Job ID = 11158504 sra ファイルのダウンロード中... Completed: 1643698K bytes transferred in 41 seconds (325012K 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 25106138 spots for /home/okishinya/chipatlas/results/dm3/SRX4279690/SRR7408112.sra Written 25106138 spots for /home/okishinya/chipatlas/results/dm3/SRX4279690/SRR7408112.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: 01:12:47 25106138 reads; of these: 25106138 (100.00%) were paired; of these: 4965448 (19.78%) aligned concordantly 0 times 17852051 (71.11%) aligned concordantly exactly 1 time 2288639 (9.12%) aligned concordantly >1 times ---- 4965448 pairs aligned concordantly 0 times; of these: 503170 (10.13%) aligned discordantly 1 time ---- 4462278 pairs aligned 0 times concordantly or discordantly; of these: 8924556 mates make up the pairs; of these: 4659953 (52.21%) aligned 0 times 1878874 (21.05%) aligned exactly 1 time 2385729 (26.73%) aligned >1 times 90.72% overall alignment rate Time searching: 01:12:48 Overall time: 01:12:48 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 20 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] 1224552 / 20224499 = 0.0605 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 11:10:55: # Command line: callpeak -t SRX4279690.bam -f BAM -g dm -n SRX4279690.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4279690.05 # format = BAM # ChIP-seq file = ['SRX4279690.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 11:10:55: # Command line: callpeak -t SRX4279690.bam -f BAM -g dm -n SRX4279690.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4279690.20 # format = BAM # ChIP-seq file = ['SRX4279690.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 11:10:55: # Command line: callpeak -t SRX4279690.bam -f BAM -g dm -n SRX4279690.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4279690.10 # format = BAM # ChIP-seq file = ['SRX4279690.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 11:10:55: #1 read tag files... INFO @ Tue, 04 Sep 2018 11:10:55: #1 read tag files... INFO @ Tue, 04 Sep 2018 11:10:55: #1 read tag files... INFO @ Tue, 04 Sep 2018 11:10:55: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 11:10:55: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 11:10:55: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 11:11:02: 1000000 INFO @ Tue, 04 Sep 2018 11:11:02: 1000000 INFO @ Tue, 04 Sep 2018 11:11:03: 1000000 INFO @ Tue, 04 Sep 2018 11:11:10: 2000000 INFO @ Tue, 04 Sep 2018 11:11:10: 2000000 INFO @ Tue, 04 Sep 2018 11:11:10: 2000000 INFO @ Tue, 04 Sep 2018 11:11:18: 3000000 INFO @ Tue, 04 Sep 2018 11:11:18: 3000000 INFO @ Tue, 04 Sep 2018 11:11:18: 3000000 INFO @ Tue, 04 Sep 2018 11:11:25: 4000000 INFO @ Tue, 04 Sep 2018 11:11:25: 4000000 INFO @ Tue, 04 Sep 2018 11:11:26: 4000000 INFO @ Tue, 04 Sep 2018 11:11:33: 5000000 INFO @ Tue, 04 Sep 2018 11:11:33: 5000000 INFO @ Tue, 04 Sep 2018 11:11:33: 5000000 INFO @ Tue, 04 Sep 2018 11:11:41: 6000000 INFO @ Tue, 04 Sep 2018 11:11:41: 6000000 INFO @ Tue, 04 Sep 2018 11:11:41: 6000000 INFO @ Tue, 04 Sep 2018 11:11:48: 7000000 INFO @ Tue, 04 Sep 2018 11:11:48: 7000000 INFO @ Tue, 04 Sep 2018 11:11:48: 7000000 INFO @ Tue, 04 Sep 2018 11:11:56: 8000000 INFO @ Tue, 04 Sep 2018 11:11:56: 8000000 INFO @ Tue, 04 Sep 2018 11:11:56: 8000000 INFO @ Tue, 04 Sep 2018 11:12:03: 9000000 INFO @ Tue, 04 Sep 2018 11:12:03: 9000000 INFO @ Tue, 04 Sep 2018 11:12:04: 9000000 INFO @ Tue, 04 Sep 2018 11:12:11: 10000000 INFO @ Tue, 04 Sep 2018 11:12:11: 10000000 INFO @ Tue, 04 Sep 2018 11:12:11: 10000000 INFO @ Tue, 04 Sep 2018 11:12:19: 11000000 INFO @ Tue, 04 Sep 2018 11:12:19: 11000000 INFO @ Tue, 04 Sep 2018 11:12:19: 11000000 INFO @ Tue, 04 Sep 2018 11:12:26: 12000000 INFO @ Tue, 04 Sep 2018 11:12:26: 12000000 INFO @ Tue, 04 Sep 2018 11:12:26: 12000000 INFO @ Tue, 04 Sep 2018 11:12:34: 13000000 INFO @ Tue, 04 Sep 2018 11:12:34: 13000000 INFO @ Tue, 04 Sep 2018 11:12:34: 13000000 INFO @ Tue, 04 Sep 2018 11:12:42: 14000000 INFO @ Tue, 04 Sep 2018 11:12:42: 14000000 INFO @ Tue, 04 Sep 2018 11:12:42: 14000000 INFO @ Tue, 04 Sep 2018 11:12:49: 15000000 INFO @ Tue, 04 Sep 2018 11:12:49: 15000000 INFO @ Tue, 04 Sep 2018 11:12:49: 15000000 INFO @ Tue, 04 Sep 2018 11:12:57: 16000000 INFO @ Tue, 04 Sep 2018 11:12:57: 16000000 INFO @ Tue, 04 Sep 2018 11:12:57: 16000000 INFO @ Tue, 04 Sep 2018 11:13:04: 17000000 INFO @ Tue, 04 Sep 2018 11:13:04: 17000000 INFO @ Tue, 04 Sep 2018 11:13:05: 17000000 INFO @ Tue, 04 Sep 2018 11:13:12: 18000000 INFO @ Tue, 04 Sep 2018 11:13:12: 18000000 INFO @ Tue, 04 Sep 2018 11:13:12: 18000000 INFO @ Tue, 04 Sep 2018 11:13:20: 19000000 INFO @ Tue, 04 Sep 2018 11:13:20: 19000000 INFO @ Tue, 04 Sep 2018 11:13:20: 19000000 INFO @ Tue, 04 Sep 2018 11:13:27: 20000000 INFO @ Tue, 04 Sep 2018 11:13:27: 20000000 INFO @ Tue, 04 Sep 2018 11:13:27: 20000000 INFO @ Tue, 04 Sep 2018 11:13:35: 21000000 INFO @ Tue, 04 Sep 2018 11:13:35: 21000000 INFO @ Tue, 04 Sep 2018 11:13:35: 21000000 INFO @ Tue, 04 Sep 2018 11:13:42: 22000000 INFO @ Tue, 04 Sep 2018 11:13:42: 22000000 INFO @ Tue, 04 Sep 2018 11:13:43: 22000000 INFO @ Tue, 04 Sep 2018 11:13:50: 23000000 INFO @ Tue, 04 Sep 2018 11:13:50: 23000000 INFO @ Tue, 04 Sep 2018 11:13:50: 23000000 INFO @ Tue, 04 Sep 2018 11:13:57: 24000000 INFO @ Tue, 04 Sep 2018 11:13:57: 24000000 INFO @ Tue, 04 Sep 2018 11:13:58: 24000000 INFO @ Tue, 04 Sep 2018 11:14:05: 25000000 INFO @ Tue, 04 Sep 2018 11:14:05: 25000000 INFO @ Tue, 04 Sep 2018 11:14:05: 25000000 INFO @ Tue, 04 Sep 2018 11:14:12: 26000000 INFO @ Tue, 04 Sep 2018 11:14:12: 26000000 INFO @ Tue, 04 Sep 2018 11:14:13: 26000000 INFO @ Tue, 04 Sep 2018 11:14:19: 27000000 INFO @ Tue, 04 Sep 2018 11:14:19: 27000000 INFO @ Tue, 04 Sep 2018 11:14:20: 27000000 INFO @ Tue, 04 Sep 2018 11:14:27: 28000000 INFO @ Tue, 04 Sep 2018 11:14:27: 28000000 INFO @ Tue, 04 Sep 2018 11:14:28: 28000000 INFO @ Tue, 04 Sep 2018 11:14:34: 29000000 INFO @ Tue, 04 Sep 2018 11:14:34: 29000000 INFO @ Tue, 04 Sep 2018 11:14:35: 29000000 INFO @ Tue, 04 Sep 2018 11:14:42: 30000000 INFO @ Tue, 04 Sep 2018 11:14:42: 30000000 INFO @ Tue, 04 Sep 2018 11:14:43: 30000000 INFO @ Tue, 04 Sep 2018 11:14:49: 31000000 INFO @ Tue, 04 Sep 2018 11:14:49: 31000000 INFO @ Tue, 04 Sep 2018 11:14:50: 31000000 INFO @ Tue, 04 Sep 2018 11:14:56: 32000000 INFO @ Tue, 04 Sep 2018 11:14:56: 32000000 INFO @ Tue, 04 Sep 2018 11:14:58: 32000000 INFO @ Tue, 04 Sep 2018 11:15:04: 33000000 INFO @ Tue, 04 Sep 2018 11:15:04: 33000000 INFO @ Tue, 04 Sep 2018 11:15:05: 33000000 INFO @ Tue, 04 Sep 2018 11:15:11: 34000000 INFO @ Tue, 04 Sep 2018 11:15:11: 34000000 INFO @ Tue, 04 Sep 2018 11:15:13: 34000000 INFO @ Tue, 04 Sep 2018 11:15:18: 35000000 INFO @ Tue, 04 Sep 2018 11:15:18: 35000000 INFO @ Tue, 04 Sep 2018 11:15:20: 35000000 INFO @ Tue, 04 Sep 2018 11:15:26: 36000000 INFO @ Tue, 04 Sep 2018 11:15:26: 36000000 INFO @ Tue, 04 Sep 2018 11:15:27: 36000000 INFO @ Tue, 04 Sep 2018 11:15:33: 37000000 INFO @ Tue, 04 Sep 2018 11:15:33: 37000000 INFO @ Tue, 04 Sep 2018 11:15:35: 37000000 INFO @ Tue, 04 Sep 2018 11:15:40: 38000000 INFO @ Tue, 04 Sep 2018 11:15:40: 38000000 INFO @ Tue, 04 Sep 2018 11:15:42: 38000000 INFO @ Tue, 04 Sep 2018 11:15:48: 39000000 INFO @ Tue, 04 Sep 2018 11:15:48: 39000000 INFO @ Tue, 04 Sep 2018 11:15:50: 39000000 INFO @ Tue, 04 Sep 2018 11:15:55: 40000000 INFO @ Tue, 04 Sep 2018 11:15:55: 40000000 INFO @ Tue, 04 Sep 2018 11:15:57: 40000000 INFO @ Tue, 04 Sep 2018 11:16:03: 41000000 INFO @ Tue, 04 Sep 2018 11:16:03: 41000000 INFO @ Tue, 04 Sep 2018 11:16:05: 41000000 INFO @ Tue, 04 Sep 2018 11:16:10: 42000000 INFO @ Tue, 04 Sep 2018 11:16:10: 42000000 INFO @ Tue, 04 Sep 2018 11:16:12: 42000000 INFO @ Tue, 04 Sep 2018 11:16:17: 43000000 INFO @ Tue, 04 Sep 2018 11:16:17: 43000000 INFO @ Tue, 04 Sep 2018 11:16:18: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 11:16:18: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 11:16:18: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 11:16:18: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 11:16:18: #1 total tags in treatment: 18920754 INFO @ Tue, 04 Sep 2018 11:16:18: #1 total tags in treatment: 18920754 INFO @ Tue, 04 Sep 2018 11:16:18: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 11:16:18: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 11:16:18: #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 11:16:18: #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 11:16:19: #1 tags after filtering in treatment: 16464781 INFO @ Tue, 04 Sep 2018 11:16:19: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 04 Sep 2018 11:16:19: #1 finished! INFO @ Tue, 04 Sep 2018 11:16:19: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 11:16:19: #1 tags after filtering in treatment: 16464781 INFO @ Tue, 04 Sep 2018 11:16:19: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 04 Sep 2018 11:16:19: #1 finished! INFO @ Tue, 04 Sep 2018 11:16:19: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 11:16:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 11:16:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 11:16:20: 43000000 INFO @ Tue, 04 Sep 2018 11:16:20: #2 number of paired peaks: 225 WARNING @ Tue, 04 Sep 2018 11:16:20: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Tue, 04 Sep 2018 11:16:20: start model_add_line... INFO @ Tue, 04 Sep 2018 11:16:20: #2 number of paired peaks: 225 WARNING @ Tue, 04 Sep 2018 11:16:20: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Tue, 04 Sep 2018 11:16:20: start model_add_line... INFO @ Tue, 04 Sep 2018 11:16:20: start X-correlation... INFO @ Tue, 04 Sep 2018 11:16:20: start X-correlation... INFO @ Tue, 04 Sep 2018 11:16:20: end of X-cor INFO @ Tue, 04 Sep 2018 11:16:20: end of X-cor INFO @ Tue, 04 Sep 2018 11:16:20: #2 finished! INFO @ Tue, 04 Sep 2018 11:16:20: #2 finished! INFO @ Tue, 04 Sep 2018 11:16:20: #2 predicted fragment length is 172 bps INFO @ Tue, 04 Sep 2018 11:16:20: #2 predicted fragment length is 172 bps INFO @ Tue, 04 Sep 2018 11:16:20: #2 alternative fragment length(s) may be 172 bps INFO @ Tue, 04 Sep 2018 11:16:20: #2 alternative fragment length(s) may be 172 bps INFO @ Tue, 04 Sep 2018 11:16:20: #2.2 Generate R script for model : SRX4279690.20_model.r INFO @ Tue, 04 Sep 2018 11:16:20: #2.2 Generate R script for model : SRX4279690.05_model.r INFO @ Tue, 04 Sep 2018 11:16:20: #3 Call peaks... INFO @ Tue, 04 Sep 2018 11:16:20: #3 Call peaks... INFO @ Tue, 04 Sep 2018 11:16:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 11:16:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 11:16:20: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 11:16:20: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 11:16:20: #1 total tags in treatment: 18920754 INFO @ Tue, 04 Sep 2018 11:16:20: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 11:16:20: #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 11:16:21: #1 tags after filtering in treatment: 16464781 INFO @ Tue, 04 Sep 2018 11:16:21: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 04 Sep 2018 11:16:21: #1 finished! INFO @ Tue, 04 Sep 2018 11:16:21: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 11:16:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 11:16:22: #2 number of paired peaks: 225 WARNING @ Tue, 04 Sep 2018 11:16:22: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Tue, 04 Sep 2018 11:16:22: start model_add_line... INFO @ Tue, 04 Sep 2018 11:16:22: start X-correlation... INFO @ Tue, 04 Sep 2018 11:16:22: end of X-cor INFO @ Tue, 04 Sep 2018 11:16:22: #2 finished! INFO @ Tue, 04 Sep 2018 11:16:22: #2 predicted fragment length is 172 bps INFO @ Tue, 04 Sep 2018 11:16:22: #2 alternative fragment length(s) may be 172 bps INFO @ Tue, 04 Sep 2018 11:16:22: #2.2 Generate R script for model : SRX4279690.10_model.r INFO @ Tue, 04 Sep 2018 11:16:22: #3 Call peaks... INFO @ Tue, 04 Sep 2018 11:16:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 11:16:58: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 11:16:59: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 11:17:02: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 11:17:21: #4 Write output xls file... SRX4279690.05_peaks.xls INFO @ Tue, 04 Sep 2018 11:17:22: #4 Write peak in narrowPeak format file... SRX4279690.05_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 11:17:22: #4 Write summits bed file... SRX4279690.05_summits.bed INFO @ Tue, 04 Sep 2018 11:17:22: Done! pass1 - making usageList (15 chroms): 8 millis pass2 - checking and writing primary data (38029 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 11:17:24: #4 Write output xls file... SRX4279690.20_peaks.xls INFO @ Tue, 04 Sep 2018 11:17:24: #4 Write peak in narrowPeak format file... SRX4279690.20_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 11:17:24: #4 Write summits bed file... SRX4279690.20_summits.bed INFO @ Tue, 04 Sep 2018 11:17:24: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (6717 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 11:17:27: #4 Write output xls file... SRX4279690.10_peaks.xls INFO @ Tue, 04 Sep 2018 11:17:27: #4 Write peak in narrowPeak format file... SRX4279690.10_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 11:17:27: #4 Write summits bed file... SRX4279690.10_summits.bed INFO @ Tue, 04 Sep 2018 11:17:27: Done! pass1 - making usageList (14 chroms): 6 millis pass2 - checking and writing primary data (21560 records, 4 fields): 25 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。