Job ID = 9371937 sra ファイルのダウンロード中... Completed: 960260K bytes transferred in 26 seconds (302198K bits/sec), in 1 file, 2 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 11113468 spots for /home/okishinya/chipatlas/results/dm3/SRX2548348/SRR5241492.sra Written 11113468 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: 01:14:07 11113468 reads; of these: 11113468 (100.00%) were paired; of these: 3731297 (33.57%) aligned concordantly 0 times 5503239 (49.52%) aligned concordantly exactly 1 time 1878932 (16.91%) aligned concordantly >1 times ---- 3731297 pairs aligned concordantly 0 times; of these: 1075302 (28.82%) aligned discordantly 1 time ---- 2655995 pairs aligned 0 times concordantly or discordantly; of these: 5311990 mates make up the pairs; of these: 4392616 (82.69%) aligned 0 times 358632 (6.75%) aligned exactly 1 time 560742 (10.56%) aligned >1 times 80.24% overall alignment rate Time searching: 01:14:07 Overall time: 01:14:07 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] 179860 / 8355744 = 0.0215 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 @ Fri, 04 Aug 2017 16:21:36: # Command line: callpeak -t SRX2548348.bam -f BAM -g dm -n SRX2548348.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2548348.20 # format = BAM # ChIP-seq file = ['SRX2548348.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 @ Fri, 04 Aug 2017 16:21:36: #1 read tag files... INFO @ Fri, 04 Aug 2017 16:21:36: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 16:21:36: # Command line: callpeak -t SRX2548348.bam -f BAM -g dm -n SRX2548348.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2548348.10 # format = BAM # ChIP-seq file = ['SRX2548348.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 @ Fri, 04 Aug 2017 16:21:36: #1 read tag files... INFO @ Fri, 04 Aug 2017 16:21:36: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 16:21:36: # Command line: callpeak -t SRX2548348.bam -f BAM -g dm -n SRX2548348.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2548348.05 # format = BAM # ChIP-seq file = ['SRX2548348.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 @ Fri, 04 Aug 2017 16:21:36: #1 read tag files... INFO @ Fri, 04 Aug 2017 16:21:36: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 16:22:04: 1000000 INFO @ Fri, 04 Aug 2017 16:22:06: 1000000 INFO @ Fri, 04 Aug 2017 16:22:08: 1000000 INFO @ Fri, 04 Aug 2017 16:22:31: 2000000 INFO @ Fri, 04 Aug 2017 16:22:35: 2000000 INFO @ Fri, 04 Aug 2017 16:22:36: 2000000 INFO @ Fri, 04 Aug 2017 16:23:00: 3000000 INFO @ Fri, 04 Aug 2017 16:23:02: 3000000 INFO @ Fri, 04 Aug 2017 16:23:02: 3000000 INFO @ Fri, 04 Aug 2017 16:23:26: 4000000 INFO @ Fri, 04 Aug 2017 16:23:26: 4000000 INFO @ Fri, 04 Aug 2017 16:23:29: 4000000 INFO @ Fri, 04 Aug 2017 16:23:53: 5000000 INFO @ Fri, 04 Aug 2017 16:23:54: 5000000 INFO @ Fri, 04 Aug 2017 16:23:59: 5000000 INFO @ Fri, 04 Aug 2017 16:24:20: 6000000 INFO @ Fri, 04 Aug 2017 16:24:20: 6000000 INFO @ Fri, 04 Aug 2017 16:24:28: 6000000 INFO @ Fri, 04 Aug 2017 16:24:45: 7000000 INFO @ Fri, 04 Aug 2017 16:24:47: 7000000 INFO @ Fri, 04 Aug 2017 16:24:56: 7000000 INFO @ Fri, 04 Aug 2017 16:25:14: 8000000 INFO @ Fri, 04 Aug 2017 16:25:14: 8000000 INFO @ Fri, 04 Aug 2017 16:25:23: 8000000 INFO @ Fri, 04 Aug 2017 16:25:43: 9000000 INFO @ Fri, 04 Aug 2017 16:25:46: 9000000 INFO @ Fri, 04 Aug 2017 16:25:53: 9000000 INFO @ Fri, 04 Aug 2017 16:26:12: 10000000 INFO @ Fri, 04 Aug 2017 16:26:16: 10000000 INFO @ Fri, 04 Aug 2017 16:26:20: 10000000 INFO @ Fri, 04 Aug 2017 16:26:35: 11000000 INFO @ Fri, 04 Aug 2017 16:26:43: 11000000 INFO @ Fri, 04 Aug 2017 16:26:51: 11000000 INFO @ Fri, 04 Aug 2017 16:27:07: 12000000 INFO @ Fri, 04 Aug 2017 16:27:11: 12000000 INFO @ Fri, 04 Aug 2017 16:27:24: 12000000 INFO @ Fri, 04 Aug 2017 16:27:36: 13000000 INFO @ Fri, 04 Aug 2017 16:27:38: 13000000 INFO @ Fri, 04 Aug 2017 16:27:49: 13000000 INFO @ Fri, 04 Aug 2017 16:28:03: 14000000 INFO @ Fri, 04 Aug 2017 16:28:09: 14000000 INFO @ Fri, 04 Aug 2017 16:28:17: 14000000 INFO @ Fri, 04 Aug 2017 16:28:31: 15000000 INFO @ Fri, 04 Aug 2017 16:28:41: 15000000 INFO @ Fri, 04 Aug 2017 16:28:44: 15000000 INFO @ Fri, 04 Aug 2017 16:29:00: 16000000 INFO @ Fri, 04 Aug 2017 16:29:10: 16000000 INFO @ Fri, 04 Aug 2017 16:29:12: 16000000 INFO @ Fri, 04 Aug 2017 16:29:28: 17000000 INFO @ Fri, 04 Aug 2017 16:29:36: 17000000 INFO @ Fri, 04 Aug 2017 16:29:36: 17000000 INFO @ Fri, 04 Aug 2017 16:29:42: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 16:29:42: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 16:29:42: #1 total tags in treatment: 7206305 INFO @ Fri, 04 Aug 2017 16:29:42: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 16:29:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 16:29:42: #1 tags after filtering in treatment: 6933662 INFO @ Fri, 04 Aug 2017 16:29:42: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 04 Aug 2017 16:29:42: #1 finished! INFO @ Fri, 04 Aug 2017 16:29:42: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 16:29:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 16:29:43: #2 number of paired peaks: 355 WARNING @ Fri, 04 Aug 2017 16:29:43: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Fri, 04 Aug 2017 16:29:43: start model_add_line... INFO @ Fri, 04 Aug 2017 16:29:43: start X-correlation... INFO @ Fri, 04 Aug 2017 16:29:43: end of X-cor INFO @ Fri, 04 Aug 2017 16:29:43: #2 finished! INFO @ Fri, 04 Aug 2017 16:29:43: #2 predicted fragment length is 167 bps INFO @ Fri, 04 Aug 2017 16:29:43: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 04 Aug 2017 16:29:43: #2.2 Generate R script for model : SRX2548348.10_model.r WARNING @ Fri, 04 Aug 2017 16:29:43: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 16:29:43: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Fri, 04 Aug 2017 16:29:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 16:29:43: #3 Call peaks... INFO @ Fri, 04 Aug 2017 16:29:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 16:29:48: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 16:29:48: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 16:29:48: #1 total tags in treatment: 7206305 INFO @ Fri, 04 Aug 2017 16:29:48: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 16:29:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 16:29:48: #1 tags after filtering in treatment: 6933662 INFO @ Fri, 04 Aug 2017 16:29:48: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 04 Aug 2017 16:29:48: #1 finished! INFO @ Fri, 04 Aug 2017 16:29:48: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 16:29:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 16:29:49: #2 number of paired peaks: 355 WARNING @ Fri, 04 Aug 2017 16:29:49: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Fri, 04 Aug 2017 16:29:49: start model_add_line... INFO @ Fri, 04 Aug 2017 16:29:49: start X-correlation... INFO @ Fri, 04 Aug 2017 16:29:49: end of X-cor INFO @ Fri, 04 Aug 2017 16:29:49: #2 finished! INFO @ Fri, 04 Aug 2017 16:29:49: #2 predicted fragment length is 167 bps INFO @ Fri, 04 Aug 2017 16:29:49: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 04 Aug 2017 16:29:49: #2.2 Generate R script for model : SRX2548348.20_model.r WARNING @ Fri, 04 Aug 2017 16:29:49: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 16:29:49: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Fri, 04 Aug 2017 16:29:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 16:29:49: #3 Call peaks... INFO @ Fri, 04 Aug 2017 16:29:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 16:29:50: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 16:29:50: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 16:29:50: #1 total tags in treatment: 7206305 INFO @ Fri, 04 Aug 2017 16:29:50: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 16:29:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 16:29:50: #1 tags after filtering in treatment: 6933662 INFO @ Fri, 04 Aug 2017 16:29:50: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 04 Aug 2017 16:29:50: #1 finished! INFO @ Fri, 04 Aug 2017 16:29:50: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 16:29:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 16:29:51: #2 number of paired peaks: 355 WARNING @ Fri, 04 Aug 2017 16:29:51: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Fri, 04 Aug 2017 16:29:51: start model_add_line... INFO @ Fri, 04 Aug 2017 16:29:51: start X-correlation... INFO @ Fri, 04 Aug 2017 16:29:51: end of X-cor INFO @ Fri, 04 Aug 2017 16:29:51: #2 finished! INFO @ Fri, 04 Aug 2017 16:29:51: #2 predicted fragment length is 167 bps INFO @ Fri, 04 Aug 2017 16:29:51: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 04 Aug 2017 16:29:51: #2.2 Generate R script for model : SRX2548348.05_model.r WARNING @ Fri, 04 Aug 2017 16:29:51: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 16:29:51: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Fri, 04 Aug 2017 16:29:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 16:29:51: #3 Call peaks... INFO @ Fri, 04 Aug 2017 16:29:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 16:30:07: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 16:30:15: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 16:30:15: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 16:30:23: #4 Write output xls file... SRX2548348.10_peaks.xls INFO @ Fri, 04 Aug 2017 16:30:23: #4 Write peak in narrowPeak format file... SRX2548348.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 16:30:23: #4 Write summits bed file... SRX2548348.10_summits.bed INFO @ Fri, 04 Aug 2017 16:30:23: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1024 records, 4 fields): 44 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 16:30:31: #4 Write output xls file... SRX2548348.20_peaks.xls INFO @ Fri, 04 Aug 2017 16:30:31: #4 Write peak in narrowPeak format file... SRX2548348.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 16:30:31: #4 Write summits bed file... SRX2548348.20_summits.bed INFO @ Fri, 04 Aug 2017 16:30:31: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (595 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 16:30:32: #4 Write output xls file... SRX2548348.05_peaks.xls INFO @ Fri, 04 Aug 2017 16:30:32: #4 Write peak in narrowPeak format file... SRX2548348.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 16:30:32: #4 Write summits bed file... SRX2548348.05_summits.bed INFO @ Fri, 04 Aug 2017 16:30:32: Done! pass1 - making usageList (14 chroms): 9 millis pass2 - checking and writing primary data (1567 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。