Job ID = 2163363 sra ファイルのダウンロード中... Completed: 1141664K bytes transferred in 11 seconds (848158K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 36207 0 36207 0 0 45531 0 --:--:-- --:--:-- --:--:-- 59945 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 17445818 spots for /home/okishinya/chipatlas/results/dm3/SRX128171/SRR442092.sra Written 17445818 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: 00:19:30 17445818 reads; of these: 17445818 (100.00%) were paired; of these: 9610263 (55.09%) aligned concordantly 0 times 5595115 (32.07%) aligned concordantly exactly 1 time 2240440 (12.84%) aligned concordantly >1 times ---- 9610263 pairs aligned concordantly 0 times; of these: 195636 (2.04%) aligned discordantly 1 time ---- 9414627 pairs aligned 0 times concordantly or discordantly; of these: 18829254 mates make up the pairs; of these: 17353244 (92.16%) aligned 0 times 561353 (2.98%) aligned exactly 1 time 914657 (4.86%) aligned >1 times 50.27% overall alignment rate Time searching: 00:19:30 Overall time: 00:19:30 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 8 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] 4364881 / 7983007 = 0.5468 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 @ Tue, 21 Apr 2015 16:32:01: # Command line: callpeak -t SRX128171.bam -f BAM -g dm -n SRX128171.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX128171.10 # format = BAM # ChIP-seq file = ['SRX128171.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 INFO @ Tue, 21 Apr 2015 16:32:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 16:32:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 16:32:01: # Command line: callpeak -t SRX128171.bam -f BAM -g dm -n SRX128171.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX128171.05 # format = BAM # ChIP-seq file = ['SRX128171.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 INFO @ Tue, 21 Apr 2015 16:32:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 16:32:01: # Command line: callpeak -t SRX128171.bam -f BAM -g dm -n SRX128171.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX128171.20 # format = BAM # ChIP-seq file = ['SRX128171.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 INFO @ Tue, 21 Apr 2015 16:32:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 16:32:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 16:32:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 16:32:06: 1000000 INFO @ Tue, 21 Apr 2015 16:32:06: 1000000 INFO @ Tue, 21 Apr 2015 16:32:06: 1000000 INFO @ Tue, 21 Apr 2015 16:32:11: 2000000 INFO @ Tue, 21 Apr 2015 16:32:11: 2000000 INFO @ Tue, 21 Apr 2015 16:32:11: 2000000 INFO @ Tue, 21 Apr 2015 16:32:16: 3000000 INFO @ Tue, 21 Apr 2015 16:32:16: 3000000 INFO @ Tue, 21 Apr 2015 16:32:17: 3000000 INFO @ Tue, 21 Apr 2015 16:32:21: 4000000 INFO @ Tue, 21 Apr 2015 16:32:21: 4000000 INFO @ Tue, 21 Apr 2015 16:32:22: 4000000 INFO @ Tue, 21 Apr 2015 16:32:26: 5000000 INFO @ Tue, 21 Apr 2015 16:32:26: 5000000 INFO @ Tue, 21 Apr 2015 16:32:27: 5000000 INFO @ Tue, 21 Apr 2015 16:32:31: 6000000 INFO @ Tue, 21 Apr 2015 16:32:31: 6000000 INFO @ Tue, 21 Apr 2015 16:32:33: 6000000 INFO @ Tue, 21 Apr 2015 16:32:36: 7000000 INFO @ Tue, 21 Apr 2015 16:32:37: 7000000 INFO @ Tue, 21 Apr 2015 16:32:38: 7000000 INFO @ Tue, 21 Apr 2015 16:32:41: 8000000 INFO @ Tue, 21 Apr 2015 16:32:42: 8000000 INFO @ Tue, 21 Apr 2015 16:32:43: 8000000 INFO @ Tue, 21 Apr 2015 16:32:45: #1 tag size is determined as 50 bps INFO @ Tue, 21 Apr 2015 16:32:45: #1 tag size = 50 INFO @ Tue, 21 Apr 2015 16:32:45: #1 total tags in treatment: 3534168 INFO @ Tue, 21 Apr 2015 16:32:45: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 16:32:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 16:32:46: #1 tags after filtering in treatment: 3311021 INFO @ Tue, 21 Apr 2015 16:32:46: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 21 Apr 2015 16:32:46: #1 finished! INFO @ Tue, 21 Apr 2015 16:32:46: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 16:32:46: #1 tag size is determined as 50 bps INFO @ Tue, 21 Apr 2015 16:32:46: #1 tag size = 50 INFO @ Tue, 21 Apr 2015 16:32:46: #1 total tags in treatment: 3534168 INFO @ Tue, 21 Apr 2015 16:32:46: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 16:32:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 16:32:47: #2 number of paired peaks: 3513 INFO @ Tue, 21 Apr 2015 16:32:47: start model_add_line... INFO @ Tue, 21 Apr 2015 16:32:47: #1 tags after filtering in treatment: 3311021 INFO @ Tue, 21 Apr 2015 16:32:47: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 21 Apr 2015 16:32:47: #1 finished! INFO @ Tue, 21 Apr 2015 16:32:47: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 16:32:48: #1 tag size is determined as 50 bps INFO @ Tue, 21 Apr 2015 16:32:48: #1 tag size = 50 INFO @ Tue, 21 Apr 2015 16:32:48: #1 total tags in treatment: 3534168 INFO @ Tue, 21 Apr 2015 16:32:48: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 16:32:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 16:32:48: #2 number of paired peaks: 3513 INFO @ Tue, 21 Apr 2015 16:32:48: start model_add_line... INFO @ Tue, 21 Apr 2015 16:32:48: #1 tags after filtering in treatment: 3311021 INFO @ Tue, 21 Apr 2015 16:32:48: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 21 Apr 2015 16:32:48: #1 finished! INFO @ Tue, 21 Apr 2015 16:32:48: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 16:32:49: #2 number of paired peaks: 3513 INFO @ Tue, 21 Apr 2015 16:32:49: start model_add_line... INFO @ Tue, 21 Apr 2015 16:32:53: start X-correlation... INFO @ Tue, 21 Apr 2015 16:32:53: end of X-cor INFO @ Tue, 21 Apr 2015 16:32:53: #2 finished! INFO @ Tue, 21 Apr 2015 16:32:53: #2 predicted fragment length is 87 bps INFO @ Tue, 21 Apr 2015 16:32:53: #2 alternative fragment length(s) may be 87 bps INFO @ Tue, 21 Apr 2015 16:32:53: #2.2 Generate R script for model : SRX128171.20_model.r WARNING @ Tue, 21 Apr 2015 16:32:53: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 16:32:53: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Tue, 21 Apr 2015 16:32:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 16:32:53: #3 Call peaks... INFO @ Tue, 21 Apr 2015 16:32:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 16:32:54: start X-correlation... INFO @ Tue, 21 Apr 2015 16:32:54: end of X-cor INFO @ Tue, 21 Apr 2015 16:32:54: #2 finished! INFO @ Tue, 21 Apr 2015 16:32:54: #2 predicted fragment length is 87 bps INFO @ Tue, 21 Apr 2015 16:32:54: #2 alternative fragment length(s) may be 87 bps INFO @ Tue, 21 Apr 2015 16:32:54: #2.2 Generate R script for model : SRX128171.10_model.r WARNING @ Tue, 21 Apr 2015 16:32:54: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 16:32:54: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Tue, 21 Apr 2015 16:32:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 16:32:54: #3 Call peaks... INFO @ Tue, 21 Apr 2015 16:32:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 16:32:56: start X-correlation... INFO @ Tue, 21 Apr 2015 16:32:56: end of X-cor INFO @ Tue, 21 Apr 2015 16:32:56: #2 finished! INFO @ Tue, 21 Apr 2015 16:32:56: #2 predicted fragment length is 87 bps INFO @ Tue, 21 Apr 2015 16:32:56: #2 alternative fragment length(s) may be 87 bps INFO @ Tue, 21 Apr 2015 16:32:56: #2.2 Generate R script for model : SRX128171.05_model.r WARNING @ Tue, 21 Apr 2015 16:32:56: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 16:32:56: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Tue, 21 Apr 2015 16:32:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 16:32:56: #3 Call peaks... INFO @ Tue, 21 Apr 2015 16:32:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 16:33:13: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 16:33:14: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 16:33:15: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 16:33:28: #4 Write output xls file... SRX128171.20_peaks.xls INFO @ Tue, 21 Apr 2015 16:33:28: #4 Write peak in narrowPeak format file... SRX128171.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 16:33:28: #4 Write summits bed file... SRX128171.20_summits.bed INFO @ Tue, 21 Apr 2015 16:33:28: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (2383 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 16:33:32: #4 Write output xls file... SRX128171.10_peaks.xls INFO @ Tue, 21 Apr 2015 16:33:32: #4 Write peak in narrowPeak format file... SRX128171.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 16:33:32: #4 Write summits bed file... SRX128171.10_summits.bed INFO @ Tue, 21 Apr 2015 16:33:32: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5900 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 16:33:33: #4 Write output xls file... SRX128171.05_peaks.xls INFO @ Tue, 21 Apr 2015 16:33:33: #4 Write peak in narrowPeak format file... SRX128171.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 16:33:33: #4 Write summits bed file... SRX128171.05_summits.bed INFO @ Tue, 21 Apr 2015 16:33:33: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (9634 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。