Job ID = 2161550 sra ファイルのダウンロード中... Completed: 8321696K bytes transferred in 116 seconds (583701K 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 36310 0 36310 0 0 52739 0 --:--:-- --:--:-- --:--:-- 73205 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 20229395 spots for /home/okishinya/chipatlas/results/dm3/SRX027826/SRR067909.sra Written 20229395 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:22 20229395 reads; of these: 20229395 (100.00%) were unpaired; of these: 2913667 (14.40%) aligned 0 times 13366491 (66.07%) aligned exactly 1 time 3949237 (19.52%) aligned >1 times 85.60% overall alignment rate Time searching: 00:05:23 Overall time: 00:05:23 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_rmdupse_core] 5258167 / 17315728 = 0.3037 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 12:57:51: # Command line: callpeak -t SRX027826.bam -f BAM -g dm -n SRX027826.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX027826.20 # format = BAM # ChIP-seq file = ['SRX027826.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 12:57:51: # Command line: callpeak -t SRX027826.bam -f BAM -g dm -n SRX027826.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX027826.10 # format = BAM # ChIP-seq file = ['SRX027826.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 12:57:51: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:57:51: # Command line: callpeak -t SRX027826.bam -f BAM -g dm -n SRX027826.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX027826.05 # format = BAM # ChIP-seq file = ['SRX027826.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 12:57:51: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:57:51: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:57:51: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:57:51: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:57:51: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:57:56: 1000000 INFO @ Tue, 21 Apr 2015 12:57:56: 1000000 INFO @ Tue, 21 Apr 2015 12:57:56: 1000000 INFO @ Tue, 21 Apr 2015 12:58:01: 2000000 INFO @ Tue, 21 Apr 2015 12:58:01: 2000000 INFO @ Tue, 21 Apr 2015 12:58:01: 2000000 INFO @ Tue, 21 Apr 2015 12:58:06: 3000000 INFO @ Tue, 21 Apr 2015 12:58:06: 3000000 INFO @ Tue, 21 Apr 2015 12:58:06: 3000000 INFO @ Tue, 21 Apr 2015 12:58:11: 4000000 INFO @ Tue, 21 Apr 2015 12:58:11: 4000000 INFO @ Tue, 21 Apr 2015 12:58:11: 4000000 INFO @ Tue, 21 Apr 2015 12:58:16: 5000000 INFO @ Tue, 21 Apr 2015 12:58:16: 5000000 INFO @ Tue, 21 Apr 2015 12:58:16: 5000000 INFO @ Tue, 21 Apr 2015 12:58:21: 6000000 INFO @ Tue, 21 Apr 2015 12:58:21: 6000000 INFO @ Tue, 21 Apr 2015 12:58:21: 6000000 INFO @ Tue, 21 Apr 2015 12:58:26: 7000000 INFO @ Tue, 21 Apr 2015 12:58:27: 7000000 INFO @ Tue, 21 Apr 2015 12:58:27: 7000000 INFO @ Tue, 21 Apr 2015 12:58:31: 8000000 INFO @ Tue, 21 Apr 2015 12:58:32: 8000000 INFO @ Tue, 21 Apr 2015 12:58:32: 8000000 INFO @ Tue, 21 Apr 2015 12:58:36: 9000000 INFO @ Tue, 21 Apr 2015 12:58:37: 9000000 INFO @ Tue, 21 Apr 2015 12:58:37: 9000000 INFO @ Tue, 21 Apr 2015 12:58:41: 10000000 INFO @ Tue, 21 Apr 2015 12:58:42: 10000000 INFO @ Tue, 21 Apr 2015 12:58:42: 10000000 INFO @ Tue, 21 Apr 2015 12:58:46: 11000000 INFO @ Tue, 21 Apr 2015 12:58:47: 11000000 INFO @ Tue, 21 Apr 2015 12:58:47: 11000000 INFO @ Tue, 21 Apr 2015 12:58:51: 12000000 INFO @ Tue, 21 Apr 2015 12:58:52: 12000000 INFO @ Tue, 21 Apr 2015 12:58:52: 12000000 INFO @ Tue, 21 Apr 2015 12:58:52: #1 tag size is determined as 38 bps INFO @ Tue, 21 Apr 2015 12:58:52: #1 tag size = 38 INFO @ Tue, 21 Apr 2015 12:58:52: #1 total tags in treatment: 12057561 INFO @ Tue, 21 Apr 2015 12:58:52: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:58:52: #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 12:58:52: #1 tag size is determined as 38 bps INFO @ Tue, 21 Apr 2015 12:58:52: #1 tag size = 38 INFO @ Tue, 21 Apr 2015 12:58:52: #1 total tags in treatment: 12057561 INFO @ Tue, 21 Apr 2015 12:58:52: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:58:52: #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 12:58:52: #1 tag size is determined as 38 bps INFO @ Tue, 21 Apr 2015 12:58:52: #1 tag size = 38 INFO @ Tue, 21 Apr 2015 12:58:52: #1 total tags in treatment: 12057561 INFO @ Tue, 21 Apr 2015 12:58:52: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:58:52: #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 12:58:54: #1 tags after filtering in treatment: 12055998 INFO @ Tue, 21 Apr 2015 12:58:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:58:54: #1 finished! INFO @ Tue, 21 Apr 2015 12:58:54: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:58:55: #1 tags after filtering in treatment: 12055998 INFO @ Tue, 21 Apr 2015 12:58:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:58:55: #1 finished! INFO @ Tue, 21 Apr 2015 12:58:55: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:58:55: #1 tags after filtering in treatment: 12055998 INFO @ Tue, 21 Apr 2015 12:58:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:58:55: #1 finished! INFO @ Tue, 21 Apr 2015 12:58:55: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:58:57: #2 number of paired peaks: 1541 INFO @ Tue, 21 Apr 2015 12:58:57: start model_add_line... INFO @ Tue, 21 Apr 2015 12:58:57: #2 number of paired peaks: 1541 INFO @ Tue, 21 Apr 2015 12:58:57: start model_add_line... INFO @ Tue, 21 Apr 2015 12:58:57: #2 number of paired peaks: 1541 INFO @ Tue, 21 Apr 2015 12:58:57: start model_add_line... INFO @ Tue, 21 Apr 2015 12:59:09: start X-correlation... INFO @ Tue, 21 Apr 2015 12:59:10: end of X-cor INFO @ Tue, 21 Apr 2015 12:59:10: #2 finished! INFO @ Tue, 21 Apr 2015 12:59:10: #2 predicted fragment length is 84 bps INFO @ Tue, 21 Apr 2015 12:59:10: #2 alternative fragment length(s) may be 84 bps INFO @ Tue, 21 Apr 2015 12:59:10: #2.2 Generate R script for model : SRX027826.10_model.r INFO @ Tue, 21 Apr 2015 12:59:10: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:59:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:59:10: start X-correlation... INFO @ Tue, 21 Apr 2015 12:59:10: end of X-cor INFO @ Tue, 21 Apr 2015 12:59:10: #2 finished! INFO @ Tue, 21 Apr 2015 12:59:10: #2 predicted fragment length is 84 bps INFO @ Tue, 21 Apr 2015 12:59:10: #2 alternative fragment length(s) may be 84 bps INFO @ Tue, 21 Apr 2015 12:59:10: #2.2 Generate R script for model : SRX027826.20_model.r INFO @ Tue, 21 Apr 2015 12:59:10: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:59:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:59:10: start X-correlation... INFO @ Tue, 21 Apr 2015 12:59:10: end of X-cor INFO @ Tue, 21 Apr 2015 12:59:10: #2 finished! INFO @ Tue, 21 Apr 2015 12:59:10: #2 predicted fragment length is 84 bps INFO @ Tue, 21 Apr 2015 12:59:10: #2 alternative fragment length(s) may be 84 bps INFO @ Tue, 21 Apr 2015 12:59:10: #2.2 Generate R script for model : SRX027826.05_model.r INFO @ Tue, 21 Apr 2015 12:59:10: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:59:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:00:13: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:00:14: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:00:14: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:01:00: #4 Write output xls file... SRX027826.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:01:01: #4 Write peak in narrowPeak format file... SRX027826.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:01:01: #4 Write summits bed file... SRX027826.10_summits.bed INFO @ Tue, 21 Apr 2015 13:01:01: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4630 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:01:03: #4 Write output xls file... SRX027826.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:01:03: #4 Write peak in narrowPeak format file... SRX027826.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:01:03: #4 Write summits bed file... SRX027826.20_summits.bed INFO @ Tue, 21 Apr 2015 13:01:03: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2621 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:01:05: #4 Write output xls file... SRX027826.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:01:05: #4 Write peak in narrowPeak format file... SRX027826.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:01:05: #4 Write summits bed file... SRX027826.05_summits.bed INFO @ Tue, 21 Apr 2015 13:01:05: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7417 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。