Job ID = 11171259 sra ファイルのダウンロード中... Completed: 888572K bytes transferred in 43 seconds (165570K 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 13445880 spots for /home/okishinya/chipatlas/results/dm3/SRX2982446/SRR5803099.sra Written 13445880 spots for /home/okishinya/chipatlas/results/dm3/SRX2982446/SRR5803099.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: 00:32:18 13445880 reads; of these: 13445880 (100.00%) were paired; of these: 1064151 (7.91%) aligned concordantly 0 times 10099640 (75.11%) aligned concordantly exactly 1 time 2282089 (16.97%) aligned concordantly >1 times ---- 1064151 pairs aligned concordantly 0 times; of these: 18578 (1.75%) aligned discordantly 1 time ---- 1045573 pairs aligned 0 times concordantly or discordantly; of these: 2091146 mates make up the pairs; of these: 1509216 (72.17%) aligned 0 times 394228 (18.85%) aligned exactly 1 time 187702 (8.98%) aligned >1 times 94.39% overall alignment rate Time searching: 00:32:19 Overall time: 00:32:19 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 12 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] 1569033 / 12384271 = 0.1267 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 14:00:59: # Command line: callpeak -t SRX2982446.bam -f BAM -g dm -n SRX2982446.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2982446.10 # format = BAM # ChIP-seq file = ['SRX2982446.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 14:00:59: # Command line: callpeak -t SRX2982446.bam -f BAM -g dm -n SRX2982446.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2982446.20 # format = BAM # ChIP-seq file = ['SRX2982446.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 14:00:59: # Command line: callpeak -t SRX2982446.bam -f BAM -g dm -n SRX2982446.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2982446.05 # format = BAM # ChIP-seq file = ['SRX2982446.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 14:00:59: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:00:59: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:00:59: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:00:59: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:00:59: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:00:59: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:01:06: 1000000 INFO @ Sat, 08 Sep 2018 14:01:06: 1000000 INFO @ Sat, 08 Sep 2018 14:01:06: 1000000 INFO @ Sat, 08 Sep 2018 14:01:12: 2000000 INFO @ Sat, 08 Sep 2018 14:01:13: 2000000 INFO @ Sat, 08 Sep 2018 14:01:13: 2000000 INFO @ Sat, 08 Sep 2018 14:01:19: 3000000 INFO @ Sat, 08 Sep 2018 14:01:20: 3000000 INFO @ Sat, 08 Sep 2018 14:01:20: 3000000 INFO @ Sat, 08 Sep 2018 14:01:26: 4000000 INFO @ Sat, 08 Sep 2018 14:01:26: 4000000 INFO @ Sat, 08 Sep 2018 14:01:27: 4000000 INFO @ Sat, 08 Sep 2018 14:01:33: 5000000 INFO @ Sat, 08 Sep 2018 14:01:33: 5000000 INFO @ Sat, 08 Sep 2018 14:01:34: 5000000 INFO @ Sat, 08 Sep 2018 14:01:40: 6000000 INFO @ Sat, 08 Sep 2018 14:01:41: 6000000 INFO @ Sat, 08 Sep 2018 14:01:41: 6000000 INFO @ Sat, 08 Sep 2018 14:01:47: 7000000 INFO @ Sat, 08 Sep 2018 14:01:48: 7000000 INFO @ Sat, 08 Sep 2018 14:01:49: 7000000 INFO @ Sat, 08 Sep 2018 14:01:53: 8000000 INFO @ Sat, 08 Sep 2018 14:01:55: 8000000 INFO @ Sat, 08 Sep 2018 14:01:56: 8000000 INFO @ Sat, 08 Sep 2018 14:02:00: 9000000 INFO @ Sat, 08 Sep 2018 14:02:03: 9000000 INFO @ Sat, 08 Sep 2018 14:02:03: 9000000 INFO @ Sat, 08 Sep 2018 14:02:07: 10000000 INFO @ Sat, 08 Sep 2018 14:02:10: 10000000 INFO @ Sat, 08 Sep 2018 14:02:11: 10000000 INFO @ Sat, 08 Sep 2018 14:02:14: 11000000 INFO @ Sat, 08 Sep 2018 14:02:17: 11000000 INFO @ Sat, 08 Sep 2018 14:02:18: 11000000 INFO @ Sat, 08 Sep 2018 14:02:20: 12000000 INFO @ Sat, 08 Sep 2018 14:02:25: 12000000 INFO @ Sat, 08 Sep 2018 14:02:25: 12000000 INFO @ Sat, 08 Sep 2018 14:02:27: 13000000 INFO @ Sat, 08 Sep 2018 14:02:32: 13000000 INFO @ Sat, 08 Sep 2018 14:02:33: 13000000 INFO @ Sat, 08 Sep 2018 14:02:34: 14000000 INFO @ Sat, 08 Sep 2018 14:02:39: 14000000 INFO @ Sat, 08 Sep 2018 14:02:40: 14000000 INFO @ Sat, 08 Sep 2018 14:02:40: 15000000 INFO @ Sat, 08 Sep 2018 14:02:47: 15000000 INFO @ Sat, 08 Sep 2018 14:02:47: 16000000 INFO @ Sat, 08 Sep 2018 14:02:47: 15000000 INFO @ Sat, 08 Sep 2018 14:02:54: 17000000 INFO @ Sat, 08 Sep 2018 14:02:54: 16000000 INFO @ Sat, 08 Sep 2018 14:02:55: 16000000 INFO @ Sat, 08 Sep 2018 14:03:01: 18000000 INFO @ Sat, 08 Sep 2018 14:03:01: 17000000 INFO @ Sat, 08 Sep 2018 14:03:02: 17000000 INFO @ Sat, 08 Sep 2018 14:03:07: 19000000 INFO @ Sat, 08 Sep 2018 14:03:09: 18000000 INFO @ Sat, 08 Sep 2018 14:03:09: 18000000 INFO @ Sat, 08 Sep 2018 14:03:14: 20000000 INFO @ Sat, 08 Sep 2018 14:03:16: 19000000 INFO @ Sat, 08 Sep 2018 14:03:17: 19000000 INFO @ Sat, 08 Sep 2018 14:03:21: 21000000 INFO @ Sat, 08 Sep 2018 14:03:23: 20000000 INFO @ Sat, 08 Sep 2018 14:03:24: 20000000 INFO @ Sat, 08 Sep 2018 14:03:27: 22000000 INFO @ Sat, 08 Sep 2018 14:03:29: #1 tag size is determined as 78 bps INFO @ Sat, 08 Sep 2018 14:03:29: #1 tag size = 78 INFO @ Sat, 08 Sep 2018 14:03:29: #1 total tags in treatment: 10813962 INFO @ Sat, 08 Sep 2018 14:03:29: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:03:29: #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 14:03:29: #1 tags after filtering in treatment: 10216068 INFO @ Sat, 08 Sep 2018 14:03:29: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 08 Sep 2018 14:03:29: #1 finished! INFO @ Sat, 08 Sep 2018 14:03:29: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:03:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:03:30: #2 number of paired peaks: 206 WARNING @ Sat, 08 Sep 2018 14:03:30: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Sat, 08 Sep 2018 14:03:30: start model_add_line... INFO @ Sat, 08 Sep 2018 14:03:30: start X-correlation... INFO @ Sat, 08 Sep 2018 14:03:30: end of X-cor INFO @ Sat, 08 Sep 2018 14:03:30: #2 finished! INFO @ Sat, 08 Sep 2018 14:03:30: #2 predicted fragment length is 189 bps INFO @ Sat, 08 Sep 2018 14:03:30: #2 alternative fragment length(s) may be 0,26,133,182,189,203,227,506,535,544,553,558,573 bps INFO @ Sat, 08 Sep 2018 14:03:30: #2.2 Generate R script for model : SRX2982446.05_model.r INFO @ Sat, 08 Sep 2018 14:03:30: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:03:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:03:31: 21000000 INFO @ Sat, 08 Sep 2018 14:03:31: 21000000 INFO @ Sat, 08 Sep 2018 14:03:38: 22000000 INFO @ Sat, 08 Sep 2018 14:03:39: 22000000 INFO @ Sat, 08 Sep 2018 14:03:40: #1 tag size is determined as 78 bps INFO @ Sat, 08 Sep 2018 14:03:40: #1 tag size = 78 INFO @ Sat, 08 Sep 2018 14:03:40: #1 total tags in treatment: 10813962 INFO @ Sat, 08 Sep 2018 14:03:40: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:03:40: #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 14:03:40: #1 tags after filtering in treatment: 10216068 INFO @ Sat, 08 Sep 2018 14:03:40: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 08 Sep 2018 14:03:40: #1 finished! INFO @ Sat, 08 Sep 2018 14:03:40: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:03:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:03:40: #1 tag size is determined as 78 bps INFO @ Sat, 08 Sep 2018 14:03:40: #1 tag size = 78 INFO @ Sat, 08 Sep 2018 14:03:40: #1 total tags in treatment: 10813962 INFO @ Sat, 08 Sep 2018 14:03:40: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:03:40: #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 14:03:40: #2 number of paired peaks: 206 WARNING @ Sat, 08 Sep 2018 14:03:40: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Sat, 08 Sep 2018 14:03:40: start model_add_line... INFO @ Sat, 08 Sep 2018 14:03:41: start X-correlation... INFO @ Sat, 08 Sep 2018 14:03:41: end of X-cor INFO @ Sat, 08 Sep 2018 14:03:41: #2 finished! INFO @ Sat, 08 Sep 2018 14:03:41: #2 predicted fragment length is 189 bps INFO @ Sat, 08 Sep 2018 14:03:41: #2 alternative fragment length(s) may be 0,26,133,182,189,203,227,506,535,544,553,558,573 bps INFO @ Sat, 08 Sep 2018 14:03:41: #2.2 Generate R script for model : SRX2982446.20_model.r INFO @ Sat, 08 Sep 2018 14:03:41: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:03:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:03:41: #1 tags after filtering in treatment: 10216068 INFO @ Sat, 08 Sep 2018 14:03:41: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 08 Sep 2018 14:03:41: #1 finished! INFO @ Sat, 08 Sep 2018 14:03:41: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:03:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:03:41: #2 number of paired peaks: 206 WARNING @ Sat, 08 Sep 2018 14:03:41: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Sat, 08 Sep 2018 14:03:41: start model_add_line... INFO @ Sat, 08 Sep 2018 14:03:41: start X-correlation... INFO @ Sat, 08 Sep 2018 14:03:41: end of X-cor INFO @ Sat, 08 Sep 2018 14:03:41: #2 finished! INFO @ Sat, 08 Sep 2018 14:03:41: #2 predicted fragment length is 189 bps INFO @ Sat, 08 Sep 2018 14:03:41: #2 alternative fragment length(s) may be 0,26,133,182,189,203,227,506,535,544,553,558,573 bps INFO @ Sat, 08 Sep 2018 14:03:41: #2.2 Generate R script for model : SRX2982446.10_model.r INFO @ Sat, 08 Sep 2018 14:03:41: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:03:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:03:55: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:04:04: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:04:04: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:04:07: #4 Write output xls file... SRX2982446.05_peaks.xls INFO @ Sat, 08 Sep 2018 14:04:07: #4 Write peak in narrowPeak format file... SRX2982446.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:04:07: #4 Write summits bed file... SRX2982446.05_summits.bed INFO @ Sat, 08 Sep 2018 14:04:07: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (347 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 14:04:15: #4 Write output xls file... SRX2982446.10_peaks.xls INFO @ Sat, 08 Sep 2018 14:04:15: #4 Write peak in narrowPeak format file... SRX2982446.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:04:15: #4 Write summits bed file... SRX2982446.10_summits.bed INFO @ Sat, 08 Sep 2018 14:04:15: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (173 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 14:04:16: #4 Write output xls file... SRX2982446.20_peaks.xls INFO @ Sat, 08 Sep 2018 14:04:16: #4 Write peak in narrowPeak format file... SRX2982446.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:04:16: #4 Write summits bed file... SRX2982446.20_summits.bed INFO @ Sat, 08 Sep 2018 14:04:16: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (61 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。