Job ID = 10043502 sra ファイルのダウンロード中... Completed: 1311189K bytes transferred in 57 seconds (188405K 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 17155473 spots for /home/okishinya/chipatlas/results/dm3/SRX2165284/SRR4244797.sra Written 17155473 spots total Written 23550796 spots for /home/okishinya/chipatlas/results/dm3/SRX2165284/SRR4244798.sra Written 23550796 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: 00:21:19 40706269 reads; of these: 40706269 (100.00%) were unpaired; of these: 4522439 (11.11%) aligned 0 times 25623602 (62.95%) aligned exactly 1 time 10560228 (25.94%) aligned >1 times 88.89% overall alignment rate Time searching: 00:21:19 Overall time: 00:21:19 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] 21142194 / 36183830 = 0.5843 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 03:59:25: # Command line: callpeak -t SRX2165284.bam -f BAM -g dm -n SRX2165284.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2165284.05 # format = BAM # ChIP-seq file = ['SRX2165284.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 03:59:25: # Command line: callpeak -t SRX2165284.bam -f BAM -g dm -n SRX2165284.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2165284.20 # format = BAM # ChIP-seq file = ['SRX2165284.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 03:59:25: #1 read tag files... INFO @ Mon, 02 Oct 2017 03:59:25: #1 read tag files... INFO @ Mon, 02 Oct 2017 03:59:25: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 03:59:25: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 03:59:25: # Command line: callpeak -t SRX2165284.bam -f BAM -g dm -n SRX2165284.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2165284.10 # format = BAM # ChIP-seq file = ['SRX2165284.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 03:59:25: #1 read tag files... INFO @ Mon, 02 Oct 2017 03:59:25: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 03:59:31: 1000000 INFO @ Mon, 02 Oct 2017 03:59:31: 1000000 INFO @ Mon, 02 Oct 2017 03:59:31: 1000000 INFO @ Mon, 02 Oct 2017 03:59:37: 2000000 INFO @ Mon, 02 Oct 2017 03:59:37: 2000000 INFO @ Mon, 02 Oct 2017 03:59:38: 2000000 INFO @ Mon, 02 Oct 2017 03:59:43: 3000000 INFO @ Mon, 02 Oct 2017 03:59:44: 3000000 INFO @ Mon, 02 Oct 2017 03:59:44: 3000000 INFO @ Mon, 02 Oct 2017 03:59:49: 4000000 INFO @ Mon, 02 Oct 2017 03:59:50: 4000000 INFO @ Mon, 02 Oct 2017 03:59:51: 4000000 INFO @ Mon, 02 Oct 2017 03:59:56: 5000000 INFO @ Mon, 02 Oct 2017 03:59:57: 5000000 INFO @ Mon, 02 Oct 2017 03:59:58: 5000000 INFO @ Mon, 02 Oct 2017 04:00:02: 6000000 INFO @ Mon, 02 Oct 2017 04:00:03: 6000000 INFO @ Mon, 02 Oct 2017 04:00:04: 6000000 INFO @ Mon, 02 Oct 2017 04:00:08: 7000000 INFO @ Mon, 02 Oct 2017 04:00:10: 7000000 INFO @ Mon, 02 Oct 2017 04:00:11: 7000000 INFO @ Mon, 02 Oct 2017 04:00:14: 8000000 INFO @ Mon, 02 Oct 2017 04:00:16: 8000000 INFO @ Mon, 02 Oct 2017 04:00:18: 8000000 INFO @ Mon, 02 Oct 2017 04:00:22: 9000000 INFO @ Mon, 02 Oct 2017 04:00:24: 9000000 INFO @ Mon, 02 Oct 2017 04:00:26: 9000000 INFO @ Mon, 02 Oct 2017 04:00:31: 10000000 INFO @ Mon, 02 Oct 2017 04:00:32: 10000000 INFO @ Mon, 02 Oct 2017 04:00:34: 10000000 INFO @ Mon, 02 Oct 2017 04:00:39: 11000000 INFO @ Mon, 02 Oct 2017 04:00:39: 11000000 INFO @ Mon, 02 Oct 2017 04:00:42: 11000000 INFO @ Mon, 02 Oct 2017 04:00:47: 12000000 INFO @ Mon, 02 Oct 2017 04:00:48: 12000000 INFO @ Mon, 02 Oct 2017 04:00:50: 12000000 INFO @ Mon, 02 Oct 2017 04:00:54: 13000000 INFO @ Mon, 02 Oct 2017 04:00:57: 13000000 INFO @ Mon, 02 Oct 2017 04:00:58: 13000000 INFO @ Mon, 02 Oct 2017 04:01:02: 14000000 INFO @ Mon, 02 Oct 2017 04:01:05: 14000000 INFO @ Mon, 02 Oct 2017 04:01:05: 14000000 INFO @ Mon, 02 Oct 2017 04:01:09: 15000000 INFO @ Mon, 02 Oct 2017 04:01:10: #1 tag size is determined as 75 bps INFO @ Mon, 02 Oct 2017 04:01:10: #1 tag size = 75 INFO @ Mon, 02 Oct 2017 04:01:10: #1 total tags in treatment: 15041636 INFO @ Mon, 02 Oct 2017 04:01:10: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 04:01:10: #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 04:01:10: #1 tags after filtering in treatment: 15041636 INFO @ Mon, 02 Oct 2017 04:01:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 04:01:10: #1 finished! INFO @ Mon, 02 Oct 2017 04:01:10: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 04:01:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 04:01:11: #2 number of paired peaks: 263 WARNING @ Mon, 02 Oct 2017 04:01:11: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Mon, 02 Oct 2017 04:01:11: start model_add_line... INFO @ Mon, 02 Oct 2017 04:01:11: start X-correlation... INFO @ Mon, 02 Oct 2017 04:01:11: end of X-cor INFO @ Mon, 02 Oct 2017 04:01:11: #2 finished! INFO @ Mon, 02 Oct 2017 04:01:11: #2 predicted fragment length is 75 bps INFO @ Mon, 02 Oct 2017 04:01:11: #2 alternative fragment length(s) may be 75 bps INFO @ Mon, 02 Oct 2017 04:01:11: #2.2 Generate R script for model : SRX2165284.20_model.r WARNING @ Mon, 02 Oct 2017 04:01:11: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 02 Oct 2017 04:01:11: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Mon, 02 Oct 2017 04:01:11: #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 04:01:11: #3 Call peaks... INFO @ Mon, 02 Oct 2017 04:01:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 02 Oct 2017 04:01:13: 15000000 INFO @ Mon, 02 Oct 2017 04:01:13: #1 tag size is determined as 75 bps INFO @ Mon, 02 Oct 2017 04:01:13: #1 tag size = 75 INFO @ Mon, 02 Oct 2017 04:01:13: #1 total tags in treatment: 15041636 INFO @ Mon, 02 Oct 2017 04:01:13: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 04:01:13: #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 04:01:14: #1 tags after filtering in treatment: 15041636 INFO @ Mon, 02 Oct 2017 04:01:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 04:01:14: #1 finished! INFO @ Mon, 02 Oct 2017 04:01:14: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 04:01:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 04:01:14: 15000000 INFO @ Mon, 02 Oct 2017 04:01:14: #1 tag size is determined as 75 bps INFO @ Mon, 02 Oct 2017 04:01:14: #1 tag size = 75 INFO @ Mon, 02 Oct 2017 04:01:14: #1 total tags in treatment: 15041636 INFO @ Mon, 02 Oct 2017 04:01:14: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 04:01:14: #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 04:01:15: #1 tags after filtering in treatment: 15041636 INFO @ Mon, 02 Oct 2017 04:01:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 04:01:15: #2 number of paired peaks: 263 INFO @ Mon, 02 Oct 2017 04:01:15: #1 finished! WARNING @ Mon, 02 Oct 2017 04:01:15: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Mon, 02 Oct 2017 04:01:15: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 04:01:15: start model_add_line... INFO @ Mon, 02 Oct 2017 04:01:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 04:01:15: start X-correlation... INFO @ Mon, 02 Oct 2017 04:01:15: end of X-cor INFO @ Mon, 02 Oct 2017 04:01:15: #2 finished! INFO @ Mon, 02 Oct 2017 04:01:15: #2 predicted fragment length is 75 bps INFO @ Mon, 02 Oct 2017 04:01:15: #2 alternative fragment length(s) may be 75 bps INFO @ Mon, 02 Oct 2017 04:01:15: #2.2 Generate R script for model : SRX2165284.10_model.r WARNING @ Mon, 02 Oct 2017 04:01:15: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 02 Oct 2017 04:01:15: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Mon, 02 Oct 2017 04:01:15: #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 04:01:15: #3 Call peaks... INFO @ Mon, 02 Oct 2017 04:01:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 02 Oct 2017 04:01:16: #2 number of paired peaks: 263 WARNING @ Mon, 02 Oct 2017 04:01:16: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Mon, 02 Oct 2017 04:01:16: start model_add_line... INFO @ Mon, 02 Oct 2017 04:01:16: start X-correlation... INFO @ Mon, 02 Oct 2017 04:01:16: end of X-cor INFO @ Mon, 02 Oct 2017 04:01:16: #2 finished! INFO @ Mon, 02 Oct 2017 04:01:16: #2 predicted fragment length is 75 bps INFO @ Mon, 02 Oct 2017 04:01:16: #2 alternative fragment length(s) may be 75 bps INFO @ Mon, 02 Oct 2017 04:01:16: #2.2 Generate R script for model : SRX2165284.05_model.r WARNING @ Mon, 02 Oct 2017 04:01:16: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 02 Oct 2017 04:01:16: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Mon, 02 Oct 2017 04:01:16: #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 04:01:16: #3 Call peaks... INFO @ Mon, 02 Oct 2017 04:01:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 02 Oct 2017 04:01:44: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 04:01:47: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 04:01:48: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 04:02:02: #4 Write output xls file... SRX2165284.20_peaks.xls INFO @ Mon, 02 Oct 2017 04:02:02: #4 Write peak in narrowPeak format file... SRX2165284.20_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 04:02:02: #4 Write summits bed file... SRX2165284.20_summits.bed INFO @ Mon, 02 Oct 2017 04:02:02: Done! pass1 - making usageList (12 chroms): 3 millis pass2 - checking and writing primary data (1170 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 02 Oct 2017 04:02:04: #4 Write output xls file... SRX2165284.10_peaks.xls INFO @ Mon, 02 Oct 2017 04:02:04: #4 Write peak in narrowPeak format file... SRX2165284.10_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 04:02:04: #4 Write summits bed file... SRX2165284.10_summits.bed INFO @ Mon, 02 Oct 2017 04:02:04: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (2886 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 02 Oct 2017 04:02:05: #4 Write output xls file... SRX2165284.05_peaks.xls INFO @ Mon, 02 Oct 2017 04:02:05: #4 Write peak in narrowPeak format file... SRX2165284.05_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 04:02:05: #4 Write summits bed file... SRX2165284.05_summits.bed INFO @ Mon, 02 Oct 2017 04:02:05: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6722 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。