Job ID = 2161339 sra ファイルのダウンロード中... Completed: 316970K bytes transferred in 7 seconds (330540K 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 36110 0 36110 0 0 48180 0 --:--:-- --:--:-- --:--:-- 64829 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 6629498 spots for /home/okishinya/chipatlas/results/dm3/SRX019955/SRR042285.sra Written 6629498 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: 00:10:35 6629498 reads; of these: 6629498 (100.00%) were paired; of these: 1195373 (18.03%) aligned concordantly 0 times 4224017 (63.72%) aligned concordantly exactly 1 time 1210108 (18.25%) aligned concordantly >1 times ---- 1195373 pairs aligned concordantly 0 times; of these: 31533 (2.64%) aligned discordantly 1 time ---- 1163840 pairs aligned 0 times concordantly or discordantly; of these: 2327680 mates make up the pairs; of these: 1678644 (72.12%) aligned 0 times 454134 (19.51%) aligned exactly 1 time 194902 (8.37%) aligned >1 times 87.34% overall alignment rate Time searching: 00:10:35 Overall time: 00:10:35 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_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] 106759 / 5443135 = 0.0196 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 12:37:23: # Command line: callpeak -t SRX019955.bam -f BAM -g dm -n SRX019955.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX019955.10 # format = BAM # ChIP-seq file = ['SRX019955.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 12:37:23: # Command line: callpeak -t SRX019955.bam -f BAM -g dm -n SRX019955.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX019955.20 # format = BAM # ChIP-seq file = ['SRX019955.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 12:37:23: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:37:23: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:37:23: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:37:23: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:37:23: # Command line: callpeak -t SRX019955.bam -f BAM -g dm -n SRX019955.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX019955.05 # format = BAM # ChIP-seq file = ['SRX019955.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 12:37:23: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:37:23: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:37:28: 1000000 INFO @ Tue, 21 Apr 2015 12:37:28: 1000000 INFO @ Tue, 21 Apr 2015 12:37:29: 1000000 INFO @ Tue, 21 Apr 2015 12:37:34: 2000000 INFO @ Tue, 21 Apr 2015 12:37:34: 2000000 INFO @ Tue, 21 Apr 2015 12:37:34: 2000000 INFO @ Tue, 21 Apr 2015 12:37:39: 3000000 INFO @ Tue, 21 Apr 2015 12:37:39: 3000000 INFO @ Tue, 21 Apr 2015 12:37:39: 3000000 INFO @ Tue, 21 Apr 2015 12:37:44: 4000000 INFO @ Tue, 21 Apr 2015 12:37:44: 4000000 INFO @ Tue, 21 Apr 2015 12:37:44: 4000000 INFO @ Tue, 21 Apr 2015 12:37:49: 5000000 INFO @ Tue, 21 Apr 2015 12:37:49: 5000000 INFO @ Tue, 21 Apr 2015 12:37:49: 5000000 INFO @ Tue, 21 Apr 2015 12:37:54: 6000000 INFO @ Tue, 21 Apr 2015 12:37:55: 6000000 INFO @ Tue, 21 Apr 2015 12:37:55: 6000000 INFO @ Tue, 21 Apr 2015 12:37:59: 7000000 INFO @ Tue, 21 Apr 2015 12:38:00: 7000000 INFO @ Tue, 21 Apr 2015 12:38:00: 7000000 INFO @ Tue, 21 Apr 2015 12:38:05: 8000000 INFO @ Tue, 21 Apr 2015 12:38:05: 8000000 INFO @ Tue, 21 Apr 2015 12:38:05: 8000000 INFO @ Tue, 21 Apr 2015 12:38:10: 9000000 INFO @ Tue, 21 Apr 2015 12:38:10: 9000000 INFO @ Tue, 21 Apr 2015 12:38:10: 9000000 INFO @ Tue, 21 Apr 2015 12:38:15: 10000000 INFO @ Tue, 21 Apr 2015 12:38:15: 10000000 INFO @ Tue, 21 Apr 2015 12:38:16: 10000000 INFO @ Tue, 21 Apr 2015 12:38:20: 11000000 INFO @ Tue, 21 Apr 2015 12:38:21: 11000000 INFO @ Tue, 21 Apr 2015 12:38:21: 11000000 INFO @ Tue, 21 Apr 2015 12:38:22: #1 tag size is determined as 35 bps INFO @ Tue, 21 Apr 2015 12:38:22: #1 tag size = 35 INFO @ Tue, 21 Apr 2015 12:38:22: #1 total tags in treatment: 5327683 INFO @ Tue, 21 Apr 2015 12:38:22: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:38:22: #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 12:38:23: #1 tags after filtering in treatment: 4916409 INFO @ Tue, 21 Apr 2015 12:38:23: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 21 Apr 2015 12:38:23: #1 finished! INFO @ Tue, 21 Apr 2015 12:38:23: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:38:23: #1 tag size is determined as 35 bps INFO @ Tue, 21 Apr 2015 12:38:23: #1 tag size = 35 INFO @ Tue, 21 Apr 2015 12:38:23: #1 total tags in treatment: 5327683 INFO @ Tue, 21 Apr 2015 12:38:23: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:38:23: #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 12:38:23: #1 tag size is determined as 35 bps INFO @ Tue, 21 Apr 2015 12:38:23: #1 tag size = 35 INFO @ Tue, 21 Apr 2015 12:38:23: #1 total tags in treatment: 5327683 INFO @ Tue, 21 Apr 2015 12:38:23: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:38:23: #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 12:38:23: #2 number of paired peaks: 300 WARNING @ Tue, 21 Apr 2015 12:38:23: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Tue, 21 Apr 2015 12:38:23: start model_add_line... INFO @ Tue, 21 Apr 2015 12:38:24: #1 tags after filtering in treatment: 4916409 INFO @ Tue, 21 Apr 2015 12:38:24: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 21 Apr 2015 12:38:24: #1 finished! INFO @ Tue, 21 Apr 2015 12:38:24: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:38:24: #1 tags after filtering in treatment: 4916409 INFO @ Tue, 21 Apr 2015 12:38:24: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 21 Apr 2015 12:38:24: #1 finished! INFO @ Tue, 21 Apr 2015 12:38:24: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:38:24: #2 number of paired peaks: 300 WARNING @ Tue, 21 Apr 2015 12:38:24: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Tue, 21 Apr 2015 12:38:24: start model_add_line... INFO @ Tue, 21 Apr 2015 12:38:25: #2 number of paired peaks: 300 WARNING @ Tue, 21 Apr 2015 12:38:25: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Tue, 21 Apr 2015 12:38:25: start model_add_line... INFO @ Tue, 21 Apr 2015 12:38:25: start X-correlation... INFO @ Tue, 21 Apr 2015 12:38:25: end of X-cor INFO @ Tue, 21 Apr 2015 12:38:25: #2 finished! INFO @ Tue, 21 Apr 2015 12:38:25: #2 predicted fragment length is 95 bps INFO @ Tue, 21 Apr 2015 12:38:25: #2 alternative fragment length(s) may be 95 bps INFO @ Tue, 21 Apr 2015 12:38:25: #2.2 Generate R script for model : SRX019955.05_model.r INFO @ Tue, 21 Apr 2015 12:38:25: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:38:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:38:26: start X-correlation... INFO @ Tue, 21 Apr 2015 12:38:26: end of X-cor INFO @ Tue, 21 Apr 2015 12:38:26: #2 finished! INFO @ Tue, 21 Apr 2015 12:38:26: #2 predicted fragment length is 95 bps INFO @ Tue, 21 Apr 2015 12:38:26: #2 alternative fragment length(s) may be 95 bps INFO @ Tue, 21 Apr 2015 12:38:26: #2.2 Generate R script for model : SRX019955.20_model.r INFO @ Tue, 21 Apr 2015 12:38:26: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:38:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:38:26: start X-correlation... INFO @ Tue, 21 Apr 2015 12:38:26: end of X-cor INFO @ Tue, 21 Apr 2015 12:38:26: #2 finished! INFO @ Tue, 21 Apr 2015 12:38:26: #2 predicted fragment length is 95 bps INFO @ Tue, 21 Apr 2015 12:38:26: #2 alternative fragment length(s) may be 95 bps INFO @ Tue, 21 Apr 2015 12:38:26: #2.2 Generate R script for model : SRX019955.10_model.r INFO @ Tue, 21 Apr 2015 12:38:26: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:38:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:38:53: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:38:54: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:38:54: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:39:14: #4 Write output xls file... SRX019955.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:39:14: #4 Write peak in narrowPeak format file... SRX019955.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:39:14: #4 Write summits bed file... SRX019955.05_summits.bed INFO @ Tue, 21 Apr 2015 12:39:14: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (846 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:39:14: #4 Write output xls file... SRX019955.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:39:14: #4 Write peak in narrowPeak format file... SRX019955.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:39:14: #4 Write summits bed file... SRX019955.10_summits.bed INFO @ Tue, 21 Apr 2015 12:39:14: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (424 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:39:15: #4 Write output xls file... SRX019955.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:39:15: #4 Write peak in narrowPeak format file... SRX019955.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:39:15: #4 Write summits bed file... SRX019955.20_summits.bed INFO @ Tue, 21 Apr 2015 12:39:15: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (173 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。