Job ID = 2161340 sra ファイルのダウンロード中... Completed: 332986K bytes transferred in 5 seconds (465856K 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 4007 0 4007 0 0 7330 0 --:--:-- --:--:-- --:--:-- 11255 100 36118 0 36118 0 0 48964 0 --:--:-- --:--:-- --:--:-- 66029 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 7010476 spots for /home/okishinya/chipatlas/results/dm3/SRX019957/SRR042287.sra Written 7010476 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:01 7010476 reads; of these: 7010476 (100.00%) were paired; of these: 1160040 (16.55%) aligned concordantly 0 times 4652926 (66.37%) aligned concordantly exactly 1 time 1197510 (17.08%) aligned concordantly >1 times ---- 1160040 pairs aligned concordantly 0 times; of these: 32291 (2.78%) aligned discordantly 1 time ---- 1127749 pairs aligned 0 times concordantly or discordantly; of these: 2255498 mates make up the pairs; of these: 1671782 (74.12%) aligned 0 times 414321 (18.37%) aligned exactly 1 time 169395 (7.51%) aligned >1 times 88.08% overall alignment rate Time searching: 00:10:02 Overall time: 00:10:02 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] 161389 / 5863860 = 0.0275 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 12:37:28: # Command line: callpeak -t SRX019957.bam -f BAM -g dm -n SRX019957.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX019957.10 # format = BAM # ChIP-seq file = ['SRX019957.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 12:37:28: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:37:28: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:37:28: # Command line: callpeak -t SRX019957.bam -f BAM -g dm -n SRX019957.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX019957.05 # format = BAM # ChIP-seq file = ['SRX019957.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 12:37:28: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:37:28: # Command line: callpeak -t SRX019957.bam -f BAM -g dm -n SRX019957.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX019957.20 # format = BAM # ChIP-seq file = ['SRX019957.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 12:37:28: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:37:28: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:37:28: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:37:34: 1000000 INFO @ Tue, 21 Apr 2015 12:37:34: 1000000 INFO @ Tue, 21 Apr 2015 12:37:34: 1000000 INFO @ Tue, 21 Apr 2015 12:37:39: 2000000 INFO @ Tue, 21 Apr 2015 12:37:41: 2000000 INFO @ Tue, 21 Apr 2015 12:37:41: 2000000 INFO @ Tue, 21 Apr 2015 12:37:44: 3000000 INFO @ Tue, 21 Apr 2015 12:37:48: 3000000 INFO @ Tue, 21 Apr 2015 12:37:48: 3000000 INFO @ Tue, 21 Apr 2015 12:37:49: 4000000 INFO @ Tue, 21 Apr 2015 12:37:54: 5000000 INFO @ Tue, 21 Apr 2015 12:37:55: 4000000 INFO @ Tue, 21 Apr 2015 12:37:55: 4000000 INFO @ Tue, 21 Apr 2015 12:38:00: 6000000 INFO @ Tue, 21 Apr 2015 12:38:02: 5000000 INFO @ Tue, 21 Apr 2015 12:38:02: 5000000 INFO @ Tue, 21 Apr 2015 12:38:05: 7000000 INFO @ Tue, 21 Apr 2015 12:38:09: 6000000 INFO @ Tue, 21 Apr 2015 12:38:09: 6000000 INFO @ Tue, 21 Apr 2015 12:38:10: 8000000 INFO @ Tue, 21 Apr 2015 12:38:15: 9000000 INFO @ Tue, 21 Apr 2015 12:38:16: 7000000 INFO @ Tue, 21 Apr 2015 12:38:16: 7000000 INFO @ Tue, 21 Apr 2015 12:38:20: 10000000 INFO @ Tue, 21 Apr 2015 12:38:23: 8000000 INFO @ Tue, 21 Apr 2015 12:38:23: 8000000 INFO @ Tue, 21 Apr 2015 12:38:26: 11000000 INFO @ Tue, 21 Apr 2015 12:38:30: 9000000 INFO @ Tue, 21 Apr 2015 12:38:30: 9000000 INFO @ Tue, 21 Apr 2015 12:38:31: 12000000 INFO @ Tue, 21 Apr 2015 12:38:31: #1 tag size is determined as 35 bps INFO @ Tue, 21 Apr 2015 12:38:31: #1 tag size = 35 INFO @ Tue, 21 Apr 2015 12:38:31: #1 total tags in treatment: 5689714 INFO @ Tue, 21 Apr 2015 12:38:31: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:38:31: #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 12:38:32: #1 tags after filtering in treatment: 5175370 INFO @ Tue, 21 Apr 2015 12:38:32: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 21 Apr 2015 12:38:32: #1 finished! INFO @ Tue, 21 Apr 2015 12:38:32: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:38:33: #2 number of paired peaks: 270 WARNING @ Tue, 21 Apr 2015 12:38:33: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Tue, 21 Apr 2015 12:38:33: start model_add_line... INFO @ Tue, 21 Apr 2015 12:38:34: start X-correlation... INFO @ Tue, 21 Apr 2015 12:38:34: end of X-cor INFO @ Tue, 21 Apr 2015 12:38:34: #2 finished! INFO @ Tue, 21 Apr 2015 12:38:34: #2 predicted fragment length is 99 bps INFO @ Tue, 21 Apr 2015 12:38:34: #2 alternative fragment length(s) may be 99 bps INFO @ Tue, 21 Apr 2015 12:38:34: #2.2 Generate R script for model : SRX019957.20_model.r INFO @ Tue, 21 Apr 2015 12:38:34: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:38:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:38:37: 10000000 INFO @ Tue, 21 Apr 2015 12:38:37: 10000000 INFO @ Tue, 21 Apr 2015 12:38:45: 11000000 INFO @ Tue, 21 Apr 2015 12:38:45: 11000000 INFO @ Tue, 21 Apr 2015 12:38:52: 12000000 INFO @ Tue, 21 Apr 2015 12:38:52: 12000000 INFO @ Tue, 21 Apr 2015 12:38:52: #1 tag size is determined as 35 bps INFO @ Tue, 21 Apr 2015 12:38:52: #1 tag size = 35 INFO @ Tue, 21 Apr 2015 12:38:52: #1 total tags in treatment: 5689714 INFO @ Tue, 21 Apr 2015 12:38:52: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:38:52: #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 12:38:52: #1 tag size is determined as 35 bps INFO @ Tue, 21 Apr 2015 12:38:52: #1 tag size = 35 INFO @ Tue, 21 Apr 2015 12:38:52: #1 total tags in treatment: 5689714 INFO @ Tue, 21 Apr 2015 12:38:52: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:38:52: #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 12:38:53: #1 tags after filtering in treatment: 5175370 INFO @ Tue, 21 Apr 2015 12:38:53: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 21 Apr 2015 12:38:53: #1 finished! INFO @ Tue, 21 Apr 2015 12:38:53: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:38:53: #1 tags after filtering in treatment: 5175370 INFO @ Tue, 21 Apr 2015 12:38:53: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 21 Apr 2015 12:38:53: #1 finished! INFO @ Tue, 21 Apr 2015 12:38:53: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:38:54: #2 number of paired peaks: 270 WARNING @ Tue, 21 Apr 2015 12:38:54: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Tue, 21 Apr 2015 12:38:54: start model_add_line... INFO @ Tue, 21 Apr 2015 12:38:54: #2 number of paired peaks: 270 WARNING @ Tue, 21 Apr 2015 12:38:54: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Tue, 21 Apr 2015 12:38:54: start model_add_line... INFO @ Tue, 21 Apr 2015 12:38:55: start X-correlation... INFO @ Tue, 21 Apr 2015 12:38:55: end of X-cor INFO @ Tue, 21 Apr 2015 12:38:55: #2 finished! INFO @ Tue, 21 Apr 2015 12:38:55: #2 predicted fragment length is 99 bps INFO @ Tue, 21 Apr 2015 12:38:55: #2 alternative fragment length(s) may be 99 bps INFO @ Tue, 21 Apr 2015 12:38:55: #2.2 Generate R script for model : SRX019957.05_model.r INFO @ Tue, 21 Apr 2015 12:38:55: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:38:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:38:55: start X-correlation... INFO @ Tue, 21 Apr 2015 12:38:55: end of X-cor INFO @ Tue, 21 Apr 2015 12:38:55: #2 finished! INFO @ Tue, 21 Apr 2015 12:38:55: #2 predicted fragment length is 99 bps INFO @ Tue, 21 Apr 2015 12:38:55: #2 alternative fragment length(s) may be 99 bps INFO @ Tue, 21 Apr 2015 12:38:55: #2.2 Generate R script for model : SRX019957.10_model.r INFO @ Tue, 21 Apr 2015 12:38:55: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:38:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:39:03: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:39:24: #4 Write output xls file... SRX019957.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:39:24: #4 Write peak in narrowPeak format file... SRX019957.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:39:24: #4 Write summits bed file... SRX019957.20_summits.bed INFO @ Tue, 21 Apr 2015 12:39:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (143 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:39:25: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:39:26: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:39:46: #4 Write output xls file... SRX019957.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:39:46: #4 Write peak in narrowPeak format file... SRX019957.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:39:46: #4 Write summits bed file... SRX019957.10_summits.bed INFO @ Tue, 21 Apr 2015 12:39:46: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (367 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:39:47: #4 Write output xls file... SRX019957.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:39:47: #4 Write peak in narrowPeak format file... SRX019957.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:39:47: #4 Write summits bed file... SRX019957.05_summits.bed INFO @ Tue, 21 Apr 2015 12:39:47: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (808 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。