Job ID = 10043498 sra ファイルのダウンロード中... Completed: 1836714K bytes transferred in 52 seconds (289098K bits/sec), in 2 files, 3 directories. 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 22140102 spots for /home/okishinya/chipatlas/results/dm3/SRX2165280/SRR4244790.sra Written 22140102 spots total Written 23652961 spots for /home/okishinya/chipatlas/results/dm3/SRX2165280/SRR4244789.sra Written 23652961 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: 00:18:33 45793063 reads; of these: 45793063 (100.00%) were unpaired; of these: 11790099 (25.75%) aligned 0 times 24145187 (52.73%) aligned exactly 1 time 9857777 (21.53%) aligned >1 times 74.25% overall alignment rate Time searching: 00:18:33 Overall time: 00:18:33 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_sort_core] merging from 16 files... [bam_rmdupse_core] 16412233 / 34002964 = 0.4827 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 @ Mon, 02 Oct 2017 03:57:17: # Command line: callpeak -t SRX2165280.bam -f BAM -g dm -n SRX2165280.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2165280.10 # format = BAM # ChIP-seq file = ['SRX2165280.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 # Paired-End mode is off INFO @ Mon, 02 Oct 2017 03:57:17: #1 read tag files... INFO @ Mon, 02 Oct 2017 03:57:17: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 03:57:17: # Command line: callpeak -t SRX2165280.bam -f BAM -g dm -n SRX2165280.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2165280.05 # format = BAM # ChIP-seq file = ['SRX2165280.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 # Paired-End mode is off INFO @ Mon, 02 Oct 2017 03:57:17: #1 read tag files... INFO @ Mon, 02 Oct 2017 03:57:17: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 03:57:17: # Command line: callpeak -t SRX2165280.bam -f BAM -g dm -n SRX2165280.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2165280.20 # format = BAM # ChIP-seq file = ['SRX2165280.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 # Paired-End mode is off INFO @ Mon, 02 Oct 2017 03:57:17: #1 read tag files... INFO @ Mon, 02 Oct 2017 03:57:17: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 03:57:23: 1000000 INFO @ Mon, 02 Oct 2017 03:57:23: 1000000 INFO @ Mon, 02 Oct 2017 03:57:23: 1000000 INFO @ Mon, 02 Oct 2017 03:57:30: 2000000 INFO @ Mon, 02 Oct 2017 03:57:30: 2000000 INFO @ Mon, 02 Oct 2017 03:57:30: 2000000 INFO @ Mon, 02 Oct 2017 03:57:37: 3000000 INFO @ Mon, 02 Oct 2017 03:57:37: 3000000 INFO @ Mon, 02 Oct 2017 03:57:37: 3000000 INFO @ Mon, 02 Oct 2017 03:57:44: 4000000 INFO @ Mon, 02 Oct 2017 03:57:44: 4000000 INFO @ Mon, 02 Oct 2017 03:57:44: 4000000 INFO @ Mon, 02 Oct 2017 03:57:51: 5000000 INFO @ Mon, 02 Oct 2017 03:57:51: 5000000 INFO @ Mon, 02 Oct 2017 03:57:52: 5000000 INFO @ Mon, 02 Oct 2017 03:57:58: 6000000 INFO @ Mon, 02 Oct 2017 03:57:59: 6000000 INFO @ Mon, 02 Oct 2017 03:58:00: 6000000 INFO @ Mon, 02 Oct 2017 03:58:05: 7000000 INFO @ Mon, 02 Oct 2017 03:58:06: 7000000 INFO @ Mon, 02 Oct 2017 03:58:07: 7000000 INFO @ Mon, 02 Oct 2017 03:58:13: 8000000 INFO @ Mon, 02 Oct 2017 03:58:14: 8000000 INFO @ Mon, 02 Oct 2017 03:58:15: 8000000 INFO @ Mon, 02 Oct 2017 03:58:21: 9000000 INFO @ Mon, 02 Oct 2017 03:58:22: 9000000 INFO @ Mon, 02 Oct 2017 03:58:23: 9000000 INFO @ Mon, 02 Oct 2017 03:58:28: 10000000 INFO @ Mon, 02 Oct 2017 03:58:30: 10000000 INFO @ Mon, 02 Oct 2017 03:58:31: 10000000 INFO @ Mon, 02 Oct 2017 03:58:36: 11000000 INFO @ Mon, 02 Oct 2017 03:58:38: 11000000 INFO @ Mon, 02 Oct 2017 03:58:40: 11000000 INFO @ Mon, 02 Oct 2017 03:58:44: 12000000 INFO @ Mon, 02 Oct 2017 03:58:46: 12000000 INFO @ Mon, 02 Oct 2017 03:58:48: 12000000 INFO @ Mon, 02 Oct 2017 03:58:53: 13000000 INFO @ Mon, 02 Oct 2017 03:58:55: 13000000 INFO @ Mon, 02 Oct 2017 03:58:56: 13000000 INFO @ Mon, 02 Oct 2017 03:59:01: 14000000 INFO @ Mon, 02 Oct 2017 03:59:03: 14000000 INFO @ Mon, 02 Oct 2017 03:59:05: 14000000 INFO @ Mon, 02 Oct 2017 03:59:09: 15000000 INFO @ Mon, 02 Oct 2017 03:59:11: 15000000 INFO @ Mon, 02 Oct 2017 03:59:13: 15000000 INFO @ Mon, 02 Oct 2017 03:59:17: 16000000 INFO @ Mon, 02 Oct 2017 03:59:19: 16000000 INFO @ Mon, 02 Oct 2017 03:59:21: 16000000 INFO @ Mon, 02 Oct 2017 03:59:25: 17000000 INFO @ Mon, 02 Oct 2017 03:59:27: 17000000 INFO @ Mon, 02 Oct 2017 03:59:29: 17000000 INFO @ Mon, 02 Oct 2017 03:59:29: #1 tag size is determined as 67 bps INFO @ Mon, 02 Oct 2017 03:59:29: #1 tag size = 67 INFO @ Mon, 02 Oct 2017 03:59:29: #1 total tags in treatment: 17590731 INFO @ Mon, 02 Oct 2017 03:59:29: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 03:59:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 02 Oct 2017 03:59:30: #1 tags after filtering in treatment: 17590731 INFO @ Mon, 02 Oct 2017 03:59:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 03:59:30: #1 finished! INFO @ Mon, 02 Oct 2017 03:59:30: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 03:59:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 03:59:31: #2 number of paired peaks: 267 WARNING @ Mon, 02 Oct 2017 03:59:31: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Mon, 02 Oct 2017 03:59:31: start model_add_line... INFO @ Mon, 02 Oct 2017 03:59:31: start X-correlation... INFO @ Mon, 02 Oct 2017 03:59:31: end of X-cor INFO @ Mon, 02 Oct 2017 03:59:31: #2 finished! INFO @ Mon, 02 Oct 2017 03:59:31: #2 predicted fragment length is 68 bps INFO @ Mon, 02 Oct 2017 03:59:31: #2 alternative fragment length(s) may be 68 bps INFO @ Mon, 02 Oct 2017 03:59:31: #2.2 Generate R script for model : SRX2165280.05_model.r WARNING @ Mon, 02 Oct 2017 03:59:31: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 02 Oct 2017 03:59:31: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Mon, 02 Oct 2017 03:59:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 02 Oct 2017 03:59:31: #3 Call peaks... INFO @ Mon, 02 Oct 2017 03:59:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 02 Oct 2017 03:59:32: #1 tag size is determined as 67 bps INFO @ Mon, 02 Oct 2017 03:59:32: #1 tag size = 67 INFO @ Mon, 02 Oct 2017 03:59:32: #1 total tags in treatment: 17590731 INFO @ Mon, 02 Oct 2017 03:59:32: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 03:59:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 02 Oct 2017 03:59:32: #1 tags after filtering in treatment: 17590731 INFO @ Mon, 02 Oct 2017 03:59:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 03:59:32: #1 finished! INFO @ Mon, 02 Oct 2017 03:59:32: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 03:59:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 03:59:34: #1 tag size is determined as 67 bps INFO @ Mon, 02 Oct 2017 03:59:34: #1 tag size = 67 INFO @ Mon, 02 Oct 2017 03:59:34: #1 total tags in treatment: 17590731 INFO @ Mon, 02 Oct 2017 03:59:34: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 03:59:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 02 Oct 2017 03:59:34: #2 number of paired peaks: 267 WARNING @ Mon, 02 Oct 2017 03:59:34: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Mon, 02 Oct 2017 03:59:34: start model_add_line... INFO @ Mon, 02 Oct 2017 03:59:34: #1 tags after filtering in treatment: 17590731 INFO @ Mon, 02 Oct 2017 03:59:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 03:59:34: #1 finished! INFO @ Mon, 02 Oct 2017 03:59:34: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 03:59:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 03:59:34: start X-correlation... INFO @ Mon, 02 Oct 2017 03:59:34: end of X-cor INFO @ Mon, 02 Oct 2017 03:59:34: #2 finished! INFO @ Mon, 02 Oct 2017 03:59:34: #2 predicted fragment length is 68 bps INFO @ Mon, 02 Oct 2017 03:59:34: #2 alternative fragment length(s) may be 68 bps INFO @ Mon, 02 Oct 2017 03:59:34: #2.2 Generate R script for model : SRX2165280.10_model.r WARNING @ Mon, 02 Oct 2017 03:59:34: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 02 Oct 2017 03:59:34: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Mon, 02 Oct 2017 03:59:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 02 Oct 2017 03:59:34: #3 Call peaks... INFO @ Mon, 02 Oct 2017 03:59:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 02 Oct 2017 03:59:35: #2 number of paired peaks: 267 WARNING @ Mon, 02 Oct 2017 03:59:35: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Mon, 02 Oct 2017 03:59:35: start model_add_line... INFO @ Mon, 02 Oct 2017 03:59:35: start X-correlation... INFO @ Mon, 02 Oct 2017 03:59:35: end of X-cor INFO @ Mon, 02 Oct 2017 03:59:35: #2 finished! INFO @ Mon, 02 Oct 2017 03:59:35: #2 predicted fragment length is 68 bps INFO @ Mon, 02 Oct 2017 03:59:35: #2 alternative fragment length(s) may be 68 bps INFO @ Mon, 02 Oct 2017 03:59:35: #2.2 Generate R script for model : SRX2165280.20_model.r WARNING @ Mon, 02 Oct 2017 03:59:35: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 02 Oct 2017 03:59:35: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Mon, 02 Oct 2017 03:59:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 02 Oct 2017 03:59:35: #3 Call peaks... INFO @ Mon, 02 Oct 2017 03:59:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 02 Oct 2017 04:00:07: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 04:00:13: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 04:00:13: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 04:00:27: #4 Write output xls file... SRX2165280.05_peaks.xls INFO @ Mon, 02 Oct 2017 04:00:27: #4 Write peak in narrowPeak format file... SRX2165280.05_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 04:00:27: #4 Write summits bed file... SRX2165280.05_summits.bed INFO @ Mon, 02 Oct 2017 04:00:27: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4253 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 02 Oct 2017 04:00:31: #4 Write output xls file... SRX2165280.20_peaks.xls INFO @ Mon, 02 Oct 2017 04:00:31: #4 Write peak in narrowPeak format file... SRX2165280.20_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 04:00:31: #4 Write summits bed file... SRX2165280.20_summits.bed INFO @ Mon, 02 Oct 2017 04:00:31: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1414 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 02 Oct 2017 04:00:32: #4 Write output xls file... SRX2165280.10_peaks.xls INFO @ Mon, 02 Oct 2017 04:00:32: #4 Write peak in narrowPeak format file... SRX2165280.10_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 04:00:32: #4 Write summits bed file... SRX2165280.10_summits.bed INFO @ Mon, 02 Oct 2017 04:00:32: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2390 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。