Job ID = 2161412 sra ファイルのダウンロード中... Completed: 399408K bytes transferred in 6 seconds (507891K 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 44427 0 44427 0 0 45741 0 --:--:-- --:--:-- --:--:-- 57030 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 16322948 spots for /home/okishinya/chipatlas/results/dm3/SRX025485/SRR063888.sra Written 16322948 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: 00:05:41 16322948 reads; of these: 16322948 (100.00%) were unpaired; of these: 933331 (5.72%) aligned 0 times 10910566 (66.84%) aligned exactly 1 time 4479051 (27.44%) aligned >1 times 94.28% overall alignment rate Time searching: 00:05:41 Overall time: 00:05:41 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] 3746814 / 15389617 = 0.2435 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 12:43:54: # Command line: callpeak -t SRX025485.bam -f BAM -g dm -n SRX025485.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX025485.10 # format = BAM # ChIP-seq file = ['SRX025485.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 12:43:54: # Command line: callpeak -t SRX025485.bam -f BAM -g dm -n SRX025485.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX025485.05 # format = BAM # ChIP-seq file = ['SRX025485.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 12:43:54: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:43:54: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:43:54: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:43:54: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:43:54: # Command line: callpeak -t SRX025485.bam -f BAM -g dm -n SRX025485.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX025485.20 # format = BAM # ChIP-seq file = ['SRX025485.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 12:43:54: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:43:54: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:44:00: 1000000 INFO @ Tue, 21 Apr 2015 12:44:00: 1000000 INFO @ Tue, 21 Apr 2015 12:44:00: 1000000 INFO @ Tue, 21 Apr 2015 12:44:05: 2000000 INFO @ Tue, 21 Apr 2015 12:44:06: 2000000 INFO @ Tue, 21 Apr 2015 12:44:06: 2000000 INFO @ Tue, 21 Apr 2015 12:44:11: 3000000 INFO @ Tue, 21 Apr 2015 12:44:13: 3000000 INFO @ Tue, 21 Apr 2015 12:44:13: 3000000 INFO @ Tue, 21 Apr 2015 12:44:17: 4000000 INFO @ Tue, 21 Apr 2015 12:44:19: 4000000 INFO @ Tue, 21 Apr 2015 12:44:19: 4000000 INFO @ Tue, 21 Apr 2015 12:44:22: 5000000 INFO @ Tue, 21 Apr 2015 12:44:25: 5000000 INFO @ Tue, 21 Apr 2015 12:44:25: 5000000 INFO @ Tue, 21 Apr 2015 12:44:28: 6000000 INFO @ Tue, 21 Apr 2015 12:44:31: 6000000 INFO @ Tue, 21 Apr 2015 12:44:31: 6000000 INFO @ Tue, 21 Apr 2015 12:44:33: 7000000 INFO @ Tue, 21 Apr 2015 12:44:37: 7000000 INFO @ Tue, 21 Apr 2015 12:44:37: 7000000 INFO @ Tue, 21 Apr 2015 12:44:39: 8000000 INFO @ Tue, 21 Apr 2015 12:44:44: 8000000 INFO @ Tue, 21 Apr 2015 12:44:44: 8000000 INFO @ Tue, 21 Apr 2015 12:44:45: 9000000 INFO @ Tue, 21 Apr 2015 12:44:50: 9000000 INFO @ Tue, 21 Apr 2015 12:44:50: 9000000 INFO @ Tue, 21 Apr 2015 12:44:50: 10000000 INFO @ Tue, 21 Apr 2015 12:44:56: 11000000 INFO @ Tue, 21 Apr 2015 12:44:56: 10000000 INFO @ Tue, 21 Apr 2015 12:44:56: 10000000 INFO @ Tue, 21 Apr 2015 12:45:00: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:45:00: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:45:00: #1 total tags in treatment: 11642803 INFO @ Tue, 21 Apr 2015 12:45:00: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:45:00: #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 12:45:02: #1 tags after filtering in treatment: 11640621 INFO @ Tue, 21 Apr 2015 12:45:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:45:02: #1 finished! INFO @ Tue, 21 Apr 2015 12:45:02: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:45:02: 11000000 INFO @ Tue, 21 Apr 2015 12:45:02: 11000000 INFO @ Tue, 21 Apr 2015 12:45:04: #2 number of paired peaks: 138 WARNING @ Tue, 21 Apr 2015 12:45:04: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Tue, 21 Apr 2015 12:45:04: start model_add_line... INFO @ Tue, 21 Apr 2015 12:45:05: start X-correlation... INFO @ Tue, 21 Apr 2015 12:45:05: end of X-cor INFO @ Tue, 21 Apr 2015 12:45:05: #2 finished! INFO @ Tue, 21 Apr 2015 12:45:05: #2 predicted fragment length is 39 bps INFO @ Tue, 21 Apr 2015 12:45:05: #2 alternative fragment length(s) may be 39 bps INFO @ Tue, 21 Apr 2015 12:45:05: #2.2 Generate R script for model : SRX025485.20_model.r WARNING @ Tue, 21 Apr 2015 12:45:05: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:45:05: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Tue, 21 Apr 2015 12:45:05: #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 12:45:05: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:45:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:45:06: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:45:06: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:45:06: #1 total tags in treatment: 11642803 INFO @ Tue, 21 Apr 2015 12:45:06: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:45:06: #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 12:45:06: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:45:06: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:45:06: #1 total tags in treatment: 11642803 INFO @ Tue, 21 Apr 2015 12:45:06: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:45:06: #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 12:45:08: #1 tags after filtering in treatment: 11640621 INFO @ Tue, 21 Apr 2015 12:45:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:45:08: #1 finished! INFO @ Tue, 21 Apr 2015 12:45:08: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:45:08: #1 tags after filtering in treatment: 11640621 INFO @ Tue, 21 Apr 2015 12:45:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:45:08: #1 finished! INFO @ Tue, 21 Apr 2015 12:45:08: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:45:10: #2 number of paired peaks: 138 WARNING @ Tue, 21 Apr 2015 12:45:10: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Tue, 21 Apr 2015 12:45:10: start model_add_line... INFO @ Tue, 21 Apr 2015 12:45:10: #2 number of paired peaks: 138 WARNING @ Tue, 21 Apr 2015 12:45:10: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Tue, 21 Apr 2015 12:45:10: start model_add_line... INFO @ Tue, 21 Apr 2015 12:45:11: start X-correlation... INFO @ Tue, 21 Apr 2015 12:45:11: end of X-cor INFO @ Tue, 21 Apr 2015 12:45:11: #2 finished! INFO @ Tue, 21 Apr 2015 12:45:11: #2 predicted fragment length is 39 bps INFO @ Tue, 21 Apr 2015 12:45:11: #2 alternative fragment length(s) may be 39 bps INFO @ Tue, 21 Apr 2015 12:45:11: #2.2 Generate R script for model : SRX025485.10_model.r WARNING @ Tue, 21 Apr 2015 12:45:11: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:45:11: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Tue, 21 Apr 2015 12:45:11: #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 12:45:11: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:45:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:45:12: start X-correlation... INFO @ Tue, 21 Apr 2015 12:45:12: end of X-cor INFO @ Tue, 21 Apr 2015 12:45:12: #2 finished! INFO @ Tue, 21 Apr 2015 12:45:12: #2 predicted fragment length is 39 bps INFO @ Tue, 21 Apr 2015 12:45:12: #2 alternative fragment length(s) may be 39 bps INFO @ Tue, 21 Apr 2015 12:45:12: #2.2 Generate R script for model : SRX025485.05_model.r WARNING @ Tue, 21 Apr 2015 12:45:12: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:45:12: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Tue, 21 Apr 2015 12:45:12: #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 12:45:12: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:45:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:46:08: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:46:12: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:46:15: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:46:54: #4 Write output xls file... SRX025485.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:46:54: #4 Write peak in narrowPeak format file... SRX025485.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:46:54: #4 Write summits bed file... SRX025485.20_summits.bed INFO @ Tue, 21 Apr 2015 12:46:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (389 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:46:56: #4 Write output xls file... SRX025485.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:46:56: #4 Write peak in narrowPeak format file... SRX025485.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:46:56: #4 Write summits bed file... SRX025485.10_summits.bed INFO @ Tue, 21 Apr 2015 12:46:56: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (559 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:47:01: #4 Write output xls file... SRX025485.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:47:01: #4 Write peak in narrowPeak format file... SRX025485.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:47:01: #4 Write summits bed file... SRX025485.05_summits.bed INFO @ Tue, 21 Apr 2015 12:47:01: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1584 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。