Job ID = 9159839 sra ファイルのダウンロード中... Completed: 1161657K bytes transferred in 13 seconds (728080K 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 17602149 spots for /home/okishinya/chipatlas/results/dm3/SRX749022/SRR1636750.sra Written 17602149 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: 00:43:56 17602149 reads; of these: 17602149 (100.00%) were paired; of these: 1391472 (7.91%) aligned concordantly 0 times 11721066 (66.59%) aligned concordantly exactly 1 time 4489611 (25.51%) aligned concordantly >1 times ---- 1391472 pairs aligned concordantly 0 times; of these: 8703 (0.63%) aligned discordantly 1 time ---- 1382769 pairs aligned 0 times concordantly or discordantly; of these: 2765538 mates make up the pairs; of these: 2330380 (84.26%) aligned 0 times 315498 (11.41%) aligned exactly 1 time 119660 (4.33%) aligned >1 times 93.38% overall alignment rate Time searching: 00:43:56 Overall time: 00:43:56 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] 4805969 / 16203109 = 0.2966 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 01:04:58: # Command line: callpeak -t SRX749022.bam -f BAM -g dm -n SRX749022.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX749022.05 # format = BAM # ChIP-seq file = ['SRX749022.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 01:04:58: # Command line: callpeak -t SRX749022.bam -f BAM -g dm -n SRX749022.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX749022.20 # format = BAM # ChIP-seq file = ['SRX749022.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 01:04:58: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:04:58: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:04:58: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:04:58: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:04:58: # Command line: callpeak -t SRX749022.bam -f BAM -g dm -n SRX749022.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX749022.10 # format = BAM # ChIP-seq file = ['SRX749022.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 01:04:58: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:04:58: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:05:05: 1000000 INFO @ Wed, 28 Jun 2017 01:05:06: 1000000 INFO @ Wed, 28 Jun 2017 01:05:06: 1000000 INFO @ Wed, 28 Jun 2017 01:05:11: 2000000 INFO @ Wed, 28 Jun 2017 01:05:13: 2000000 INFO @ Wed, 28 Jun 2017 01:05:13: 2000000 INFO @ Wed, 28 Jun 2017 01:05:18: 3000000 INFO @ Wed, 28 Jun 2017 01:05:20: 3000000 INFO @ Wed, 28 Jun 2017 01:05:20: 3000000 INFO @ Wed, 28 Jun 2017 01:05:24: 4000000 INFO @ Wed, 28 Jun 2017 01:05:28: 4000000 INFO @ Wed, 28 Jun 2017 01:05:28: 4000000 INFO @ Wed, 28 Jun 2017 01:05:31: 5000000 INFO @ Wed, 28 Jun 2017 01:05:35: 5000000 INFO @ Wed, 28 Jun 2017 01:05:35: 5000000 INFO @ Wed, 28 Jun 2017 01:05:37: 6000000 INFO @ Wed, 28 Jun 2017 01:05:42: 6000000 INFO @ Wed, 28 Jun 2017 01:05:42: 6000000 INFO @ Wed, 28 Jun 2017 01:05:44: 7000000 INFO @ Wed, 28 Jun 2017 01:05:49: 7000000 INFO @ Wed, 28 Jun 2017 01:05:49: 7000000 INFO @ Wed, 28 Jun 2017 01:05:50: 8000000 INFO @ Wed, 28 Jun 2017 01:05:57: 9000000 INFO @ Wed, 28 Jun 2017 01:05:57: 8000000 INFO @ Wed, 28 Jun 2017 01:05:57: 8000000 INFO @ Wed, 28 Jun 2017 01:06:03: 10000000 INFO @ Wed, 28 Jun 2017 01:06:04: 9000000 INFO @ Wed, 28 Jun 2017 01:06:04: 9000000 INFO @ Wed, 28 Jun 2017 01:06:10: 11000000 INFO @ Wed, 28 Jun 2017 01:06:11: 10000000 INFO @ Wed, 28 Jun 2017 01:06:11: 10000000 INFO @ Wed, 28 Jun 2017 01:06:16: 12000000 INFO @ Wed, 28 Jun 2017 01:06:19: 11000000 INFO @ Wed, 28 Jun 2017 01:06:19: 11000000 INFO @ Wed, 28 Jun 2017 01:06:23: 13000000 INFO @ Wed, 28 Jun 2017 01:06:26: 12000000 INFO @ Wed, 28 Jun 2017 01:06:26: 12000000 INFO @ Wed, 28 Jun 2017 01:06:29: 14000000 INFO @ Wed, 28 Jun 2017 01:06:33: 13000000 INFO @ Wed, 28 Jun 2017 01:06:33: 13000000 INFO @ Wed, 28 Jun 2017 01:06:36: 15000000 INFO @ Wed, 28 Jun 2017 01:06:40: 14000000 INFO @ Wed, 28 Jun 2017 01:06:40: 14000000 INFO @ Wed, 28 Jun 2017 01:06:42: 16000000 INFO @ Wed, 28 Jun 2017 01:06:48: 15000000 INFO @ Wed, 28 Jun 2017 01:06:48: 15000000 INFO @ Wed, 28 Jun 2017 01:06:49: 17000000 INFO @ Wed, 28 Jun 2017 01:06:55: 16000000 INFO @ Wed, 28 Jun 2017 01:06:55: 16000000 INFO @ Wed, 28 Jun 2017 01:06:55: 18000000 INFO @ Wed, 28 Jun 2017 01:07:02: 19000000 INFO @ Wed, 28 Jun 2017 01:07:02: 17000000 INFO @ Wed, 28 Jun 2017 01:07:02: 17000000 INFO @ Wed, 28 Jun 2017 01:07:08: 20000000 INFO @ Wed, 28 Jun 2017 01:07:09: 18000000 INFO @ Wed, 28 Jun 2017 01:07:10: 18000000 INFO @ Wed, 28 Jun 2017 01:07:15: 21000000 INFO @ Wed, 28 Jun 2017 01:07:17: 19000000 INFO @ Wed, 28 Jun 2017 01:07:17: 19000000 INFO @ Wed, 28 Jun 2017 01:07:22: 22000000 INFO @ Wed, 28 Jun 2017 01:07:24: 20000000 INFO @ Wed, 28 Jun 2017 01:07:24: 20000000 INFO @ Wed, 28 Jun 2017 01:07:28: 23000000 INFO @ Wed, 28 Jun 2017 01:07:30: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:07:30: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:07:30: #1 total tags in treatment: 11406502 INFO @ Wed, 28 Jun 2017 01:07:30: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:07:30: #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 01:07:30: #1 tags after filtering in treatment: 10645199 INFO @ Wed, 28 Jun 2017 01:07:30: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 28 Jun 2017 01:07:30: #1 finished! INFO @ Wed, 28 Jun 2017 01:07:30: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:07:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:07:31: #2 number of paired peaks: 754 WARNING @ Wed, 28 Jun 2017 01:07:31: Fewer paired peaks (754) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 754 pairs to build model! INFO @ Wed, 28 Jun 2017 01:07:31: start model_add_line... INFO @ Wed, 28 Jun 2017 01:07:31: start X-correlation... INFO @ Wed, 28 Jun 2017 01:07:31: end of X-cor INFO @ Wed, 28 Jun 2017 01:07:31: #2 finished! INFO @ Wed, 28 Jun 2017 01:07:31: #2 predicted fragment length is 125 bps INFO @ Wed, 28 Jun 2017 01:07:31: #2 alternative fragment length(s) may be 125 bps INFO @ Wed, 28 Jun 2017 01:07:31: #2.2 Generate R script for model : SRX749022.05_model.r INFO @ Wed, 28 Jun 2017 01:07:31: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:07:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:07:31: 21000000 INFO @ Wed, 28 Jun 2017 01:07:31: 21000000 INFO @ Wed, 28 Jun 2017 01:07:38: 22000000 INFO @ Wed, 28 Jun 2017 01:07:39: 22000000 INFO @ Wed, 28 Jun 2017 01:07:46: 23000000 INFO @ Wed, 28 Jun 2017 01:07:46: 23000000 INFO @ Wed, 28 Jun 2017 01:07:48: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:07:48: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:07:48: #1 total tags in treatment: 11406502 INFO @ Wed, 28 Jun 2017 01:07:48: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:07:48: #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 01:07:48: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:07:48: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:07:48: #1 total tags in treatment: 11406502 INFO @ Wed, 28 Jun 2017 01:07:48: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:07:48: #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 01:07:48: #1 tags after filtering in treatment: 10645199 INFO @ Wed, 28 Jun 2017 01:07:48: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 28 Jun 2017 01:07:48: #1 finished! INFO @ Wed, 28 Jun 2017 01:07:48: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:07:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:07:48: #1 tags after filtering in treatment: 10645199 INFO @ Wed, 28 Jun 2017 01:07:48: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 28 Jun 2017 01:07:48: #1 finished! INFO @ Wed, 28 Jun 2017 01:07:48: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:07:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:07:49: #2 number of paired peaks: 754 WARNING @ Wed, 28 Jun 2017 01:07:49: Fewer paired peaks (754) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 754 pairs to build model! INFO @ Wed, 28 Jun 2017 01:07:49: start model_add_line... INFO @ Wed, 28 Jun 2017 01:07:49: #2 number of paired peaks: 754 WARNING @ Wed, 28 Jun 2017 01:07:49: Fewer paired peaks (754) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 754 pairs to build model! INFO @ Wed, 28 Jun 2017 01:07:49: start model_add_line... INFO @ Wed, 28 Jun 2017 01:07:49: start X-correlation... INFO @ Wed, 28 Jun 2017 01:07:49: end of X-cor INFO @ Wed, 28 Jun 2017 01:07:49: #2 finished! INFO @ Wed, 28 Jun 2017 01:07:49: #2 predicted fragment length is 125 bps INFO @ Wed, 28 Jun 2017 01:07:49: #2 alternative fragment length(s) may be 125 bps INFO @ Wed, 28 Jun 2017 01:07:49: #2.2 Generate R script for model : SRX749022.10_model.r INFO @ Wed, 28 Jun 2017 01:07:49: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:07:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:07:49: start X-correlation... INFO @ Wed, 28 Jun 2017 01:07:49: end of X-cor INFO @ Wed, 28 Jun 2017 01:07:49: #2 finished! INFO @ Wed, 28 Jun 2017 01:07:49: #2 predicted fragment length is 125 bps INFO @ Wed, 28 Jun 2017 01:07:49: #2 alternative fragment length(s) may be 125 bps INFO @ Wed, 28 Jun 2017 01:07:49: #2.2 Generate R script for model : SRX749022.20_model.r INFO @ Wed, 28 Jun 2017 01:07:49: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:07:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:07:57: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:08:12: #4 Write output xls file... SRX749022.05_peaks.xls INFO @ Wed, 28 Jun 2017 01:08:12: #4 Write peak in narrowPeak format file... SRX749022.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:08:12: #4 Write summits bed file... SRX749022.05_summits.bed INFO @ Wed, 28 Jun 2017 01:08:12: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4581 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:08:13: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:08:14: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:08:26: #4 Write output xls file... SRX749022.10_peaks.xls INFO @ Wed, 28 Jun 2017 01:08:26: #4 Write peak in narrowPeak format file... SRX749022.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:08:26: #4 Write summits bed file... SRX749022.10_summits.bed INFO @ Wed, 28 Jun 2017 01:08:26: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2579 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:08:26: #4 Write output xls file... SRX749022.20_peaks.xls INFO @ Wed, 28 Jun 2017 01:08:26: #4 Write peak in narrowPeak format file... SRX749022.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:08:26: #4 Write summits bed file... SRX749022.20_summits.bed INFO @ Wed, 28 Jun 2017 01:08:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1256 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。