Job ID = 11158495 sra ファイルのダウンロード中... Completed: 1433551K bytes transferred in 29 seconds (400843K 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 21596848 spots for /home/okishinya/chipatlas/results/dm3/SRX4279676/SRR7408126.sra Written 21596848 spots for /home/okishinya/chipatlas/results/dm3/SRX4279676/SRR7408126.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: 01:12:48 21596848 reads; of these: 21596848 (100.00%) were paired; of these: 6142585 (28.44%) aligned concordantly 0 times 13310832 (61.63%) aligned concordantly exactly 1 time 2143431 (9.92%) aligned concordantly >1 times ---- 6142585 pairs aligned concordantly 0 times; of these: 955385 (15.55%) aligned discordantly 1 time ---- 5187200 pairs aligned 0 times concordantly or discordantly; of these: 10374400 mates make up the pairs; of these: 5065130 (48.82%) aligned 0 times 2479517 (23.90%) aligned exactly 1 time 2829753 (27.28%) aligned >1 times 88.27% overall alignment rate Time searching: 01:12:49 Overall time: 01:12:49 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] 1110730 / 15623478 = 0.0711 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, 04 Sep 2018 11:07:25: # Command line: callpeak -t SRX4279676.bam -f BAM -g dm -n SRX4279676.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4279676.10 # format = BAM # ChIP-seq file = ['SRX4279676.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, 04 Sep 2018 11:07:25: #1 read tag files... INFO @ Tue, 04 Sep 2018 11:07:25: # Command line: callpeak -t SRX4279676.bam -f BAM -g dm -n SRX4279676.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4279676.20 # format = BAM # ChIP-seq file = ['SRX4279676.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, 04 Sep 2018 11:07:25: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 11:07:25: #1 read tag files... INFO @ Tue, 04 Sep 2018 11:07:25: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 11:07:25: # Command line: callpeak -t SRX4279676.bam -f BAM -g dm -n SRX4279676.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4279676.05 # format = BAM # ChIP-seq file = ['SRX4279676.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, 04 Sep 2018 11:07:25: #1 read tag files... INFO @ Tue, 04 Sep 2018 11:07:25: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 11:07:32: 1000000 INFO @ Tue, 04 Sep 2018 11:07:32: 1000000 INFO @ Tue, 04 Sep 2018 11:07:33: 1000000 INFO @ Tue, 04 Sep 2018 11:07:39: 2000000 INFO @ Tue, 04 Sep 2018 11:07:40: 2000000 INFO @ Tue, 04 Sep 2018 11:07:40: 2000000 INFO @ Tue, 04 Sep 2018 11:07:47: 3000000 INFO @ Tue, 04 Sep 2018 11:07:48: 3000000 INFO @ Tue, 04 Sep 2018 11:07:48: 3000000 INFO @ Tue, 04 Sep 2018 11:07:54: 4000000 INFO @ Tue, 04 Sep 2018 11:07:56: 4000000 INFO @ Tue, 04 Sep 2018 11:07:56: 4000000 INFO @ Tue, 04 Sep 2018 11:08:02: 5000000 INFO @ Tue, 04 Sep 2018 11:08:04: 5000000 INFO @ Tue, 04 Sep 2018 11:08:04: 5000000 INFO @ Tue, 04 Sep 2018 11:08:09: 6000000 INFO @ Tue, 04 Sep 2018 11:08:11: 6000000 INFO @ Tue, 04 Sep 2018 11:08:12: 6000000 INFO @ Tue, 04 Sep 2018 11:08:16: 7000000 INFO @ Tue, 04 Sep 2018 11:08:19: 7000000 INFO @ Tue, 04 Sep 2018 11:08:19: 7000000 INFO @ Tue, 04 Sep 2018 11:08:24: 8000000 INFO @ Tue, 04 Sep 2018 11:08:27: 8000000 INFO @ Tue, 04 Sep 2018 11:08:27: 8000000 INFO @ Tue, 04 Sep 2018 11:08:31: 9000000 INFO @ Tue, 04 Sep 2018 11:08:35: 9000000 INFO @ Tue, 04 Sep 2018 11:08:35: 9000000 INFO @ Tue, 04 Sep 2018 11:08:39: 10000000 INFO @ Tue, 04 Sep 2018 11:08:43: 10000000 INFO @ Tue, 04 Sep 2018 11:08:43: 10000000 INFO @ Tue, 04 Sep 2018 11:08:46: 11000000 INFO @ Tue, 04 Sep 2018 11:08:50: 11000000 INFO @ Tue, 04 Sep 2018 11:08:51: 11000000 INFO @ Tue, 04 Sep 2018 11:08:54: 12000000 INFO @ Tue, 04 Sep 2018 11:08:58: 12000000 INFO @ Tue, 04 Sep 2018 11:08:59: 12000000 INFO @ Tue, 04 Sep 2018 11:09:01: 13000000 INFO @ Tue, 04 Sep 2018 11:09:06: 13000000 INFO @ Tue, 04 Sep 2018 11:09:06: 13000000 INFO @ Tue, 04 Sep 2018 11:09:09: 14000000 INFO @ Tue, 04 Sep 2018 11:09:14: 14000000 INFO @ Tue, 04 Sep 2018 11:09:14: 14000000 INFO @ Tue, 04 Sep 2018 11:09:16: 15000000 INFO @ Tue, 04 Sep 2018 11:09:21: 15000000 INFO @ Tue, 04 Sep 2018 11:09:22: 15000000 INFO @ Tue, 04 Sep 2018 11:09:24: 16000000 INFO @ Tue, 04 Sep 2018 11:09:29: 16000000 INFO @ Tue, 04 Sep 2018 11:09:30: 16000000 INFO @ Tue, 04 Sep 2018 11:09:31: 17000000 INFO @ Tue, 04 Sep 2018 11:09:37: 17000000 INFO @ Tue, 04 Sep 2018 11:09:37: 17000000 INFO @ Tue, 04 Sep 2018 11:09:38: 18000000 INFO @ Tue, 04 Sep 2018 11:09:44: 18000000 INFO @ Tue, 04 Sep 2018 11:09:45: 18000000 INFO @ Tue, 04 Sep 2018 11:09:46: 19000000 INFO @ Tue, 04 Sep 2018 11:09:52: 19000000 INFO @ Tue, 04 Sep 2018 11:09:53: 19000000 INFO @ Tue, 04 Sep 2018 11:09:53: 20000000 INFO @ Tue, 04 Sep 2018 11:10:00: 20000000 INFO @ Tue, 04 Sep 2018 11:10:00: 20000000 INFO @ Tue, 04 Sep 2018 11:10:00: 21000000 INFO @ Tue, 04 Sep 2018 11:10:07: 21000000 INFO @ Tue, 04 Sep 2018 11:10:08: 22000000 INFO @ Tue, 04 Sep 2018 11:10:08: 21000000 INFO @ Tue, 04 Sep 2018 11:10:15: 22000000 INFO @ Tue, 04 Sep 2018 11:10:15: 23000000 INFO @ Tue, 04 Sep 2018 11:10:15: 22000000 INFO @ Tue, 04 Sep 2018 11:10:22: 24000000 INFO @ Tue, 04 Sep 2018 11:10:23: 23000000 INFO @ Tue, 04 Sep 2018 11:10:23: 23000000 INFO @ Tue, 04 Sep 2018 11:10:30: 25000000 INFO @ Tue, 04 Sep 2018 11:10:30: 24000000 INFO @ Tue, 04 Sep 2018 11:10:31: 24000000 INFO @ Tue, 04 Sep 2018 11:10:37: 26000000 INFO @ Tue, 04 Sep 2018 11:10:38: 25000000 INFO @ Tue, 04 Sep 2018 11:10:38: 25000000 INFO @ Tue, 04 Sep 2018 11:10:44: 27000000 INFO @ Tue, 04 Sep 2018 11:10:45: 26000000 INFO @ Tue, 04 Sep 2018 11:10:46: 26000000 INFO @ Tue, 04 Sep 2018 11:10:52: 28000000 INFO @ Tue, 04 Sep 2018 11:10:53: 27000000 INFO @ Tue, 04 Sep 2018 11:10:53: 27000000 INFO @ Tue, 04 Sep 2018 11:10:59: 29000000 INFO @ Tue, 04 Sep 2018 11:11:01: 28000000 INFO @ Tue, 04 Sep 2018 11:11:01: 28000000 INFO @ Tue, 04 Sep 2018 11:11:06: 30000000 INFO @ Tue, 04 Sep 2018 11:11:08: 29000000 INFO @ Tue, 04 Sep 2018 11:11:08: 29000000 INFO @ Tue, 04 Sep 2018 11:11:13: 31000000 INFO @ Tue, 04 Sep 2018 11:11:15: 30000000 INFO @ Tue, 04 Sep 2018 11:11:16: 30000000 INFO @ Tue, 04 Sep 2018 11:11:21: 32000000 INFO @ Tue, 04 Sep 2018 11:11:23: 31000000 INFO @ Tue, 04 Sep 2018 11:11:24: 31000000 INFO @ Tue, 04 Sep 2018 11:11:28: 33000000 INFO @ Tue, 04 Sep 2018 11:11:31: 32000000 INFO @ Tue, 04 Sep 2018 11:11:31: 32000000 INFO @ Tue, 04 Sep 2018 11:11:35: 34000000 INFO @ Tue, 04 Sep 2018 11:11:38: 33000000 INFO @ Tue, 04 Sep 2018 11:11:39: 33000000 INFO @ Tue, 04 Sep 2018 11:11:43: 35000000 INFO @ Tue, 04 Sep 2018 11:11:46: 34000000 INFO @ Tue, 04 Sep 2018 11:11:46: 34000000 INFO @ Tue, 04 Sep 2018 11:11:49: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 11:11:49: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 11:11:49: #1 total tags in treatment: 14350477 INFO @ Tue, 04 Sep 2018 11:11:49: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 11:11:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 11:11:50: #1 tags after filtering in treatment: 12289941 INFO @ Tue, 04 Sep 2018 11:11:50: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 04 Sep 2018 11:11:50: #1 finished! INFO @ Tue, 04 Sep 2018 11:11:50: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 11:11:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 11:11:51: #2 number of paired peaks: 1621 INFO @ Tue, 04 Sep 2018 11:11:51: start model_add_line... INFO @ Tue, 04 Sep 2018 11:11:51: start X-correlation... INFO @ Tue, 04 Sep 2018 11:11:51: end of X-cor INFO @ Tue, 04 Sep 2018 11:11:51: #2 finished! INFO @ Tue, 04 Sep 2018 11:11:51: #2 predicted fragment length is 174 bps INFO @ Tue, 04 Sep 2018 11:11:51: #2 alternative fragment length(s) may be 174 bps INFO @ Tue, 04 Sep 2018 11:11:51: #2.2 Generate R script for model : SRX4279676.10_model.r INFO @ Tue, 04 Sep 2018 11:11:51: #3 Call peaks... INFO @ Tue, 04 Sep 2018 11:11:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 11:11:53: 35000000 INFO @ Tue, 04 Sep 2018 11:11:54: 35000000 INFO @ Tue, 04 Sep 2018 11:12:00: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 11:12:00: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 11:12:00: #1 total tags in treatment: 14350477 INFO @ Tue, 04 Sep 2018 11:12:00: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 11:12:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 11:12:00: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 11:12:00: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 11:12:00: #1 total tags in treatment: 14350477 INFO @ Tue, 04 Sep 2018 11:12:00: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 11:12:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 11:12:01: #1 tags after filtering in treatment: 12289941 INFO @ Tue, 04 Sep 2018 11:12:01: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 04 Sep 2018 11:12:01: #1 finished! INFO @ Tue, 04 Sep 2018 11:12:01: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 11:12:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 11:12:01: #1 tags after filtering in treatment: 12289941 INFO @ Tue, 04 Sep 2018 11:12:01: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 04 Sep 2018 11:12:01: #1 finished! INFO @ Tue, 04 Sep 2018 11:12:01: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 11:12:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 11:12:02: #2 number of paired peaks: 1621 INFO @ Tue, 04 Sep 2018 11:12:02: start model_add_line... INFO @ Tue, 04 Sep 2018 11:12:02: start X-correlation... INFO @ Tue, 04 Sep 2018 11:12:02: end of X-cor INFO @ Tue, 04 Sep 2018 11:12:02: #2 finished! INFO @ Tue, 04 Sep 2018 11:12:02: #2 predicted fragment length is 174 bps INFO @ Tue, 04 Sep 2018 11:12:02: #2 alternative fragment length(s) may be 174 bps INFO @ Tue, 04 Sep 2018 11:12:02: #2.2 Generate R script for model : SRX4279676.05_model.r INFO @ Tue, 04 Sep 2018 11:12:02: #3 Call peaks... INFO @ Tue, 04 Sep 2018 11:12:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 11:12:02: #2 number of paired peaks: 1621 INFO @ Tue, 04 Sep 2018 11:12:02: start model_add_line... INFO @ Tue, 04 Sep 2018 11:12:02: start X-correlation... INFO @ Tue, 04 Sep 2018 11:12:02: end of X-cor INFO @ Tue, 04 Sep 2018 11:12:02: #2 finished! INFO @ Tue, 04 Sep 2018 11:12:02: #2 predicted fragment length is 174 bps INFO @ Tue, 04 Sep 2018 11:12:02: #2 alternative fragment length(s) may be 174 bps INFO @ Tue, 04 Sep 2018 11:12:02: #2.2 Generate R script for model : SRX4279676.20_model.r INFO @ Tue, 04 Sep 2018 11:12:02: #3 Call peaks... INFO @ Tue, 04 Sep 2018 11:12:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 11:12:24: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 11:12:33: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 11:12:33: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 11:12:42: #4 Write output xls file... SRX4279676.10_peaks.xls INFO @ Tue, 04 Sep 2018 11:12:42: #4 Write peak in narrowPeak format file... SRX4279676.10_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 11:12:42: #4 Write summits bed file... SRX4279676.10_summits.bed INFO @ Tue, 04 Sep 2018 11:12:42: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (21539 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 11:12:49: #4 Write output xls file... SRX4279676.20_peaks.xls INFO @ Tue, 04 Sep 2018 11:12:49: #4 Write peak in narrowPeak format file... SRX4279676.20_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 11:12:49: #4 Write summits bed file... SRX4279676.20_summits.bed INFO @ Tue, 04 Sep 2018 11:12:49: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9792 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 11:12:52: #4 Write output xls file... SRX4279676.05_peaks.xls INFO @ Tue, 04 Sep 2018 11:12:52: #4 Write peak in narrowPeak format file... SRX4279676.05_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 11:12:52: #4 Write summits bed file... SRX4279676.05_summits.bed INFO @ Tue, 04 Sep 2018 11:12:52: Done! pass1 - making usageList (15 chroms): 7 millis pass2 - checking and writing primary data (33097 records, 4 fields): 36 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。