Job ID = 9158414 sra ファイルのダウンロード中... Completed: 1720436K bytes transferred in 12 seconds (1101136K 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 27119779 spots for /home/okishinya/chipatlas/results/dm3/SRX1179571/SRR2232432.sra Written 27119779 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: 01:44:50 27119779 reads; of these: 27119779 (100.00%) were paired; of these: 945975 (3.49%) aligned concordantly 0 times 16501514 (60.85%) aligned concordantly exactly 1 time 9672290 (35.67%) aligned concordantly >1 times ---- 945975 pairs aligned concordantly 0 times; of these: 11703 (1.24%) aligned discordantly 1 time ---- 934272 pairs aligned 0 times concordantly or discordantly; of these: 1868544 mates make up the pairs; of these: 1037599 (55.53%) aligned 0 times 558153 (29.87%) aligned exactly 1 time 272792 (14.60%) aligned >1 times 98.09% overall alignment rate Time searching: 01:44:50 Overall time: 01:44:50 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 24 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] 12490768 / 26069198 = 0.4791 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 @ Tue, 27 Jun 2017 18:35:18: # Command line: callpeak -t SRX1179571.bam -f BAM -g dm -n SRX1179571.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1179571.10 # format = BAM # ChIP-seq file = ['SRX1179571.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 @ Tue, 27 Jun 2017 18:35:18: #1 read tag files... INFO @ Tue, 27 Jun 2017 18:35:18: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 18:35:18: # Command line: callpeak -t SRX1179571.bam -f BAM -g dm -n SRX1179571.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1179571.05 # format = BAM # ChIP-seq file = ['SRX1179571.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 @ Tue, 27 Jun 2017 18:35:18: #1 read tag files... INFO @ Tue, 27 Jun 2017 18:35:18: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 18:35:18: # Command line: callpeak -t SRX1179571.bam -f BAM -g dm -n SRX1179571.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1179571.20 # format = BAM # ChIP-seq file = ['SRX1179571.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 @ Tue, 27 Jun 2017 18:35:18: #1 read tag files... INFO @ Tue, 27 Jun 2017 18:35:18: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 18:35:26: 1000000 INFO @ Tue, 27 Jun 2017 18:35:27: 1000000 INFO @ Tue, 27 Jun 2017 18:35:27: 1000000 INFO @ Tue, 27 Jun 2017 18:35:33: 2000000 INFO @ Tue, 27 Jun 2017 18:35:36: 2000000 INFO @ Tue, 27 Jun 2017 18:35:36: 2000000 INFO @ Tue, 27 Jun 2017 18:35:42: 3000000 INFO @ Tue, 27 Jun 2017 18:35:44: 3000000 INFO @ Tue, 27 Jun 2017 18:35:45: 3000000 INFO @ Tue, 27 Jun 2017 18:35:50: 4000000 INFO @ Tue, 27 Jun 2017 18:35:52: 4000000 INFO @ Tue, 27 Jun 2017 18:35:54: 4000000 INFO @ Tue, 27 Jun 2017 18:35:58: 5000000 INFO @ Tue, 27 Jun 2017 18:36:00: 5000000 INFO @ Tue, 27 Jun 2017 18:36:03: 5000000 INFO @ Tue, 27 Jun 2017 18:36:06: 6000000 INFO @ Tue, 27 Jun 2017 18:36:09: 6000000 INFO @ Tue, 27 Jun 2017 18:36:12: 6000000 INFO @ Tue, 27 Jun 2017 18:36:14: 7000000 INFO @ Tue, 27 Jun 2017 18:36:18: 7000000 INFO @ Tue, 27 Jun 2017 18:36:21: 7000000 INFO @ Tue, 27 Jun 2017 18:36:21: 8000000 INFO @ Tue, 27 Jun 2017 18:36:28: 8000000 INFO @ Tue, 27 Jun 2017 18:36:30: 9000000 INFO @ Tue, 27 Jun 2017 18:36:30: 8000000 INFO @ Tue, 27 Jun 2017 18:36:36: 9000000 INFO @ Tue, 27 Jun 2017 18:36:38: 9000000 INFO @ Tue, 27 Jun 2017 18:36:38: 10000000 INFO @ Tue, 27 Jun 2017 18:36:45: 10000000 INFO @ Tue, 27 Jun 2017 18:36:46: 10000000 INFO @ Tue, 27 Jun 2017 18:36:47: 11000000 INFO @ Tue, 27 Jun 2017 18:36:54: 11000000 INFO @ Tue, 27 Jun 2017 18:36:54: 11000000 INFO @ Tue, 27 Jun 2017 18:36:55: 12000000 INFO @ Tue, 27 Jun 2017 18:37:02: 12000000 INFO @ Tue, 27 Jun 2017 18:37:02: 12000000 INFO @ Tue, 27 Jun 2017 18:37:04: 13000000 INFO @ Tue, 27 Jun 2017 18:37:10: 13000000 INFO @ Tue, 27 Jun 2017 18:37:11: 13000000 INFO @ Tue, 27 Jun 2017 18:37:13: 14000000 INFO @ Tue, 27 Jun 2017 18:37:18: 14000000 INFO @ Tue, 27 Jun 2017 18:37:19: 14000000 INFO @ Tue, 27 Jun 2017 18:37:21: 15000000 INFO @ Tue, 27 Jun 2017 18:37:25: 15000000 INFO @ Tue, 27 Jun 2017 18:37:28: 15000000 INFO @ Tue, 27 Jun 2017 18:37:30: 16000000 INFO @ Tue, 27 Jun 2017 18:37:33: 16000000 INFO @ Tue, 27 Jun 2017 18:37:37: 16000000 INFO @ Tue, 27 Jun 2017 18:37:38: 17000000 INFO @ Tue, 27 Jun 2017 18:37:41: 17000000 INFO @ Tue, 27 Jun 2017 18:37:45: 17000000 INFO @ Tue, 27 Jun 2017 18:37:47: 18000000 INFO @ Tue, 27 Jun 2017 18:37:49: 18000000 INFO @ Tue, 27 Jun 2017 18:37:54: 18000000 INFO @ Tue, 27 Jun 2017 18:37:55: 19000000 INFO @ Tue, 27 Jun 2017 18:37:57: 19000000 INFO @ Tue, 27 Jun 2017 18:38:02: 19000000 INFO @ Tue, 27 Jun 2017 18:38:04: 20000000 INFO @ Tue, 27 Jun 2017 18:38:04: 20000000 INFO @ Tue, 27 Jun 2017 18:38:11: 20000000 INFO @ Tue, 27 Jun 2017 18:38:12: 21000000 INFO @ Tue, 27 Jun 2017 18:38:13: 21000000 INFO @ Tue, 27 Jun 2017 18:38:19: 21000000 INFO @ Tue, 27 Jun 2017 18:38:20: 22000000 INFO @ Tue, 27 Jun 2017 18:38:21: 22000000 INFO @ Tue, 27 Jun 2017 18:38:28: 23000000 INFO @ Tue, 27 Jun 2017 18:38:28: 22000000 INFO @ Tue, 27 Jun 2017 18:38:30: 23000000 INFO @ Tue, 27 Jun 2017 18:38:35: 24000000 INFO @ Tue, 27 Jun 2017 18:38:37: 23000000 INFO @ Tue, 27 Jun 2017 18:38:39: 24000000 INFO @ Tue, 27 Jun 2017 18:38:43: 25000000 INFO @ Tue, 27 Jun 2017 18:38:45: 24000000 INFO @ Tue, 27 Jun 2017 18:38:47: 25000000 INFO @ Tue, 27 Jun 2017 18:38:51: 26000000 INFO @ Tue, 27 Jun 2017 18:38:54: 25000000 INFO @ Tue, 27 Jun 2017 18:38:56: 26000000 INFO @ Tue, 27 Jun 2017 18:38:59: 27000000 INFO @ Tue, 27 Jun 2017 18:39:03: 26000000 INFO @ Tue, 27 Jun 2017 18:39:04: 27000000 INFO @ Tue, 27 Jun 2017 18:39:07: 28000000 INFO @ Tue, 27 Jun 2017 18:39:09: #1 tag size is determined as 76 bps INFO @ Tue, 27 Jun 2017 18:39:09: #1 tag size = 76 INFO @ Tue, 27 Jun 2017 18:39:09: #1 total tags in treatment: 13688571 INFO @ Tue, 27 Jun 2017 18:39:09: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 18:39:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 18:39:09: #1 tags after filtering in treatment: 10840938 INFO @ Tue, 27 Jun 2017 18:39:09: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 27 Jun 2017 18:39:09: #1 finished! INFO @ Tue, 27 Jun 2017 18:39:09: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 18:39:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 18:39:10: #2 number of paired peaks: 1419 INFO @ Tue, 27 Jun 2017 18:39:10: start model_add_line... INFO @ Tue, 27 Jun 2017 18:39:10: start X-correlation... INFO @ Tue, 27 Jun 2017 18:39:10: end of X-cor INFO @ Tue, 27 Jun 2017 18:39:10: #2 finished! INFO @ Tue, 27 Jun 2017 18:39:10: #2 predicted fragment length is 147 bps INFO @ Tue, 27 Jun 2017 18:39:10: #2 alternative fragment length(s) may be 4,147 bps INFO @ Tue, 27 Jun 2017 18:39:10: #2.2 Generate R script for model : SRX1179571.05_model.r WARNING @ Tue, 27 Jun 2017 18:39:10: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 18:39:10: #2 You may need to consider one of the other alternative d(s): 4,147 WARNING @ Tue, 27 Jun 2017 18:39:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 18:39:10: #3 Call peaks... INFO @ Tue, 27 Jun 2017 18:39:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 18:39:11: 27000000 INFO @ Tue, 27 Jun 2017 18:39:13: 28000000 INFO @ Tue, 27 Jun 2017 18:39:15: #1 tag size is determined as 76 bps INFO @ Tue, 27 Jun 2017 18:39:15: #1 tag size = 76 INFO @ Tue, 27 Jun 2017 18:39:15: #1 total tags in treatment: 13688571 INFO @ Tue, 27 Jun 2017 18:39:15: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 18:39:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 18:39:15: #1 tags after filtering in treatment: 10840938 INFO @ Tue, 27 Jun 2017 18:39:15: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 27 Jun 2017 18:39:15: #1 finished! INFO @ Tue, 27 Jun 2017 18:39:15: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 18:39:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 18:39:16: #2 number of paired peaks: 1419 INFO @ Tue, 27 Jun 2017 18:39:16: start model_add_line... INFO @ Tue, 27 Jun 2017 18:39:16: start X-correlation... INFO @ Tue, 27 Jun 2017 18:39:16: end of X-cor INFO @ Tue, 27 Jun 2017 18:39:16: #2 finished! INFO @ Tue, 27 Jun 2017 18:39:16: #2 predicted fragment length is 147 bps INFO @ Tue, 27 Jun 2017 18:39:16: #2 alternative fragment length(s) may be 4,147 bps INFO @ Tue, 27 Jun 2017 18:39:16: #2.2 Generate R script for model : SRX1179571.10_model.r WARNING @ Tue, 27 Jun 2017 18:39:16: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 18:39:16: #2 You may need to consider one of the other alternative d(s): 4,147 WARNING @ Tue, 27 Jun 2017 18:39:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 18:39:16: #3 Call peaks... INFO @ Tue, 27 Jun 2017 18:39:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 18:39:19: 28000000 INFO @ Tue, 27 Jun 2017 18:39:20: #1 tag size is determined as 76 bps INFO @ Tue, 27 Jun 2017 18:39:20: #1 tag size = 76 INFO @ Tue, 27 Jun 2017 18:39:20: #1 total tags in treatment: 13688571 INFO @ Tue, 27 Jun 2017 18:39:20: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 18:39:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 18:39:21: #1 tags after filtering in treatment: 10840938 INFO @ Tue, 27 Jun 2017 18:39:21: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 27 Jun 2017 18:39:21: #1 finished! INFO @ Tue, 27 Jun 2017 18:39:21: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 18:39:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 18:39:22: #2 number of paired peaks: 1419 INFO @ Tue, 27 Jun 2017 18:39:22: start model_add_line... INFO @ Tue, 27 Jun 2017 18:39:22: start X-correlation... INFO @ Tue, 27 Jun 2017 18:39:22: end of X-cor INFO @ Tue, 27 Jun 2017 18:39:22: #2 finished! INFO @ Tue, 27 Jun 2017 18:39:22: #2 predicted fragment length is 147 bps INFO @ Tue, 27 Jun 2017 18:39:22: #2 alternative fragment length(s) may be 4,147 bps INFO @ Tue, 27 Jun 2017 18:39:22: #2.2 Generate R script for model : SRX1179571.20_model.r WARNING @ Tue, 27 Jun 2017 18:39:22: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 18:39:22: #2 You may need to consider one of the other alternative d(s): 4,147 WARNING @ Tue, 27 Jun 2017 18:39:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 18:39:22: #3 Call peaks... INFO @ Tue, 27 Jun 2017 18:39:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 18:39:37: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 18:39:43: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 18:39:48: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 18:39:53: #4 Write output xls file... SRX1179571.05_peaks.xls INFO @ Tue, 27 Jun 2017 18:39:53: #4 Write peak in narrowPeak format file... SRX1179571.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 18:39:53: #4 Write summits bed file... SRX1179571.05_summits.bed INFO @ Tue, 27 Jun 2017 18:39:53: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4032 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 18:39:59: #4 Write output xls file... SRX1179571.10_peaks.xls INFO @ Tue, 27 Jun 2017 18:39:59: #4 Write peak in narrowPeak format file... SRX1179571.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 18:39:59: #4 Write summits bed file... SRX1179571.10_summits.bed INFO @ Tue, 27 Jun 2017 18:39:59: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1945 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 18:40:02: #4 Write output xls file... SRX1179571.20_peaks.xls INFO @ Tue, 27 Jun 2017 18:40:02: #4 Write peak in narrowPeak format file... SRX1179571.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 18:40:02: #4 Write summits bed file... SRX1179571.20_summits.bed INFO @ Tue, 27 Jun 2017 18:40:02: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (970 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。