Job ID = 10845222 sra ファイルのダウンロード中... Completed: 892632K bytes transferred in 52 seconds (139404K bits/sec), in 1 file. 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... Read 16981582 spots for /home/okishinya/chipatlas/results/dm3/SRX3632920/SRR6655572.sra Written 16981582 spots for /home/okishinya/chipatlas/results/dm3/SRX3632920/SRR6655572.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:27:53 16981582 reads; of these: 16981582 (100.00%) were paired; of these: 851576 (5.01%) aligned concordantly 0 times 14480273 (85.27%) aligned concordantly exactly 1 time 1649733 (9.71%) aligned concordantly >1 times ---- 851576 pairs aligned concordantly 0 times; of these: 255903 (30.05%) aligned discordantly 1 time ---- 595673 pairs aligned 0 times concordantly or discordantly; of these: 1191346 mates make up the pairs; of these: 675338 (56.69%) aligned 0 times 390966 (32.82%) aligned exactly 1 time 125042 (10.50%) aligned >1 times 98.01% overall alignment rate Time searching: 00:27:54 Overall time: 00:27:54 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_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] 843259 / 16341954 = 0.0516 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, 04 Jul 2018 10:09:07: # Command line: callpeak -t SRX3632920.bam -f BAM -g dm -n SRX3632920.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3632920.10 # format = BAM # ChIP-seq file = ['SRX3632920.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, 04 Jul 2018 10:09:07: #1 read tag files... INFO @ Wed, 04 Jul 2018 10:09:07: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 10:09:07: # Command line: callpeak -t SRX3632920.bam -f BAM -g dm -n SRX3632920.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3632920.20 # format = BAM # ChIP-seq file = ['SRX3632920.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, 04 Jul 2018 10:09:07: #1 read tag files... INFO @ Wed, 04 Jul 2018 10:09:07: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 10:09:07: # Command line: callpeak -t SRX3632920.bam -f BAM -g dm -n SRX3632920.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3632920.05 # format = BAM # ChIP-seq file = ['SRX3632920.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, 04 Jul 2018 10:09:07: #1 read tag files... INFO @ Wed, 04 Jul 2018 10:09:07: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 10:09:13: 1000000 INFO @ Wed, 04 Jul 2018 10:09:14: 1000000 INFO @ Wed, 04 Jul 2018 10:09:14: 1000000 INFO @ Wed, 04 Jul 2018 10:09:20: 2000000 INFO @ Wed, 04 Jul 2018 10:09:20: 2000000 INFO @ Wed, 04 Jul 2018 10:09:20: 2000000 INFO @ Wed, 04 Jul 2018 10:09:26: 3000000 INFO @ Wed, 04 Jul 2018 10:09:27: 3000000 INFO @ Wed, 04 Jul 2018 10:09:27: 3000000 INFO @ Wed, 04 Jul 2018 10:09:32: 4000000 INFO @ Wed, 04 Jul 2018 10:09:33: 4000000 INFO @ Wed, 04 Jul 2018 10:09:34: 4000000 INFO @ Wed, 04 Jul 2018 10:09:38: 5000000 INFO @ Wed, 04 Jul 2018 10:09:40: 5000000 INFO @ Wed, 04 Jul 2018 10:09:40: 5000000 INFO @ Wed, 04 Jul 2018 10:09:45: 6000000 INFO @ Wed, 04 Jul 2018 10:09:46: 6000000 INFO @ Wed, 04 Jul 2018 10:09:47: 6000000 INFO @ Wed, 04 Jul 2018 10:09:51: 7000000 INFO @ Wed, 04 Jul 2018 10:09:53: 7000000 INFO @ Wed, 04 Jul 2018 10:09:54: 7000000 INFO @ Wed, 04 Jul 2018 10:09:57: 8000000 INFO @ Wed, 04 Jul 2018 10:10:00: 8000000 INFO @ Wed, 04 Jul 2018 10:10:01: 8000000 INFO @ Wed, 04 Jul 2018 10:10:03: 9000000 INFO @ Wed, 04 Jul 2018 10:10:06: 9000000 INFO @ Wed, 04 Jul 2018 10:10:07: 9000000 INFO @ Wed, 04 Jul 2018 10:10:10: 10000000 INFO @ Wed, 04 Jul 2018 10:10:13: 10000000 INFO @ Wed, 04 Jul 2018 10:10:14: 10000000 INFO @ Wed, 04 Jul 2018 10:10:17: 11000000 INFO @ Wed, 04 Jul 2018 10:10:20: 11000000 INFO @ Wed, 04 Jul 2018 10:10:20: 11000000 INFO @ Wed, 04 Jul 2018 10:10:24: 12000000 INFO @ Wed, 04 Jul 2018 10:10:26: 12000000 INFO @ Wed, 04 Jul 2018 10:10:27: 12000000 INFO @ Wed, 04 Jul 2018 10:10:30: 13000000 INFO @ Wed, 04 Jul 2018 10:10:32: 13000000 INFO @ Wed, 04 Jul 2018 10:10:34: 13000000 INFO @ Wed, 04 Jul 2018 10:10:37: 14000000 INFO @ Wed, 04 Jul 2018 10:10:38: 14000000 INFO @ Wed, 04 Jul 2018 10:10:41: 14000000 INFO @ Wed, 04 Jul 2018 10:10:44: 15000000 INFO @ Wed, 04 Jul 2018 10:10:45: 15000000 INFO @ Wed, 04 Jul 2018 10:10:48: 15000000 INFO @ Wed, 04 Jul 2018 10:10:51: 16000000 INFO @ Wed, 04 Jul 2018 10:10:51: 16000000 INFO @ Wed, 04 Jul 2018 10:10:55: 16000000 INFO @ Wed, 04 Jul 2018 10:10:58: 17000000 INFO @ Wed, 04 Jul 2018 10:10:58: 17000000 INFO @ Wed, 04 Jul 2018 10:11:02: 17000000 INFO @ Wed, 04 Jul 2018 10:11:04: 18000000 INFO @ Wed, 04 Jul 2018 10:11:05: 18000000 INFO @ Wed, 04 Jul 2018 10:11:09: 18000000 INFO @ Wed, 04 Jul 2018 10:11:10: 19000000 INFO @ Wed, 04 Jul 2018 10:11:12: 19000000 INFO @ Wed, 04 Jul 2018 10:11:16: 19000000 INFO @ Wed, 04 Jul 2018 10:11:17: 20000000 INFO @ Wed, 04 Jul 2018 10:11:19: 20000000 INFO @ Wed, 04 Jul 2018 10:11:23: 21000000 INFO @ Wed, 04 Jul 2018 10:11:23: 20000000 INFO @ Wed, 04 Jul 2018 10:11:26: 21000000 INFO @ Wed, 04 Jul 2018 10:11:29: 22000000 INFO @ Wed, 04 Jul 2018 10:11:30: 21000000 INFO @ Wed, 04 Jul 2018 10:11:33: 22000000 INFO @ Wed, 04 Jul 2018 10:11:35: 23000000 INFO @ Wed, 04 Jul 2018 10:11:37: 22000000 INFO @ Wed, 04 Jul 2018 10:11:40: 23000000 INFO @ Wed, 04 Jul 2018 10:11:42: 24000000 INFO @ Wed, 04 Jul 2018 10:11:44: 23000000 INFO @ Wed, 04 Jul 2018 10:11:47: 24000000 INFO @ Wed, 04 Jul 2018 10:11:48: 25000000 INFO @ Wed, 04 Jul 2018 10:11:51: 24000000 INFO @ Wed, 04 Jul 2018 10:11:53: 25000000 INFO @ Wed, 04 Jul 2018 10:11:54: 26000000 INFO @ Wed, 04 Jul 2018 10:11:58: 25000000 INFO @ Wed, 04 Jul 2018 10:12:00: 26000000 INFO @ Wed, 04 Jul 2018 10:12:00: 27000000 INFO @ Wed, 04 Jul 2018 10:12:05: 26000000 INFO @ Wed, 04 Jul 2018 10:12:07: 28000000 INFO @ Wed, 04 Jul 2018 10:12:07: 27000000 INFO @ Wed, 04 Jul 2018 10:12:12: 27000000 INFO @ Wed, 04 Jul 2018 10:12:13: 29000000 INFO @ Wed, 04 Jul 2018 10:12:14: 28000000 INFO @ Wed, 04 Jul 2018 10:12:19: 28000000 INFO @ Wed, 04 Jul 2018 10:12:19: 30000000 INFO @ Wed, 04 Jul 2018 10:12:21: 29000000 INFO @ Wed, 04 Jul 2018 10:12:25: 31000000 INFO @ Wed, 04 Jul 2018 10:12:25: 29000000 INFO @ Wed, 04 Jul 2018 10:12:28: 30000000 INFO @ Wed, 04 Jul 2018 10:12:29: #1 tag size is determined as 75 bps INFO @ Wed, 04 Jul 2018 10:12:29: #1 tag size = 75 INFO @ Wed, 04 Jul 2018 10:12:29: #1 total tags in treatment: 15294661 INFO @ Wed, 04 Jul 2018 10:12:29: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 10:12:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 10:12:29: #1 tags after filtering in treatment: 12657905 INFO @ Wed, 04 Jul 2018 10:12:29: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 04 Jul 2018 10:12:29: #1 finished! INFO @ Wed, 04 Jul 2018 10:12:29: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 10:12:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 10:12:30: #2 number of paired peaks: 128 WARNING @ Wed, 04 Jul 2018 10:12:30: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Wed, 04 Jul 2018 10:12:30: start model_add_line... INFO @ Wed, 04 Jul 2018 10:12:30: start X-correlation... INFO @ Wed, 04 Jul 2018 10:12:30: end of X-cor INFO @ Wed, 04 Jul 2018 10:12:30: #2 finished! INFO @ Wed, 04 Jul 2018 10:12:30: #2 predicted fragment length is 205 bps INFO @ Wed, 04 Jul 2018 10:12:30: #2 alternative fragment length(s) may be 4,161,205,230,249 bps INFO @ Wed, 04 Jul 2018 10:12:30: #2.2 Generate R script for model : SRX3632920.10_model.r INFO @ Wed, 04 Jul 2018 10:12:30: #3 Call peaks... INFO @ Wed, 04 Jul 2018 10:12:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 10:12:32: 30000000 INFO @ Wed, 04 Jul 2018 10:12:35: 31000000 INFO @ Wed, 04 Jul 2018 10:12:38: #1 tag size is determined as 75 bps INFO @ Wed, 04 Jul 2018 10:12:38: #1 tag size = 75 INFO @ Wed, 04 Jul 2018 10:12:38: #1 total tags in treatment: 15294661 INFO @ Wed, 04 Jul 2018 10:12:38: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 10:12:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 10:12:39: #1 tags after filtering in treatment: 12657905 INFO @ Wed, 04 Jul 2018 10:12:39: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 04 Jul 2018 10:12:39: #1 finished! INFO @ Wed, 04 Jul 2018 10:12:39: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 10:12:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 10:12:39: 31000000 INFO @ Wed, 04 Jul 2018 10:12:39: #2 number of paired peaks: 128 WARNING @ Wed, 04 Jul 2018 10:12:39: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Wed, 04 Jul 2018 10:12:39: start model_add_line... INFO @ Wed, 04 Jul 2018 10:12:40: start X-correlation... INFO @ Wed, 04 Jul 2018 10:12:40: end of X-cor INFO @ Wed, 04 Jul 2018 10:12:40: #2 finished! INFO @ Wed, 04 Jul 2018 10:12:40: #2 predicted fragment length is 205 bps INFO @ Wed, 04 Jul 2018 10:12:40: #2 alternative fragment length(s) may be 4,161,205,230,249 bps INFO @ Wed, 04 Jul 2018 10:12:40: #2.2 Generate R script for model : SRX3632920.05_model.r INFO @ Wed, 04 Jul 2018 10:12:40: #3 Call peaks... INFO @ Wed, 04 Jul 2018 10:12:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 10:12:43: #1 tag size is determined as 75 bps INFO @ Wed, 04 Jul 2018 10:12:43: #1 tag size = 75 INFO @ Wed, 04 Jul 2018 10:12:43: #1 total tags in treatment: 15294661 INFO @ Wed, 04 Jul 2018 10:12:43: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 10:12:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 10:12:43: #1 tags after filtering in treatment: 12657905 INFO @ Wed, 04 Jul 2018 10:12:43: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 04 Jul 2018 10:12:43: #1 finished! INFO @ Wed, 04 Jul 2018 10:12:43: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 10:12:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 10:12:44: #2 number of paired peaks: 128 WARNING @ Wed, 04 Jul 2018 10:12:44: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Wed, 04 Jul 2018 10:12:44: start model_add_line... INFO @ Wed, 04 Jul 2018 10:12:44: start X-correlation... INFO @ Wed, 04 Jul 2018 10:12:44: end of X-cor INFO @ Wed, 04 Jul 2018 10:12:44: #2 finished! INFO @ Wed, 04 Jul 2018 10:12:44: #2 predicted fragment length is 205 bps INFO @ Wed, 04 Jul 2018 10:12:44: #2 alternative fragment length(s) may be 4,161,205,230,249 bps INFO @ Wed, 04 Jul 2018 10:12:44: #2.2 Generate R script for model : SRX3632920.20_model.r INFO @ Wed, 04 Jul 2018 10:12:44: #3 Call peaks... INFO @ Wed, 04 Jul 2018 10:12:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 10:12:59: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 10:13:09: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 10:13:13: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 10:13:15: #4 Write output xls file... SRX3632920.10_peaks.xls INFO @ Wed, 04 Jul 2018 10:13:15: #4 Write peak in narrowPeak format file... SRX3632920.10_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 10:13:15: #4 Write summits bed file... SRX3632920.10_summits.bed INFO @ Wed, 04 Jul 2018 10:13:15: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1603 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 10:13:24: #4 Write output xls file... SRX3632920.05_peaks.xls INFO @ Wed, 04 Jul 2018 10:13:24: #4 Write peak in narrowPeak format file... SRX3632920.05_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 10:13:24: #4 Write summits bed file... SRX3632920.05_summits.bed INFO @ Wed, 04 Jul 2018 10:13:24: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4015 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 10:13:29: #4 Write output xls file... SRX3632920.20_peaks.xls INFO @ Wed, 04 Jul 2018 10:13:29: #4 Write peak in narrowPeak format file... SRX3632920.20_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 10:13:29: #4 Write summits bed file... SRX3632920.20_summits.bed INFO @ Wed, 04 Jul 2018 10:13:29: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (318 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。