Job ID = 2161067 sra ファイルのダウンロード中... Completed: 148105K bytes transferred in 5 seconds (232964K 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 16350 0 16350 0 0 23692 0 --:--:-- --:--:-- --:--:-- 32765 100 34830 0 34830 0 0 50410 0 --:--:-- --:--:-- --:--:-- 69660 sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 6793597 spots for /home/okishinya/chipatlas/results/dm3/SRX013005/SRR030271.sra Written 6793597 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: 00:01:33 6793597 reads; of these: 6793597 (100.00%) were unpaired; of these: 228767 (3.37%) aligned 0 times 5939243 (87.42%) aligned exactly 1 time 625587 (9.21%) aligned >1 times 96.63% overall alignment rate Time searching: 00:01:33 Overall time: 00:01:33 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_rmdupse_core] 928412 / 6564830 = 0.1414 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 11:55:58: # Command line: callpeak -t SRX013005.bam -f BAM -g dm -n SRX013005.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013005.05 # format = BAM # ChIP-seq file = ['SRX013005.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 11:55:58: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:55:58: # Command line: callpeak -t SRX013005.bam -f BAM -g dm -n SRX013005.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013005.10 # format = BAM # ChIP-seq file = ['SRX013005.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 11:55:58: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 11:55:58: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:55:58: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 11:55:58: # Command line: callpeak -t SRX013005.bam -f BAM -g dm -n SRX013005.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013005.20 # format = BAM # ChIP-seq file = ['SRX013005.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 11:55:58: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:55:58: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 11:56:03: 1000000 INFO @ Tue, 21 Apr 2015 11:56:03: 1000000 INFO @ Tue, 21 Apr 2015 11:56:03: 1000000 INFO @ Tue, 21 Apr 2015 11:56:08: 2000000 INFO @ Tue, 21 Apr 2015 11:56:09: 2000000 INFO @ Tue, 21 Apr 2015 11:56:09: 2000000 INFO @ Tue, 21 Apr 2015 11:56:13: 3000000 INFO @ Tue, 21 Apr 2015 11:56:14: 3000000 INFO @ Tue, 21 Apr 2015 11:56:14: 3000000 INFO @ Tue, 21 Apr 2015 11:56:18: 4000000 INFO @ Tue, 21 Apr 2015 11:56:19: 4000000 INFO @ Tue, 21 Apr 2015 11:56:19: 4000000 INFO @ Tue, 21 Apr 2015 11:56:23: 5000000 INFO @ Tue, 21 Apr 2015 11:56:24: 5000000 INFO @ Tue, 21 Apr 2015 11:56:24: 5000000 INFO @ Tue, 21 Apr 2015 11:56:26: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 11:56:26: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 11:56:26: #1 total tags in treatment: 5636418 INFO @ Tue, 21 Apr 2015 11:56:26: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 11:56:26: #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 11:56:27: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 11:56:27: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 11:56:27: #1 total tags in treatment: 5636418 INFO @ Tue, 21 Apr 2015 11:56:27: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 11:56:27: #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 11:56:27: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 11:56:27: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 11:56:27: #1 total tags in treatment: 5636418 INFO @ Tue, 21 Apr 2015 11:56:27: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 11:56:27: #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 11:56:28: #1 tags after filtering in treatment: 5635958 INFO @ Tue, 21 Apr 2015 11:56:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 11:56:28: #1 finished! INFO @ Tue, 21 Apr 2015 11:56:28: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 11:56:28: #1 tags after filtering in treatment: 5635958 INFO @ Tue, 21 Apr 2015 11:56:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 11:56:28: #1 finished! INFO @ Tue, 21 Apr 2015 11:56:28: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 11:56:28: #1 tags after filtering in treatment: 5635958 INFO @ Tue, 21 Apr 2015 11:56:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 11:56:28: #1 finished! INFO @ Tue, 21 Apr 2015 11:56:28: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 11:56:29: #2 number of paired peaks: 7399 INFO @ Tue, 21 Apr 2015 11:56:29: start model_add_line... INFO @ Tue, 21 Apr 2015 11:56:30: #2 number of paired peaks: 7399 INFO @ Tue, 21 Apr 2015 11:56:30: start model_add_line... INFO @ Tue, 21 Apr 2015 11:56:30: #2 number of paired peaks: 7399 INFO @ Tue, 21 Apr 2015 11:56:30: start model_add_line... INFO @ Tue, 21 Apr 2015 11:57:01: start X-correlation... INFO @ Tue, 21 Apr 2015 11:57:01: end of X-cor INFO @ Tue, 21 Apr 2015 11:57:01: #2 finished! INFO @ Tue, 21 Apr 2015 11:57:01: #2 predicted fragment length is 145 bps INFO @ Tue, 21 Apr 2015 11:57:01: #2 alternative fragment length(s) may be 145 bps INFO @ Tue, 21 Apr 2015 11:57:01: #2.2 Generate R script for model : SRX013005.20_model.r INFO @ Tue, 21 Apr 2015 11:57:01: #3 Call peaks... INFO @ Tue, 21 Apr 2015 11:57:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 11:57:03: start X-correlation... INFO @ Tue, 21 Apr 2015 11:57:03: end of X-cor INFO @ Tue, 21 Apr 2015 11:57:03: #2 finished! INFO @ Tue, 21 Apr 2015 11:57:03: #2 predicted fragment length is 145 bps INFO @ Tue, 21 Apr 2015 11:57:03: #2 alternative fragment length(s) may be 145 bps INFO @ Tue, 21 Apr 2015 11:57:03: #2.2 Generate R script for model : SRX013005.05_model.r INFO @ Tue, 21 Apr 2015 11:57:03: #3 Call peaks... INFO @ Tue, 21 Apr 2015 11:57:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 11:57:03: start X-correlation... INFO @ Tue, 21 Apr 2015 11:57:03: end of X-cor INFO @ Tue, 21 Apr 2015 11:57:03: #2 finished! INFO @ Tue, 21 Apr 2015 11:57:03: #2 predicted fragment length is 145 bps INFO @ Tue, 21 Apr 2015 11:57:03: #2 alternative fragment length(s) may be 145 bps INFO @ Tue, 21 Apr 2015 11:57:03: #2.2 Generate R script for model : SRX013005.10_model.r INFO @ Tue, 21 Apr 2015 11:57:03: #3 Call peaks... INFO @ Tue, 21 Apr 2015 11:57:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 11:57:33: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 11:57:35: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 11:57:36: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 21 Apr 2015 11:58:00: #4 Write output xls file... SRX013005.20_peaks.xls INFO @ Tue, 21 Apr 2015 11:58:00: #4 Write peak in narrowPeak format file... SRX013005.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 11:58:01: #4 Write summits bed file... SRX013005.20_summits.bed INFO @ Tue, 21 Apr 2015 11:58:01: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (4940 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 11:58:07: #4 Write output xls file... SRX013005.10_peaks.xls INFO @ Tue, 21 Apr 2015 11:58:07: #4 Write peak in narrowPeak format file... SRX013005.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 11:58:07: #4 Write summits bed file... SRX013005.10_summits.bed INFO @ Tue, 21 Apr 2015 11:58:07: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6923 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 11:58:09: #4 Write output xls file... SRX013005.05_peaks.xls INFO @ Tue, 21 Apr 2015 11:58:09: #4 Write peak in narrowPeak format file... SRX013005.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 11:58:09: #4 Write summits bed file... SRX013005.05_summits.bed INFO @ Tue, 21 Apr 2015 11:58:09: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (8968 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。