Job ID = 9033014 sra ファイルのダウンロード中... Completed: 1233334K bytes transferred in 11 seconds (908096K 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 --:--:-- 0:00:06 --:--:-- 0 100 7663 0 7663 0 0 1045 0 --:--:-- 0:00:07 --:--:-- 8024 100 46317 0 46317 0 0 5538 0 --:--:-- 0:00:08 --:--:-- 23274 100 106k 0 106k 0 0 11906 0 --:--:-- 0:00:09 --:--:-- 38828 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 38537934 spots for /home/okishinya/chipatlas/results/dm3/SRX886165/SRR1813779.sra Written 38537934 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: 00:11:09 38537934 reads; of these: 38537934 (100.00%) were unpaired; of these: 11838538 (30.72%) aligned 0 times 19463151 (50.50%) aligned exactly 1 time 7236245 (18.78%) aligned >1 times 69.28% overall alignment rate Time searching: 00:11:09 Overall time: 00:11:09 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 12 files... [bam_rmdupse_core] 19874919 / 26699396 = 0.7444 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 @ Sun, 04 Jun 2017 00:18:17: # Command line: callpeak -t SRX886165.bam -f BAM -g dm -n SRX886165.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX886165.20 # format = BAM # ChIP-seq file = ['SRX886165.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 @ Sun, 04 Jun 2017 00:18:17: # Command line: callpeak -t SRX886165.bam -f BAM -g dm -n SRX886165.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX886165.05 # format = BAM # ChIP-seq file = ['SRX886165.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 @ Sun, 04 Jun 2017 00:18:17: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:18:17: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:18:17: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:18:17: # Command line: callpeak -t SRX886165.bam -f BAM -g dm -n SRX886165.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX886165.10 # format = BAM # ChIP-seq file = ['SRX886165.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 @ Sun, 04 Jun 2017 00:18:17: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:18:17: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:18:17: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:18:22: 1000000 INFO @ Sun, 04 Jun 2017 00:18:22: 1000000 INFO @ Sun, 04 Jun 2017 00:18:22: 1000000 INFO @ Sun, 04 Jun 2017 00:18:28: 2000000 INFO @ Sun, 04 Jun 2017 00:18:28: 2000000 INFO @ Sun, 04 Jun 2017 00:18:28: 2000000 INFO @ Sun, 04 Jun 2017 00:18:34: 3000000 INFO @ Sun, 04 Jun 2017 00:18:34: 3000000 INFO @ Sun, 04 Jun 2017 00:18:34: 3000000 INFO @ Sun, 04 Jun 2017 00:18:39: 4000000 INFO @ Sun, 04 Jun 2017 00:18:39: 4000000 INFO @ Sun, 04 Jun 2017 00:18:40: 4000000 INFO @ Sun, 04 Jun 2017 00:18:45: 5000000 INFO @ Sun, 04 Jun 2017 00:18:45: 5000000 INFO @ Sun, 04 Jun 2017 00:18:46: 5000000 INFO @ Sun, 04 Jun 2017 00:18:52: 6000000 INFO @ Sun, 04 Jun 2017 00:18:52: 6000000 INFO @ Sun, 04 Jun 2017 00:18:53: 6000000 INFO @ Sun, 04 Jun 2017 00:18:57: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 00:18:57: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 00:18:57: #1 total tags in treatment: 6824477 INFO @ Sun, 04 Jun 2017 00:18:57: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:18:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:18:58: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 00:18:58: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 00:18:58: #1 total tags in treatment: 6824477 INFO @ Sun, 04 Jun 2017 00:18:58: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:18:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:18:58: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 00:18:58: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 00:18:58: #1 total tags in treatment: 6824477 INFO @ Sun, 04 Jun 2017 00:18:58: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:18:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:18:59: #1 tags after filtering in treatment: 6822003 INFO @ Sun, 04 Jun 2017 00:18:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:18:59: #1 finished! INFO @ Sun, 04 Jun 2017 00:18:59: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:18:59: #1 tags after filtering in treatment: 6822003 INFO @ Sun, 04 Jun 2017 00:18:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:18:59: #1 finished! INFO @ Sun, 04 Jun 2017 00:18:59: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:18:59: #1 tags after filtering in treatment: 6822003 INFO @ Sun, 04 Jun 2017 00:18:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:18:59: #1 finished! INFO @ Sun, 04 Jun 2017 00:18:59: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:19:00: #2 number of paired peaks: 4108 INFO @ Sun, 04 Jun 2017 00:19:00: start model_add_line... INFO @ Sun, 04 Jun 2017 00:19:01: #2 number of paired peaks: 4108 INFO @ Sun, 04 Jun 2017 00:19:01: start model_add_line... INFO @ Sun, 04 Jun 2017 00:19:01: #2 number of paired peaks: 4108 INFO @ Sun, 04 Jun 2017 00:19:01: start model_add_line... INFO @ Sun, 04 Jun 2017 00:19:30: start X-correlation... INFO @ Sun, 04 Jun 2017 00:19:30: end of X-cor INFO @ Sun, 04 Jun 2017 00:19:30: #2 finished! INFO @ Sun, 04 Jun 2017 00:19:30: #2 predicted fragment length is 61 bps INFO @ Sun, 04 Jun 2017 00:19:30: #2 alternative fragment length(s) may be 4,61 bps INFO @ Sun, 04 Jun 2017 00:19:30: #2.2 Generate R script for model : SRX886165.05_model.r WARNING @ Sun, 04 Jun 2017 00:19:30: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 00:19:30: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Sun, 04 Jun 2017 00:19:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 00:19:30: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:19:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:19:30: start X-correlation... INFO @ Sun, 04 Jun 2017 00:19:30: end of X-cor INFO @ Sun, 04 Jun 2017 00:19:30: #2 finished! INFO @ Sun, 04 Jun 2017 00:19:30: #2 predicted fragment length is 61 bps INFO @ Sun, 04 Jun 2017 00:19:30: #2 alternative fragment length(s) may be 4,61 bps INFO @ Sun, 04 Jun 2017 00:19:30: #2.2 Generate R script for model : SRX886165.10_model.r WARNING @ Sun, 04 Jun 2017 00:19:30: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 00:19:30: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Sun, 04 Jun 2017 00:19:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 00:19:30: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:19:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:19:30: start X-correlation... INFO @ Sun, 04 Jun 2017 00:19:30: end of X-cor INFO @ Sun, 04 Jun 2017 00:19:30: #2 finished! INFO @ Sun, 04 Jun 2017 00:19:30: #2 predicted fragment length is 61 bps INFO @ Sun, 04 Jun 2017 00:19:30: #2 alternative fragment length(s) may be 4,61 bps INFO @ Sun, 04 Jun 2017 00:19:30: #2.2 Generate R script for model : SRX886165.20_model.r WARNING @ Sun, 04 Jun 2017 00:19:30: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 00:19:30: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Sun, 04 Jun 2017 00:19:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 00:19:30: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:19:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:20:07: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:20:10: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:20:10: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:20:38: #4 Write output xls file... SRX886165.05_peaks.xls INFO @ Sun, 04 Jun 2017 00:20:38: #4 Write peak in narrowPeak format file... SRX886165.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:20:38: #4 Write summits bed file... SRX886165.05_summits.bed INFO @ Sun, 04 Jun 2017 00:20:38: Done! INFO @ Sun, 04 Jun 2017 00:20:38: #4 Write output xls file... SRX886165.20_peaks.xls INFO @ Sun, 04 Jun 2017 00:20:39: #4 Write peak in narrowPeak format file... SRX886165.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:20:39: #4 Write summits bed file... SRX886165.20_summits.bed INFO @ Sun, 04 Jun 2017 00:20:39: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6981 records, 4 fields): 10 millis CompletedMACS2peakCalling pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3021 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:20:40: #4 Write output xls file... SRX886165.10_peaks.xls INFO @ Sun, 04 Jun 2017 00:20:40: #4 Write peak in narrowPeak format file... SRX886165.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:20:40: #4 Write summits bed file... SRX886165.10_summits.bed INFO @ Sun, 04 Jun 2017 00:20:40: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4531 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。