Job ID = 9159812 sra ファイルのダウンロード中... Completed: 1120174K bytes transferred in 12 seconds (732146K 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: PAIRED fastq に変換中... Written 4179321 spots for /home/okishinya/chipatlas/results/dm3/SRX699105/SRR1573142.sra Written 4179321 spots total Written 4231263 spots for /home/okishinya/chipatlas/results/dm3/SRX699105/SRR1573141.sra Written 4231263 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: 00:24:25 8410584 reads; of these: 8410584 (100.00%) were paired; of these: 238473 (2.84%) aligned concordantly 0 times 6977241 (82.96%) aligned concordantly exactly 1 time 1194870 (14.21%) aligned concordantly >1 times ---- 238473 pairs aligned concordantly 0 times; of these: 17032 (7.14%) aligned discordantly 1 time ---- 221441 pairs aligned 0 times concordantly or discordantly; of these: 442882 mates make up the pairs; of these: 230045 (51.94%) aligned 0 times 137791 (31.11%) aligned exactly 1 time 75046 (16.94%) aligned >1 times 98.63% overall alignment rate Time searching: 00:24:25 Overall time: 00:24:25 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 8 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 571247 / 8178293 = 0.0698 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 @ Wed, 28 Jun 2017 00:20:02: # Command line: callpeak -t SRX699105.bam -f BAM -g dm -n SRX699105.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX699105.10 # format = BAM # ChIP-seq file = ['SRX699105.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 @ Wed, 28 Jun 2017 00:20:02: # Command line: callpeak -t SRX699105.bam -f BAM -g dm -n SRX699105.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX699105.05 # format = BAM # ChIP-seq file = ['SRX699105.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 @ Wed, 28 Jun 2017 00:20:02: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:20:02: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:20:02: # Command line: callpeak -t SRX699105.bam -f BAM -g dm -n SRX699105.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX699105.20 # format = BAM # ChIP-seq file = ['SRX699105.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 @ Wed, 28 Jun 2017 00:20:02: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:20:02: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:20:02: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:20:02: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:20:09: 1000000 INFO @ Wed, 28 Jun 2017 00:20:10: 1000000 INFO @ Wed, 28 Jun 2017 00:20:10: 1000000 INFO @ Wed, 28 Jun 2017 00:20:17: 2000000 INFO @ Wed, 28 Jun 2017 00:20:18: 2000000 INFO @ Wed, 28 Jun 2017 00:20:18: 2000000 INFO @ Wed, 28 Jun 2017 00:20:25: 3000000 INFO @ Wed, 28 Jun 2017 00:20:26: 3000000 INFO @ Wed, 28 Jun 2017 00:20:26: 3000000 INFO @ Wed, 28 Jun 2017 00:20:34: 4000000 INFO @ Wed, 28 Jun 2017 00:20:34: 4000000 INFO @ Wed, 28 Jun 2017 00:20:35: 4000000 INFO @ Wed, 28 Jun 2017 00:20:42: 5000000 INFO @ Wed, 28 Jun 2017 00:20:42: 5000000 INFO @ Wed, 28 Jun 2017 00:20:43: 5000000 INFO @ Wed, 28 Jun 2017 00:20:50: 6000000 INFO @ Wed, 28 Jun 2017 00:20:51: 6000000 INFO @ Wed, 28 Jun 2017 00:20:52: 6000000 INFO @ Wed, 28 Jun 2017 00:20:59: 7000000 INFO @ Wed, 28 Jun 2017 00:20:59: 7000000 INFO @ Wed, 28 Jun 2017 00:21:00: 7000000 INFO @ Wed, 28 Jun 2017 00:21:07: 8000000 INFO @ Wed, 28 Jun 2017 00:21:07: 8000000 INFO @ Wed, 28 Jun 2017 00:21:09: 8000000 INFO @ Wed, 28 Jun 2017 00:21:14: 9000000 INFO @ Wed, 28 Jun 2017 00:21:15: 9000000 INFO @ Wed, 28 Jun 2017 00:21:17: 9000000 INFO @ Wed, 28 Jun 2017 00:21:22: 10000000 INFO @ Wed, 28 Jun 2017 00:21:23: 10000000 INFO @ Wed, 28 Jun 2017 00:21:25: 10000000 INFO @ Wed, 28 Jun 2017 00:21:31: 11000000 INFO @ Wed, 28 Jun 2017 00:21:31: 11000000 INFO @ Wed, 28 Jun 2017 00:21:34: 11000000 INFO @ Wed, 28 Jun 2017 00:21:39: 12000000 INFO @ Wed, 28 Jun 2017 00:21:39: 12000000 INFO @ Wed, 28 Jun 2017 00:21:42: 12000000 INFO @ Wed, 28 Jun 2017 00:21:47: 13000000 INFO @ Wed, 28 Jun 2017 00:21:47: 13000000 INFO @ Wed, 28 Jun 2017 00:21:51: 13000000 INFO @ Wed, 28 Jun 2017 00:21:55: 14000000 INFO @ Wed, 28 Jun 2017 00:21:56: 14000000 INFO @ Wed, 28 Jun 2017 00:21:59: 14000000 INFO @ Wed, 28 Jun 2017 00:22:04: 15000000 INFO @ Wed, 28 Jun 2017 00:22:04: 15000000 INFO @ Wed, 28 Jun 2017 00:22:07: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 00:22:07: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 00:22:07: #1 total tags in treatment: 7601291 INFO @ Wed, 28 Jun 2017 00:22:07: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:22:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 00:22:07: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 00:22:07: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 00:22:07: #1 total tags in treatment: 7601291 INFO @ Wed, 28 Jun 2017 00:22:07: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:22:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 00:22:08: 15000000 INFO @ Wed, 28 Jun 2017 00:22:08: #1 tags after filtering in treatment: 6848438 INFO @ Wed, 28 Jun 2017 00:22:08: #1 Redundant rate of treatment: 0.10 INFO @ Wed, 28 Jun 2017 00:22:08: #1 finished! INFO @ Wed, 28 Jun 2017 00:22:08: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:22:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:22:08: #1 tags after filtering in treatment: 6848438 INFO @ Wed, 28 Jun 2017 00:22:08: #1 Redundant rate of treatment: 0.10 INFO @ Wed, 28 Jun 2017 00:22:08: #1 finished! INFO @ Wed, 28 Jun 2017 00:22:08: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:22:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:22:08: #2 number of paired peaks: 2609 INFO @ Wed, 28 Jun 2017 00:22:08: start model_add_line... INFO @ Wed, 28 Jun 2017 00:22:08: start X-correlation... INFO @ Wed, 28 Jun 2017 00:22:08: #2 number of paired peaks: 2609 INFO @ Wed, 28 Jun 2017 00:22:08: start model_add_line... INFO @ Wed, 28 Jun 2017 00:22:08: end of X-cor INFO @ Wed, 28 Jun 2017 00:22:08: #2 finished! INFO @ Wed, 28 Jun 2017 00:22:08: #2 predicted fragment length is 176 bps INFO @ Wed, 28 Jun 2017 00:22:08: #2 alternative fragment length(s) may be 176 bps INFO @ Wed, 28 Jun 2017 00:22:08: #2.2 Generate R script for model : SRX699105.05_model.r WARNING @ Wed, 28 Jun 2017 00:22:08: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 00:22:08: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Wed, 28 Jun 2017 00:22:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 00:22:08: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:22:08: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:22:08: start X-correlation... INFO @ Wed, 28 Jun 2017 00:22:09: end of X-cor INFO @ Wed, 28 Jun 2017 00:22:09: #2 finished! INFO @ Wed, 28 Jun 2017 00:22:09: #2 predicted fragment length is 176 bps INFO @ Wed, 28 Jun 2017 00:22:09: #2 alternative fragment length(s) may be 176 bps INFO @ Wed, 28 Jun 2017 00:22:09: #2.2 Generate R script for model : SRX699105.10_model.r WARNING @ Wed, 28 Jun 2017 00:22:09: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 00:22:09: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Wed, 28 Jun 2017 00:22:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 00:22:09: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:22:09: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:22:11: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 00:22:11: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 00:22:11: #1 total tags in treatment: 7601291 INFO @ Wed, 28 Jun 2017 00:22:11: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:22:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 00:22:11: #1 tags after filtering in treatment: 6848438 INFO @ Wed, 28 Jun 2017 00:22:11: #1 Redundant rate of treatment: 0.10 INFO @ Wed, 28 Jun 2017 00:22:11: #1 finished! INFO @ Wed, 28 Jun 2017 00:22:11: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:22:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:22:12: #2 number of paired peaks: 2609 INFO @ Wed, 28 Jun 2017 00:22:12: start model_add_line... INFO @ Wed, 28 Jun 2017 00:22:12: start X-correlation... INFO @ Wed, 28 Jun 2017 00:22:12: end of X-cor INFO @ Wed, 28 Jun 2017 00:22:12: #2 finished! INFO @ Wed, 28 Jun 2017 00:22:12: #2 predicted fragment length is 176 bps INFO @ Wed, 28 Jun 2017 00:22:12: #2 alternative fragment length(s) may be 176 bps INFO @ Wed, 28 Jun 2017 00:22:12: #2.2 Generate R script for model : SRX699105.20_model.r WARNING @ Wed, 28 Jun 2017 00:22:12: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 00:22:12: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Wed, 28 Jun 2017 00:22:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 00:22:12: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:22:12: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:22:28: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:22:29: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:22:32: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:22:39: #4 Write output xls file... SRX699105.05_peaks.xls INFO @ Wed, 28 Jun 2017 00:22:40: #4 Write peak in narrowPeak format file... SRX699105.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:22:40: #4 Write summits bed file... SRX699105.05_summits.bed INFO @ Wed, 28 Jun 2017 00:22:40: Done! INFO @ Wed, 28 Jun 2017 00:22:40: #4 Write output xls file... SRX699105.10_peaks.xls INFO @ Wed, 28 Jun 2017 00:22:40: #4 Write peak in narrowPeak format file... SRX699105.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:22:40: #4 Write summits bed file... SRX699105.10_summits.bed INFO @ Wed, 28 Jun 2017 00:22:40: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (12956 records, 4 fields): 19 millis pass1 - making usageList (14 chroms): 1 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (4891 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:22:43: #4 Write output xls file... SRX699105.20_peaks.xls INFO @ Wed, 28 Jun 2017 00:22:43: #4 Write peak in narrowPeak format file... SRX699105.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:22:43: #4 Write summits bed file... SRX699105.20_summits.bed INFO @ Wed, 28 Jun 2017 00:22:43: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1298 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。