Job ID = 11171263 sra ファイルのダウンロード中... Completed: 1687989K bytes transferred in 60 seconds (230359K 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 25568395 spots for /home/okishinya/chipatlas/results/dm3/SRX2985882/SRR5806895.sra Written 25568395 spots for /home/okishinya/chipatlas/results/dm3/SRX2985882/SRR5806895.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:03:37 25568395 reads; of these: 25568395 (100.00%) were paired; of these: 2083279 (8.15%) aligned concordantly 0 times 18529313 (72.47%) aligned concordantly exactly 1 time 4955803 (19.38%) aligned concordantly >1 times ---- 2083279 pairs aligned concordantly 0 times; of these: 37053 (1.78%) aligned discordantly 1 time ---- 2046226 pairs aligned 0 times concordantly or discordantly; of these: 4092452 mates make up the pairs; of these: 2898172 (70.82%) aligned 0 times 783558 (19.15%) aligned exactly 1 time 410722 (10.04%) aligned >1 times 94.33% overall alignment rate Time searching: 01:03:37 Overall time: 01:03:37 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] 5699155 / 23490580 = 0.2426 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 @ Sat, 08 Sep 2018 14:43:46: # Command line: callpeak -t SRX2985882.bam -f BAM -g dm -n SRX2985882.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2985882.20 # format = BAM # ChIP-seq file = ['SRX2985882.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 @ Sat, 08 Sep 2018 14:43:46: # Command line: callpeak -t SRX2985882.bam -f BAM -g dm -n SRX2985882.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2985882.05 # format = BAM # ChIP-seq file = ['SRX2985882.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 @ Sat, 08 Sep 2018 14:43:46: # Command line: callpeak -t SRX2985882.bam -f BAM -g dm -n SRX2985882.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2985882.10 # format = BAM # ChIP-seq file = ['SRX2985882.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 @ Sat, 08 Sep 2018 14:43:46: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:43:46: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:43:46: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:43:46: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:43:46: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:43:46: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:43:53: 1000000 INFO @ Sat, 08 Sep 2018 14:43:53: 1000000 INFO @ Sat, 08 Sep 2018 14:43:53: 1000000 INFO @ Sat, 08 Sep 2018 14:44:00: 2000000 INFO @ Sat, 08 Sep 2018 14:44:01: 2000000 INFO @ Sat, 08 Sep 2018 14:44:01: 2000000 INFO @ Sat, 08 Sep 2018 14:44:07: 3000000 INFO @ Sat, 08 Sep 2018 14:44:07: 3000000 INFO @ Sat, 08 Sep 2018 14:44:07: 3000000 INFO @ Sat, 08 Sep 2018 14:44:13: 4000000 INFO @ Sat, 08 Sep 2018 14:44:14: 4000000 INFO @ Sat, 08 Sep 2018 14:44:14: 4000000 INFO @ Sat, 08 Sep 2018 14:44:20: 5000000 INFO @ Sat, 08 Sep 2018 14:44:21: 5000000 INFO @ Sat, 08 Sep 2018 14:44:21: 5000000 INFO @ Sat, 08 Sep 2018 14:44:27: 6000000 INFO @ Sat, 08 Sep 2018 14:44:28: 6000000 INFO @ Sat, 08 Sep 2018 14:44:28: 6000000 INFO @ Sat, 08 Sep 2018 14:44:33: 7000000 INFO @ Sat, 08 Sep 2018 14:44:35: 7000000 INFO @ Sat, 08 Sep 2018 14:44:35: 7000000 INFO @ Sat, 08 Sep 2018 14:44:40: 8000000 INFO @ Sat, 08 Sep 2018 14:44:42: 8000000 INFO @ Sat, 08 Sep 2018 14:44:42: 8000000 INFO @ Sat, 08 Sep 2018 14:44:47: 9000000 INFO @ Sat, 08 Sep 2018 14:44:49: 9000000 INFO @ Sat, 08 Sep 2018 14:44:49: 9000000 INFO @ Sat, 08 Sep 2018 14:44:54: 10000000 INFO @ Sat, 08 Sep 2018 14:44:56: 10000000 INFO @ Sat, 08 Sep 2018 14:44:56: 10000000 INFO @ Sat, 08 Sep 2018 14:45:00: 11000000 INFO @ Sat, 08 Sep 2018 14:45:03: 11000000 INFO @ Sat, 08 Sep 2018 14:45:03: 11000000 INFO @ Sat, 08 Sep 2018 14:45:07: 12000000 INFO @ Sat, 08 Sep 2018 14:45:10: 12000000 INFO @ Sat, 08 Sep 2018 14:45:10: 12000000 INFO @ Sat, 08 Sep 2018 14:45:14: 13000000 INFO @ Sat, 08 Sep 2018 14:45:17: 13000000 INFO @ Sat, 08 Sep 2018 14:45:17: 13000000 INFO @ Sat, 08 Sep 2018 14:45:20: 14000000 INFO @ Sat, 08 Sep 2018 14:45:23: 14000000 INFO @ Sat, 08 Sep 2018 14:45:23: 14000000 INFO @ Sat, 08 Sep 2018 14:45:27: 15000000 INFO @ Sat, 08 Sep 2018 14:45:30: 15000000 INFO @ Sat, 08 Sep 2018 14:45:30: 15000000 INFO @ Sat, 08 Sep 2018 14:45:34: 16000000 INFO @ Sat, 08 Sep 2018 14:45:37: 16000000 INFO @ Sat, 08 Sep 2018 14:45:37: 16000000 INFO @ Sat, 08 Sep 2018 14:45:40: 17000000 INFO @ Sat, 08 Sep 2018 14:45:44: 17000000 INFO @ Sat, 08 Sep 2018 14:45:44: 17000000 INFO @ Sat, 08 Sep 2018 14:45:47: 18000000 INFO @ Sat, 08 Sep 2018 14:45:51: 18000000 INFO @ Sat, 08 Sep 2018 14:45:51: 18000000 INFO @ Sat, 08 Sep 2018 14:45:53: 19000000 INFO @ Sat, 08 Sep 2018 14:45:58: 19000000 INFO @ Sat, 08 Sep 2018 14:45:58: 19000000 INFO @ Sat, 08 Sep 2018 14:46:00: 20000000 INFO @ Sat, 08 Sep 2018 14:46:05: 20000000 INFO @ Sat, 08 Sep 2018 14:46:05: 20000000 INFO @ Sat, 08 Sep 2018 14:46:07: 21000000 INFO @ Sat, 08 Sep 2018 14:46:12: 21000000 INFO @ Sat, 08 Sep 2018 14:46:12: 21000000 INFO @ Sat, 08 Sep 2018 14:46:13: 22000000 INFO @ Sat, 08 Sep 2018 14:46:19: 22000000 INFO @ Sat, 08 Sep 2018 14:46:20: 22000000 INFO @ Sat, 08 Sep 2018 14:46:20: 23000000 INFO @ Sat, 08 Sep 2018 14:46:26: 23000000 INFO @ Sat, 08 Sep 2018 14:46:27: 23000000 INFO @ Sat, 08 Sep 2018 14:46:27: 24000000 INFO @ Sat, 08 Sep 2018 14:46:33: 25000000 INFO @ Sat, 08 Sep 2018 14:46:33: 24000000 INFO @ Sat, 08 Sep 2018 14:46:34: 24000000 INFO @ Sat, 08 Sep 2018 14:46:40: 26000000 INFO @ Sat, 08 Sep 2018 14:46:40: 25000000 INFO @ Sat, 08 Sep 2018 14:46:41: 25000000 INFO @ Sat, 08 Sep 2018 14:46:46: 27000000 INFO @ Sat, 08 Sep 2018 14:46:47: 26000000 INFO @ Sat, 08 Sep 2018 14:46:48: 26000000 INFO @ Sat, 08 Sep 2018 14:46:53: 28000000 INFO @ Sat, 08 Sep 2018 14:46:54: 27000000 INFO @ Sat, 08 Sep 2018 14:46:54: 27000000 INFO @ Sat, 08 Sep 2018 14:46:59: 29000000 INFO @ Sat, 08 Sep 2018 14:47:01: 28000000 INFO @ Sat, 08 Sep 2018 14:47:01: 28000000 INFO @ Sat, 08 Sep 2018 14:47:06: 30000000 INFO @ Sat, 08 Sep 2018 14:47:08: 29000000 INFO @ Sat, 08 Sep 2018 14:47:08: 29000000 INFO @ Sat, 08 Sep 2018 14:47:13: 31000000 INFO @ Sat, 08 Sep 2018 14:47:15: 30000000 INFO @ Sat, 08 Sep 2018 14:47:15: 30000000 INFO @ Sat, 08 Sep 2018 14:47:19: 32000000 INFO @ Sat, 08 Sep 2018 14:47:22: 31000000 INFO @ Sat, 08 Sep 2018 14:47:23: 31000000 INFO @ Sat, 08 Sep 2018 14:47:26: 33000000 INFO @ Sat, 08 Sep 2018 14:47:29: 32000000 INFO @ Sat, 08 Sep 2018 14:47:30: 32000000 INFO @ Sat, 08 Sep 2018 14:47:33: 34000000 INFO @ Sat, 08 Sep 2018 14:47:36: 33000000 INFO @ Sat, 08 Sep 2018 14:47:37: 33000000 INFO @ Sat, 08 Sep 2018 14:47:39: 35000000 INFO @ Sat, 08 Sep 2018 14:47:44: 34000000 INFO @ Sat, 08 Sep 2018 14:47:44: 34000000 INFO @ Sat, 08 Sep 2018 14:47:46: 36000000 INFO @ Sat, 08 Sep 2018 14:47:51: 35000000 INFO @ Sat, 08 Sep 2018 14:47:51: 35000000 INFO @ Sat, 08 Sep 2018 14:47:52: #1 tag size is determined as 78 bps INFO @ Sat, 08 Sep 2018 14:47:52: #1 tag size = 78 INFO @ Sat, 08 Sep 2018 14:47:52: #1 total tags in treatment: 17791029 INFO @ Sat, 08 Sep 2018 14:47:52: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:47:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:47:52: #1 tags after filtering in treatment: 16268525 INFO @ Sat, 08 Sep 2018 14:47:52: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 08 Sep 2018 14:47:52: #1 finished! INFO @ Sat, 08 Sep 2018 14:47:52: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:47:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:47:53: #2 number of paired peaks: 199 WARNING @ Sat, 08 Sep 2018 14:47:53: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Sat, 08 Sep 2018 14:47:53: start model_add_line... INFO @ Sat, 08 Sep 2018 14:47:53: start X-correlation... INFO @ Sat, 08 Sep 2018 14:47:53: end of X-cor INFO @ Sat, 08 Sep 2018 14:47:53: #2 finished! INFO @ Sat, 08 Sep 2018 14:47:53: #2 predicted fragment length is 175 bps INFO @ Sat, 08 Sep 2018 14:47:53: #2 alternative fragment length(s) may be 2,108,175,198,217,240,258,284,586 bps INFO @ Sat, 08 Sep 2018 14:47:53: #2.2 Generate R script for model : SRX2985882.20_model.r INFO @ Sat, 08 Sep 2018 14:47:53: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:47:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:47:58: 36000000 INFO @ Sat, 08 Sep 2018 14:47:58: 36000000 INFO @ Sat, 08 Sep 2018 14:48:04: #1 tag size is determined as 78 bps INFO @ Sat, 08 Sep 2018 14:48:04: #1 tag size = 78 INFO @ Sat, 08 Sep 2018 14:48:04: #1 total tags in treatment: 17791029 INFO @ Sat, 08 Sep 2018 14:48:04: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:48:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:48:04: #1 tag size is determined as 78 bps INFO @ Sat, 08 Sep 2018 14:48:04: #1 tag size = 78 INFO @ Sat, 08 Sep 2018 14:48:04: #1 total tags in treatment: 17791029 INFO @ Sat, 08 Sep 2018 14:48:04: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:48:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:48:04: #1 tags after filtering in treatment: 16268525 INFO @ Sat, 08 Sep 2018 14:48:04: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 08 Sep 2018 14:48:04: #1 finished! INFO @ Sat, 08 Sep 2018 14:48:04: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:48:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:48:04: #1 tags after filtering in treatment: 16268525 INFO @ Sat, 08 Sep 2018 14:48:04: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 08 Sep 2018 14:48:04: #1 finished! INFO @ Sat, 08 Sep 2018 14:48:04: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:48:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:48:05: #2 number of paired peaks: 199 WARNING @ Sat, 08 Sep 2018 14:48:05: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Sat, 08 Sep 2018 14:48:05: start model_add_line... INFO @ Sat, 08 Sep 2018 14:48:05: start X-correlation... INFO @ Sat, 08 Sep 2018 14:48:05: end of X-cor INFO @ Sat, 08 Sep 2018 14:48:05: #2 finished! INFO @ Sat, 08 Sep 2018 14:48:05: #2 predicted fragment length is 175 bps INFO @ Sat, 08 Sep 2018 14:48:05: #2 alternative fragment length(s) may be 2,108,175,198,217,240,258,284,586 bps INFO @ Sat, 08 Sep 2018 14:48:05: #2.2 Generate R script for model : SRX2985882.05_model.r INFO @ Sat, 08 Sep 2018 14:48:05: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:48:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:48:06: #2 number of paired peaks: 199 WARNING @ Sat, 08 Sep 2018 14:48:06: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Sat, 08 Sep 2018 14:48:06: start model_add_line... INFO @ Sat, 08 Sep 2018 14:48:06: start X-correlation... INFO @ Sat, 08 Sep 2018 14:48:06: end of X-cor INFO @ Sat, 08 Sep 2018 14:48:06: #2 finished! INFO @ Sat, 08 Sep 2018 14:48:06: #2 predicted fragment length is 175 bps INFO @ Sat, 08 Sep 2018 14:48:06: #2 alternative fragment length(s) may be 2,108,175,198,217,240,258,284,586 bps INFO @ Sat, 08 Sep 2018 14:48:06: #2.2 Generate R script for model : SRX2985882.10_model.r INFO @ Sat, 08 Sep 2018 14:48:06: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:48:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:48:27: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:48:41: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:48:42: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:48:47: #4 Write output xls file... SRX2985882.20_peaks.xls INFO @ Sat, 08 Sep 2018 14:48:47: #4 Write peak in narrowPeak format file... SRX2985882.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:48:47: #4 Write summits bed file... SRX2985882.20_summits.bed INFO @ Sat, 08 Sep 2018 14:48:47: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (116 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 14:48:59: #4 Write output xls file... SRX2985882.05_peaks.xls INFO @ Sat, 08 Sep 2018 14:48:59: #4 Write peak in narrowPeak format file... SRX2985882.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:48:59: #4 Write summits bed file... SRX2985882.05_summits.bed INFO @ Sat, 08 Sep 2018 14:49:00: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (843 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 14:49:01: #4 Write output xls file... SRX2985882.10_peaks.xls INFO @ Sat, 08 Sep 2018 14:49:01: #4 Write peak in narrowPeak format file... SRX2985882.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:49:01: #4 Write summits bed file... SRX2985882.10_summits.bed INFO @ Sat, 08 Sep 2018 14:49:01: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (331 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。