Job ID = 9159855 sra ファイルのダウンロード中... Completed: 713392K bytes transferred in 9 seconds (635344K bits/sec), in 1 file, 2 directories. 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... Written 11172518 spots for /home/okishinya/chipatlas/results/dm3/SRX749049/SRR1636777.sra Written 11172518 spots total 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: 00:25:45 11172518 reads; of these: 11172518 (100.00%) were paired; of these: 1106536 (9.90%) aligned concordantly 0 times 7972881 (71.36%) aligned concordantly exactly 1 time 2093101 (18.73%) aligned concordantly >1 times ---- 1106536 pairs aligned concordantly 0 times; of these: 394546 (35.66%) aligned discordantly 1 time ---- 711990 pairs aligned 0 times concordantly or discordantly; of these: 1423980 mates make up the pairs; of these: 728353 (51.15%) aligned 0 times 390565 (27.43%) aligned exactly 1 time 305062 (21.42%) aligned >1 times 96.74% overall alignment rate Time searching: 00:25:45 Overall time: 00:25:45 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] 92818 / 10454243 = 0.0089 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, 28 Jun 2017 00:52:07: # Command line: callpeak -t SRX749049.bam -f BAM -g dm -n SRX749049.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX749049.10 # format = BAM # ChIP-seq file = ['SRX749049.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, 28 Jun 2017 00:52:07: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:52:07: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:52:07: # Command line: callpeak -t SRX749049.bam -f BAM -g dm -n SRX749049.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX749049.20 # format = BAM # ChIP-seq file = ['SRX749049.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, 28 Jun 2017 00:52:07: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:52:07: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:52:07: # Command line: callpeak -t SRX749049.bam -f BAM -g dm -n SRX749049.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX749049.05 # format = BAM # ChIP-seq file = ['SRX749049.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, 28 Jun 2017 00:52:07: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:52:07: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:52:14: 1000000 INFO @ Wed, 28 Jun 2017 00:52:14: 1000000 INFO @ Wed, 28 Jun 2017 00:52:14: 1000000 INFO @ Wed, 28 Jun 2017 00:52:20: 2000000 INFO @ Wed, 28 Jun 2017 00:52:20: 2000000 INFO @ Wed, 28 Jun 2017 00:52:20: 2000000 INFO @ Wed, 28 Jun 2017 00:52:26: 3000000 INFO @ Wed, 28 Jun 2017 00:52:26: 3000000 INFO @ Wed, 28 Jun 2017 00:52:26: 3000000 INFO @ Wed, 28 Jun 2017 00:52:32: 4000000 INFO @ Wed, 28 Jun 2017 00:52:33: 4000000 INFO @ Wed, 28 Jun 2017 00:52:33: 4000000 INFO @ Wed, 28 Jun 2017 00:52:38: 5000000 INFO @ Wed, 28 Jun 2017 00:52:39: 5000000 INFO @ Wed, 28 Jun 2017 00:52:40: 5000000 INFO @ Wed, 28 Jun 2017 00:52:44: 6000000 INFO @ Wed, 28 Jun 2017 00:52:46: 6000000 INFO @ Wed, 28 Jun 2017 00:52:46: 6000000 INFO @ Wed, 28 Jun 2017 00:52:50: 7000000 INFO @ Wed, 28 Jun 2017 00:52:52: 7000000 INFO @ Wed, 28 Jun 2017 00:52:53: 7000000 INFO @ Wed, 28 Jun 2017 00:52:56: 8000000 INFO @ Wed, 28 Jun 2017 00:52:59: 8000000 INFO @ Wed, 28 Jun 2017 00:53:00: 8000000 INFO @ Wed, 28 Jun 2017 00:53:02: 9000000 INFO @ Wed, 28 Jun 2017 00:53:05: 9000000 INFO @ Wed, 28 Jun 2017 00:53:06: 9000000 INFO @ Wed, 28 Jun 2017 00:53:08: 10000000 INFO @ Wed, 28 Jun 2017 00:53:12: 10000000 INFO @ Wed, 28 Jun 2017 00:53:13: 10000000 INFO @ Wed, 28 Jun 2017 00:53:14: 11000000 INFO @ Wed, 28 Jun 2017 00:53:18: 11000000 INFO @ Wed, 28 Jun 2017 00:53:20: 11000000 INFO @ Wed, 28 Jun 2017 00:53:20: 12000000 INFO @ Wed, 28 Jun 2017 00:53:25: 12000000 INFO @ Wed, 28 Jun 2017 00:53:26: 13000000 INFO @ Wed, 28 Jun 2017 00:53:26: 12000000 INFO @ Wed, 28 Jun 2017 00:53:31: 13000000 INFO @ Wed, 28 Jun 2017 00:53:32: 14000000 INFO @ Wed, 28 Jun 2017 00:53:33: 13000000 INFO @ Wed, 28 Jun 2017 00:53:38: 14000000 INFO @ Wed, 28 Jun 2017 00:53:38: 15000000 INFO @ Wed, 28 Jun 2017 00:53:40: 14000000 INFO @ Wed, 28 Jun 2017 00:53:44: 16000000 INFO @ Wed, 28 Jun 2017 00:53:44: 15000000 INFO @ Wed, 28 Jun 2017 00:53:47: 15000000 INFO @ Wed, 28 Jun 2017 00:53:50: 17000000 INFO @ Wed, 28 Jun 2017 00:53:51: 16000000 INFO @ Wed, 28 Jun 2017 00:53:54: 16000000 INFO @ Wed, 28 Jun 2017 00:53:56: 18000000 INFO @ Wed, 28 Jun 2017 00:53:57: 17000000 INFO @ Wed, 28 Jun 2017 00:54:00: 17000000 INFO @ Wed, 28 Jun 2017 00:54:01: 19000000 INFO @ Wed, 28 Jun 2017 00:54:04: 18000000 INFO @ Wed, 28 Jun 2017 00:54:07: 18000000 INFO @ Wed, 28 Jun 2017 00:54:07: 20000000 INFO @ Wed, 28 Jun 2017 00:54:10: 19000000 INFO @ Wed, 28 Jun 2017 00:54:13: 21000000 INFO @ Wed, 28 Jun 2017 00:54:14: 19000000 INFO @ Wed, 28 Jun 2017 00:54:16: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:54:16: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:54:16: #1 total tags in treatment: 9974192 INFO @ Wed, 28 Jun 2017 00:54:16: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:54:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 00:54:16: #1 tags after filtering in treatment: 9511731 INFO @ Wed, 28 Jun 2017 00:54:16: #1 Redundant rate of treatment: 0.05 INFO @ Wed, 28 Jun 2017 00:54:16: #1 finished! INFO @ Wed, 28 Jun 2017 00:54:16: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:54:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:54:17: #2 number of paired peaks: 775 WARNING @ Wed, 28 Jun 2017 00:54:17: Fewer paired peaks (775) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 775 pairs to build model! INFO @ Wed, 28 Jun 2017 00:54:17: start model_add_line... INFO @ Wed, 28 Jun 2017 00:54:17: 20000000 INFO @ Wed, 28 Jun 2017 00:54:17: start X-correlation... INFO @ Wed, 28 Jun 2017 00:54:17: end of X-cor INFO @ Wed, 28 Jun 2017 00:54:17: #2 finished! INFO @ Wed, 28 Jun 2017 00:54:17: #2 predicted fragment length is 190 bps INFO @ Wed, 28 Jun 2017 00:54:17: #2 alternative fragment length(s) may be 4,190 bps INFO @ Wed, 28 Jun 2017 00:54:17: #2.2 Generate R script for model : SRX749049.20_model.r INFO @ Wed, 28 Jun 2017 00:54:17: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:54:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:54:20: 20000000 INFO @ Wed, 28 Jun 2017 00:54:23: 21000000 INFO @ Wed, 28 Jun 2017 00:54:26: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:54:26: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:54:26: #1 total tags in treatment: 9974192 INFO @ Wed, 28 Jun 2017 00:54:26: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:54:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 00:54:26: #1 tags after filtering in treatment: 9511731 INFO @ Wed, 28 Jun 2017 00:54:26: #1 Redundant rate of treatment: 0.05 INFO @ Wed, 28 Jun 2017 00:54:26: #1 finished! INFO @ Wed, 28 Jun 2017 00:54:26: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:54:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:54:27: 21000000 INFO @ Wed, 28 Jun 2017 00:54:27: #2 number of paired peaks: 775 WARNING @ Wed, 28 Jun 2017 00:54:27: Fewer paired peaks (775) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 775 pairs to build model! INFO @ Wed, 28 Jun 2017 00:54:27: start model_add_line... INFO @ Wed, 28 Jun 2017 00:54:27: start X-correlation... INFO @ Wed, 28 Jun 2017 00:54:27: end of X-cor INFO @ Wed, 28 Jun 2017 00:54:27: #2 finished! INFO @ Wed, 28 Jun 2017 00:54:27: #2 predicted fragment length is 190 bps INFO @ Wed, 28 Jun 2017 00:54:27: #2 alternative fragment length(s) may be 4,190 bps INFO @ Wed, 28 Jun 2017 00:54:27: #2.2 Generate R script for model : SRX749049.10_model.r INFO @ Wed, 28 Jun 2017 00:54:27: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:54:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:54:29: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:54:29: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:54:29: #1 total tags in treatment: 9974192 INFO @ Wed, 28 Jun 2017 00:54:29: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:54:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 00:54:30: #1 tags after filtering in treatment: 9511731 INFO @ Wed, 28 Jun 2017 00:54:30: #1 Redundant rate of treatment: 0.05 INFO @ Wed, 28 Jun 2017 00:54:30: #1 finished! INFO @ Wed, 28 Jun 2017 00:54:30: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:54:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:54:30: #2 number of paired peaks: 775 WARNING @ Wed, 28 Jun 2017 00:54:30: Fewer paired peaks (775) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 775 pairs to build model! INFO @ Wed, 28 Jun 2017 00:54:30: start model_add_line... INFO @ Wed, 28 Jun 2017 00:54:31: start X-correlation... INFO @ Wed, 28 Jun 2017 00:54:31: end of X-cor INFO @ Wed, 28 Jun 2017 00:54:31: #2 finished! INFO @ Wed, 28 Jun 2017 00:54:31: #2 predicted fragment length is 190 bps INFO @ Wed, 28 Jun 2017 00:54:31: #2 alternative fragment length(s) may be 4,190 bps INFO @ Wed, 28 Jun 2017 00:54:31: #2.2 Generate R script for model : SRX749049.05_model.r INFO @ Wed, 28 Jun 2017 00:54:31: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:54:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:54:40: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:54:50: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:54:54: #4 Write output xls file... SRX749049.20_peaks.xls INFO @ Wed, 28 Jun 2017 00:54:54: #4 Write peak in narrowPeak format file... SRX749049.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:54:54: #4 Write summits bed file... SRX749049.20_summits.bed INFO @ Wed, 28 Jun 2017 00:54:54: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (465 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:54:56: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:55:04: #4 Write output xls file... SRX749049.10_peaks.xls INFO @ Wed, 28 Jun 2017 00:55:04: #4 Write peak in narrowPeak format file... SRX749049.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:55:04: #4 Write summits bed file... SRX749049.10_summits.bed INFO @ Wed, 28 Jun 2017 00:55:04: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1212 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:55:09: #4 Write output xls file... SRX749049.05_peaks.xls INFO @ Wed, 28 Jun 2017 00:55:09: #4 Write peak in narrowPeak format file... SRX749049.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:55:09: #4 Write summits bed file... SRX749049.05_summits.bed INFO @ Wed, 28 Jun 2017 00:55:09: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3768 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。