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 694 pairs to build model! INFO @ Tue, 21 Apr 2015 12:29:34: start model_add_line... INFO @ Tue, 21 Apr 2015 12:29:37: start X-correlation... INFO @ Tue, 21 Apr 2015 12:29:37: end of X-cor INFO @ Tue, 21 Apr 2015 12:29:37: #2 finished! INFO @ Tue, 21 Apr 2015 12:29:37: #2 predicted fragment length is 55 bps INFO @ Tue, 21 Apr 2015 12:29:37: #2 alternative fragment length(s) may be 55 bps INFO @ Tue, 21 Apr 2015 12:29:37: #2.2 Generate R script for model : SRX018632.20_model.r WARNING @ Tue, 21 Apr 2015 12:29:37: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:29:37: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Tue, 21 Apr 2015 12:29:37: #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 12:29:37: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:29:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:29:39: start X-correlation... INFO @ Tue, 21 Apr 2015 12:29:39: end of X-cor INFO @ Tue, 21 Apr 2015 12:29:39: #2 finished! INFO @ Tue, 21 Apr 2015 12:29:39: #2 predicted fragment length is 55 bps INFO @ Tue, 21 Apr 2015 12:29:39: #2 alternative fragment length(s) may be 55 bps INFO @ Tue, 21 Apr 2015 12:29:39: #2.2 Generate R script for model : SRX018632.10_model.r WARNING @ Tue, 21 Apr 2015 12:29:39: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:29:39: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Tue, 21 Apr 2015 12:29:39: #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 12:29:39: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:29:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:30:17: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:30:23: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:30:26: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:30:49: #4 Write output xls file... SRX018632.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:30:49: #4 Write peak in narrowPeak format file... SRX018632.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:30:49: #4 Write summits bed file... SRX018632.05_summits.bed INFO @ Tue, 21 Apr 2015 12:30:49: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2647 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:30:57: #4 Write output xls file... SRX018632.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:30:57: #4 Write peak in narrowPeak format file... SRX018632.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:30:57: #4 Write summits bed file... SRX018632.20_summits.bed INFO @ Tue, 21 Apr 2015 12:30:57: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (880 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:31:00: #4 Write output xls file... SRX018632.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:31:00: #4 Write peak in narrowPeak format file... SRX018632.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:31:00: #4 Write summits bed file... SRX018632.10_summits.bed INFO @ Tue, 21 Apr 2015 12:31:00: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1591 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。