Job ID = 6983659 sra ファイルのダウンロード中... Completed: 345853K bytes transferred in 7 seconds (395056K 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 35556 0 35556 0 0 37427 0 --:--:-- --:--:-- --:--:-- 59458 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 16963039 spots for /home/okishinya/chipatlas/results/dm3/SRX017469/SRR037526.sra Written 16963039 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: 00:05:03 16963039 reads; of these: 16963039 (100.00%) were unpaired; of these: 995584 (5.87%) aligned 0 times 11827766 (69.73%) aligned exactly 1 time 4139689 (24.40%) aligned >1 times 94.13% overall alignment rate Time searching: 00:05:03 Overall time: 00:05:03 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] 2156973 / 15967455 = 0.1351 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 @ Sun, 05 Jun 2016 15:42:34: # Command line: callpeak -t SRX017469.bam -f BAM -g dm -n SRX017469.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX017469.05 # format = BAM # ChIP-seq file = ['SRX017469.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 @ Sun, 05 Jun 2016 15:42:34: # Command line: callpeak -t SRX017469.bam -f BAM -g dm -n SRX017469.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX017469.10 # format = BAM # ChIP-seq file = ['SRX017469.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 @ Sun, 05 Jun 2016 15:42:34: # Command line: callpeak -t SRX017469.bam -f BAM -g dm -n SRX017469.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX017469.20 # format = BAM # ChIP-seq file = ['SRX017469.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 @ Sun, 05 Jun 2016 15:42:34: #1 read tag files... INFO @ Sun, 05 Jun 2016 15:42:34: #1 read tag files... INFO @ Sun, 05 Jun 2016 15:42:34: #1 read tag files... INFO @ Sun, 05 Jun 2016 15:42:34: #1 read treatment tags... INFO @ Sun, 05 Jun 2016 15:42:34: #1 read treatment tags... INFO @ Sun, 05 Jun 2016 15:42:34: #1 read treatment tags... INFO @ Sun, 05 Jun 2016 15:42:40: 1000000 INFO @ Sun, 05 Jun 2016 15:42:40: 1000000 INFO @ Sun, 05 Jun 2016 15:42:40: 1000000 INFO @ Sun, 05 Jun 2016 15:42:45: 2000000 INFO @ Sun, 05 Jun 2016 15:42:45: 2000000 INFO @ Sun, 05 Jun 2016 15:42:45: 2000000 INFO @ Sun, 05 Jun 2016 15:42:51: 3000000 INFO @ Sun, 05 Jun 2016 15:42:51: 3000000 INFO @ Sun, 05 Jun 2016 15:42:51: 3000000 INFO @ Sun, 05 Jun 2016 15:42:56: 4000000 INFO @ Sun, 05 Jun 2016 15:42:57: 4000000 INFO @ Sun, 05 Jun 2016 15:42:57: 4000000 INFO @ Sun, 05 Jun 2016 15:43:02: 5000000 INFO @ Sun, 05 Jun 2016 15:43:02: 5000000 INFO @ Sun, 05 Jun 2016 15:43:02: 5000000 INFO @ Sun, 05 Jun 2016 15:43:07: 6000000 INFO @ Sun, 05 Jun 2016 15:43:08: 6000000 INFO @ Sun, 05 Jun 2016 15:43:08: 6000000 INFO @ Sun, 05 Jun 2016 15:43:12: 7000000 INFO @ Sun, 05 Jun 2016 15:43:13: 7000000 INFO @ Sun, 05 Jun 2016 15:43:13: 7000000 INFO @ Sun, 05 Jun 2016 15:43:18: 8000000 INFO @ Sun, 05 Jun 2016 15:43:19: 8000000 INFO @ Sun, 05 Jun 2016 15:43:19: 8000000 INFO @ Sun, 05 Jun 2016 15:43:23: 9000000 INFO @ Sun, 05 Jun 2016 15:43:24: 9000000 INFO @ Sun, 05 Jun 2016 15:43:24: 9000000 INFO @ Sun, 05 Jun 2016 15:43:29: 10000000 INFO @ Sun, 05 Jun 2016 15:43:30: 10000000 INFO @ Sun, 05 Jun 2016 15:43:30: 10000000 INFO @ Sun, 05 Jun 2016 15:43:34: 11000000 INFO @ Sun, 05 Jun 2016 15:43:35: 11000000 INFO @ Sun, 05 Jun 2016 15:43:35: 11000000 INFO @ Sun, 05 Jun 2016 15:43:40: 12000000 INFO @ Sun, 05 Jun 2016 15:43:40: 12000000 INFO @ Sun, 05 Jun 2016 15:43:41: 12000000 INFO @ Sun, 05 Jun 2016 15:43:45: 13000000 INFO @ Sun, 05 Jun 2016 15:43:45: 13000000 INFO @ Sun, 05 Jun 2016 15:43:47: 13000000 INFO @ Sun, 05 Jun 2016 15:43:50: #1 tag size is determined as 36 bps INFO @ Sun, 05 Jun 2016 15:43:50: #1 tag size = 36 INFO @ Sun, 05 Jun 2016 15:43:50: #1 total tags in treatment: 13810482 INFO @ Sun, 05 Jun 2016 15:43:50: #1 user defined the maximum tags... INFO @ Sun, 05 Jun 2016 15:43:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 05 Jun 2016 15:43:50: #1 tag size is determined as 36 bps INFO @ Sun, 05 Jun 2016 15:43:50: #1 tag size = 36 INFO @ Sun, 05 Jun 2016 15:43:50: #1 total tags in treatment: 13810482 INFO @ Sun, 05 Jun 2016 15:43:50: #1 user defined the maximum tags... INFO @ Sun, 05 Jun 2016 15:43:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 05 Jun 2016 15:43:51: #1 tag size is determined as 36 bps INFO @ Sun, 05 Jun 2016 15:43:51: #1 tag size = 36 INFO @ Sun, 05 Jun 2016 15:43:51: #1 total tags in treatment: 13810482 INFO @ Sun, 05 Jun 2016 15:43:51: #1 user defined the maximum tags... INFO @ Sun, 05 Jun 2016 15:43:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 05 Jun 2016 15:43:52: #1 tags after filtering in treatment: 13809046 INFO @ Sun, 05 Jun 2016 15:43:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 05 Jun 2016 15:43:52: #1 finished! INFO @ Sun, 05 Jun 2016 15:43:52: #2 Build Peak Model... INFO @ Sun, 05 Jun 2016 15:43:53: #1 tags after filtering in treatment: 13809046 INFO @ Sun, 05 Jun 2016 15:43:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 05 Jun 2016 15:43:53: #1 finished! INFO @ Sun, 05 Jun 2016 15:43:53: #2 Build Peak Model... INFO @ Sun, 05 Jun 2016 15:43:54: #1 tags after filtering in treatment: 13809046 INFO @ Sun, 05 Jun 2016 15:43:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 05 Jun 2016 15:43:54: #1 finished! INFO @ Sun, 05 Jun 2016 15:43:54: #2 Build Peak Model... INFO @ Sun, 05 Jun 2016 15:43:55: #2 number of paired peaks: 127 WARNING @ Sun, 05 Jun 2016 15:43:55: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Sun, 05 Jun 2016 15:43:55: start model_add_line... INFO @ Sun, 05 Jun 2016 15:43:55: #2 number of paired peaks: 127 WARNING @ Sun, 05 Jun 2016 15:43:55: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Sun, 05 Jun 2016 15:43:55: start model_add_line... INFO @ Sun, 05 Jun 2016 15:43:56: #2 number of paired peaks: 127 WARNING @ Sun, 05 Jun 2016 15:43:56: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Sun, 05 Jun 2016 15:43:56: start model_add_line... INFO @ Sun, 05 Jun 2016 15:43:57: start X-correlation... INFO @ Sun, 05 Jun 2016 15:43:57: end of X-cor INFO @ Sun, 05 Jun 2016 15:43:57: #2 finished! INFO @ Sun, 05 Jun 2016 15:43:57: #2 predicted fragment length is 59 bps INFO @ Sun, 05 Jun 2016 15:43:57: #2 alternative fragment length(s) may be 59 bps INFO @ Sun, 05 Jun 2016 15:43:57: #2.2 Generate R script for model : SRX017469.20_model.r WARNING @ Sun, 05 Jun 2016 15:43:57: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 05 Jun 2016 15:43:57: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Sun, 05 Jun 2016 15:43:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 05 Jun 2016 15:43:57: #3 Call peaks... INFO @ Sun, 05 Jun 2016 15:43:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 05 Jun 2016 15:43:57: start X-correlation... INFO @ Sun, 05 Jun 2016 15:43:57: end of X-cor INFO @ Sun, 05 Jun 2016 15:43:57: #2 finished! INFO @ Sun, 05 Jun 2016 15:43:57: #2 predicted fragment length is 59 bps INFO @ Sun, 05 Jun 2016 15:43:57: #2 alternative fragment length(s) may be 59 bps INFO @ Sun, 05 Jun 2016 15:43:57: #2.2 Generate R script for model : SRX017469.05_model.r WARNING @ Sun, 05 Jun 2016 15:43:57: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 05 Jun 2016 15:43:57: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Sun, 05 Jun 2016 15:43:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 05 Jun 2016 15:43:57: #3 Call peaks... INFO @ Sun, 05 Jun 2016 15:43:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 05 Jun 2016 15:43:58: start X-correlation... INFO @ Sun, 05 Jun 2016 15:43:58: end of X-cor INFO @ Sun, 05 Jun 2016 15:43:58: #2 finished! INFO @ Sun, 05 Jun 2016 15:43:58: #2 predicted fragment length is 59 bps INFO @ Sun, 05 Jun 2016 15:43:58: #2 alternative fragment length(s) may be 59 bps INFO @ Sun, 05 Jun 2016 15:43:58: #2.2 Generate R script for model : SRX017469.10_model.r WARNING @ Sun, 05 Jun 2016 15:43:58: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 05 Jun 2016 15:43:58: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Sun, 05 Jun 2016 15:43:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 05 Jun 2016 15:43:58: #3 Call peaks... INFO @ Sun, 05 Jun 2016 15:43:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 05 Jun 2016 15:45:10: #3 Call peaks for each chromosome... INFO @ Sun, 05 Jun 2016 15:45:11: #3 Call peaks for each chromosome... INFO @ Sun, 05 Jun 2016 15:45:12: #3 Call peaks for each chromosome... INFO @ Sun, 05 Jun 2016 15:46:04: #4 Write output xls file... SRX017469.10_peaks.xls INFO @ Sun, 05 Jun 2016 15:46:04: #4 Write peak in narrowPeak format file... SRX017469.10_peaks.narrowPeak INFO @ Sun, 05 Jun 2016 15:46:04: #4 Write summits bed file... SRX017469.10_summits.bed INFO @ Sun, 05 Jun 2016 15:46:04: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3122 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 05 Jun 2016 15:46:05: #4 Write output xls file... SRX017469.20_peaks.xls INFO @ Sun, 05 Jun 2016 15:46:05: #4 Write peak in narrowPeak format file... SRX017469.20_peaks.narrowPeak INFO @ Sun, 05 Jun 2016 15:46:05: #4 Write summits bed file... SRX017469.20_summits.bed INFO @ Sun, 05 Jun 2016 15:46:05: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (944 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 05 Jun 2016 15:46:11: #4 Write output xls file... SRX017469.05_peaks.xls INFO @ Sun, 05 Jun 2016 15:46:11: #4 Write peak in narrowPeak format file... SRX017469.05_peaks.narrowPeak INFO @ Sun, 05 Jun 2016 15:46:11: #4 Write summits bed file... SRX017469.05_summits.bed INFO @ Sun, 05 Jun 2016 15:46:11: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7338 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。