Job ID = 9159796 sra ファイルのダウンロード中... Completed: 2759070K bytes transferred in 25 seconds (875524K 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 42948360 spots for /home/okishinya/chipatlas/results/dm3/SRX683493/SRR1554219.sra Written 42948360 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: 00:52:06 42948360 reads; of these: 42948360 (100.00%) were paired; of these: 26813168 (62.43%) aligned concordantly 0 times 11968200 (27.87%) aligned concordantly exactly 1 time 4166992 (9.70%) aligned concordantly >1 times ---- 26813168 pairs aligned concordantly 0 times; of these: 99314 (0.37%) aligned discordantly 1 time ---- 26713854 pairs aligned 0 times concordantly or discordantly; of these: 53427708 mates make up the pairs; of these: 52853839 (98.93%) aligned 0 times 410217 (0.77%) aligned exactly 1 time 163652 (0.31%) aligned >1 times 38.47% overall alignment rate Time searching: 00:52:06 Overall time: 00:52:06 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] 13954595 / 16223516 = 0.8601 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 00:47:08: # Command line: callpeak -t SRX683493.bam -f BAM -g dm -n SRX683493.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX683493.05 # format = BAM # ChIP-seq file = ['SRX683493.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 00:47:08: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:47:08: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:47:08: # Command line: callpeak -t SRX683493.bam -f BAM -g dm -n SRX683493.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX683493.10 # format = BAM # ChIP-seq file = ['SRX683493.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 00:47:08: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:47:08: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:47:08: # Command line: callpeak -t SRX683493.bam -f BAM -g dm -n SRX683493.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX683493.20 # format = BAM # ChIP-seq file = ['SRX683493.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 00:47:08: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:47:08: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:47:14: 1000000 INFO @ Wed, 28 Jun 2017 00:47:15: 1000000 INFO @ Wed, 28 Jun 2017 00:47:15: 1000000 INFO @ Wed, 28 Jun 2017 00:47:21: 2000000 INFO @ Wed, 28 Jun 2017 00:47:23: 2000000 INFO @ Wed, 28 Jun 2017 00:47:23: 2000000 INFO @ Wed, 28 Jun 2017 00:47:28: 3000000 INFO @ Wed, 28 Jun 2017 00:47:31: 3000000 INFO @ Wed, 28 Jun 2017 00:47:31: 3000000 INFO @ Wed, 28 Jun 2017 00:47:34: 4000000 INFO @ Wed, 28 Jun 2017 00:47:39: 4000000 INFO @ Wed, 28 Jun 2017 00:47:39: 4000000 INFO @ Wed, 28 Jun 2017 00:47:41: 5000000 INFO @ Wed, 28 Jun 2017 00:47:42: #1 tag size is determined as 51 bps INFO @ Wed, 28 Jun 2017 00:47:42: #1 tag size = 51 INFO @ Wed, 28 Jun 2017 00:47:42: #1 total tags in treatment: 2252544 INFO @ Wed, 28 Jun 2017 00:47:42: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:47:42: #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 00:47:42: #1 tags after filtering in treatment: 2131038 INFO @ Wed, 28 Jun 2017 00:47:42: #1 Redundant rate of treatment: 0.05 INFO @ Wed, 28 Jun 2017 00:47:42: #1 finished! INFO @ Wed, 28 Jun 2017 00:47:42: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:47:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:47:42: #2 number of paired peaks: 3925 INFO @ Wed, 28 Jun 2017 00:47:42: start model_add_line... INFO @ Wed, 28 Jun 2017 00:47:42: start X-correlation... INFO @ Wed, 28 Jun 2017 00:47:42: end of X-cor INFO @ Wed, 28 Jun 2017 00:47:42: #2 finished! INFO @ Wed, 28 Jun 2017 00:47:42: #2 predicted fragment length is 145 bps INFO @ Wed, 28 Jun 2017 00:47:42: #2 alternative fragment length(s) may be 145 bps INFO @ Wed, 28 Jun 2017 00:47:42: #2.2 Generate R script for model : SRX683493.05_model.r INFO @ Wed, 28 Jun 2017 00:47:42: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:47:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:47:47: 5000000 INFO @ Wed, 28 Jun 2017 00:47:47: 5000000 INFO @ Wed, 28 Jun 2017 00:47:48: #1 tag size is determined as 51 bps INFO @ Wed, 28 Jun 2017 00:47:48: #1 tag size = 51 INFO @ Wed, 28 Jun 2017 00:47:48: #1 total tags in treatment: 2252544 INFO @ Wed, 28 Jun 2017 00:47:48: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:47:48: #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 00:47:48: #1 tag size is determined as 51 bps INFO @ Wed, 28 Jun 2017 00:47:48: #1 tag size = 51 INFO @ Wed, 28 Jun 2017 00:47:48: #1 total tags in treatment: 2252544 INFO @ Wed, 28 Jun 2017 00:47:48: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:47:48: #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 00:47:48: #1 tags after filtering in treatment: 2131038 INFO @ Wed, 28 Jun 2017 00:47:48: #1 Redundant rate of treatment: 0.05 INFO @ Wed, 28 Jun 2017 00:47:48: #1 finished! INFO @ Wed, 28 Jun 2017 00:47:48: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:47:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:47:48: #1 tags after filtering in treatment: 2131038 INFO @ Wed, 28 Jun 2017 00:47:48: #1 Redundant rate of treatment: 0.05 INFO @ Wed, 28 Jun 2017 00:47:48: #1 finished! INFO @ Wed, 28 Jun 2017 00:47:48: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:47:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:47:48: #2 number of paired peaks: 3925 INFO @ Wed, 28 Jun 2017 00:47:48: start model_add_line... INFO @ Wed, 28 Jun 2017 00:47:48: #2 number of paired peaks: 3925 INFO @ Wed, 28 Jun 2017 00:47:48: start model_add_line... INFO @ Wed, 28 Jun 2017 00:47:48: start X-correlation... INFO @ Wed, 28 Jun 2017 00:47:48: end of X-cor INFO @ Wed, 28 Jun 2017 00:47:48: #2 finished! INFO @ Wed, 28 Jun 2017 00:47:48: #2 predicted fragment length is 145 bps INFO @ Wed, 28 Jun 2017 00:47:48: #2 alternative fragment length(s) may be 145 bps INFO @ Wed, 28 Jun 2017 00:47:48: #2.2 Generate R script for model : SRX683493.20_model.r INFO @ Wed, 28 Jun 2017 00:47:48: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:47:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:47:48: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:47:48: start X-correlation... INFO @ Wed, 28 Jun 2017 00:47:48: end of X-cor INFO @ Wed, 28 Jun 2017 00:47:48: #2 finished! INFO @ Wed, 28 Jun 2017 00:47:48: #2 predicted fragment length is 145 bps INFO @ Wed, 28 Jun 2017 00:47:48: #2 alternative fragment length(s) may be 145 bps INFO @ Wed, 28 Jun 2017 00:47:48: #2.2 Generate R script for model : SRX683493.10_model.r INFO @ Wed, 28 Jun 2017 00:47:48: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:47:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:47:52: #4 Write output xls file... SRX683493.05_peaks.xls INFO @ Wed, 28 Jun 2017 00:47:52: #4 Write peak in narrowPeak format file... SRX683493.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:47:52: #4 Write summits bed file... SRX683493.05_summits.bed INFO @ Wed, 28 Jun 2017 00:47:52: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3569 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:47:54: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:47:54: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:47:58: #4 Write output xls file... SRX683493.20_peaks.xls INFO @ Wed, 28 Jun 2017 00:47:58: #4 Write peak in narrowPeak format file... SRX683493.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:47:58: #4 Write summits bed file... SRX683493.20_summits.bed INFO @ Wed, 28 Jun 2017 00:47:58: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (865 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:47:58: #4 Write output xls file... SRX683493.10_peaks.xls INFO @ Wed, 28 Jun 2017 00:47:58: #4 Write peak in narrowPeak format file... SRX683493.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:47:58: #4 Write summits bed file... SRX683493.10_summits.bed INFO @ Wed, 28 Jun 2017 00:47:58: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1726 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。