Job ID = 9029249 sra ファイルのダウンロード中... Completed: 517970K bytes transferred in 10 seconds (413386K 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 1068 0 --:--:-- 0:00:07 --:--:-- 11041 100 30318 0 30318 0 0 3789 0 --:--:-- 0:00:08 --:--:-- 19893 100 80775 0 80775 0 0 9145 0 --:--:-- 0:00:08 --:--:-- 34299 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 27003446 spots for /home/okishinya/chipatlas/results/dm3/SRX1433398/SRR2919814.sra Written 27003446 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: 00:10:48 27003446 reads; of these: 27003446 (100.00%) were unpaired; of these: 1696340 (6.28%) aligned 0 times 17968684 (66.54%) aligned exactly 1 time 7338422 (27.18%) aligned >1 times 93.72% overall alignment rate Time searching: 00:10:48 Overall time: 00:10:48 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] 14484359 / 25307106 = 0.5723 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 @ Sat, 03 Jun 2017 13:10:06: # Command line: callpeak -t SRX1433398.bam -f BAM -g dm -n SRX1433398.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1433398.05 # format = BAM # ChIP-seq file = ['SRX1433398.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 @ Sat, 03 Jun 2017 13:10:06: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:10:06: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:10:06: # Command line: callpeak -t SRX1433398.bam -f BAM -g dm -n SRX1433398.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1433398.10 # format = BAM # ChIP-seq file = ['SRX1433398.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 @ Sat, 03 Jun 2017 13:10:06: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:10:06: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:10:06: # Command line: callpeak -t SRX1433398.bam -f BAM -g dm -n SRX1433398.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1433398.20 # format = BAM # ChIP-seq file = ['SRX1433398.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 @ Sat, 03 Jun 2017 13:10:06: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:10:06: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:10:13: 1000000 INFO @ Sat, 03 Jun 2017 13:10:13: 1000000 INFO @ Sat, 03 Jun 2017 13:10:13: 1000000 INFO @ Sat, 03 Jun 2017 13:10:20: 2000000 INFO @ Sat, 03 Jun 2017 13:10:20: 2000000 INFO @ Sat, 03 Jun 2017 13:10:20: 2000000 INFO @ Sat, 03 Jun 2017 13:10:27: 3000000 INFO @ Sat, 03 Jun 2017 13:10:27: 3000000 INFO @ Sat, 03 Jun 2017 13:10:27: 3000000 INFO @ Sat, 03 Jun 2017 13:10:34: 4000000 INFO @ Sat, 03 Jun 2017 13:10:34: 4000000 INFO @ Sat, 03 Jun 2017 13:10:34: 4000000 INFO @ Sat, 03 Jun 2017 13:10:40: 5000000 INFO @ Sat, 03 Jun 2017 13:10:41: 5000000 INFO @ Sat, 03 Jun 2017 13:10:41: 5000000 INFO @ Sat, 03 Jun 2017 13:10:47: 6000000 INFO @ Sat, 03 Jun 2017 13:10:47: 6000000 INFO @ Sat, 03 Jun 2017 13:10:47: 6000000 INFO @ Sat, 03 Jun 2017 13:10:54: 7000000 INFO @ Sat, 03 Jun 2017 13:10:54: 7000000 INFO @ Sat, 03 Jun 2017 13:10:54: 7000000 INFO @ Sat, 03 Jun 2017 13:11:00: 8000000 INFO @ Sat, 03 Jun 2017 13:11:01: 8000000 INFO @ Sat, 03 Jun 2017 13:11:01: 8000000 INFO @ Sat, 03 Jun 2017 13:11:07: 9000000 INFO @ Sat, 03 Jun 2017 13:11:08: 9000000 INFO @ Sat, 03 Jun 2017 13:11:08: 9000000 INFO @ Sat, 03 Jun 2017 13:11:14: 10000000 INFO @ Sat, 03 Jun 2017 13:11:15: 10000000 INFO @ Sat, 03 Jun 2017 13:11:15: 10000000 INFO @ Sat, 03 Jun 2017 13:11:19: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 13:11:19: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 13:11:19: #1 total tags in treatment: 10822747 INFO @ Sat, 03 Jun 2017 13:11:19: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:11:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:11:20: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 13:11:20: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 13:11:20: #1 total tags in treatment: 10822747 INFO @ Sat, 03 Jun 2017 13:11:20: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:11:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:11:20: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 13:11:20: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 13:11:20: #1 total tags in treatment: 10822747 INFO @ Sat, 03 Jun 2017 13:11:20: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:11:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:11:21: #1 tags after filtering in treatment: 10819714 INFO @ Sat, 03 Jun 2017 13:11:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:11:21: #1 finished! INFO @ Sat, 03 Jun 2017 13:11:21: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:11:22: #1 tags after filtering in treatment: 10819714 INFO @ Sat, 03 Jun 2017 13:11:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:11:22: #1 finished! INFO @ Sat, 03 Jun 2017 13:11:22: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:11:22: #1 tags after filtering in treatment: 10819714 INFO @ Sat, 03 Jun 2017 13:11:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:11:22: #1 finished! INFO @ Sat, 03 Jun 2017 13:11:22: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:11:23: #2 number of paired peaks: 1944 INFO @ Sat, 03 Jun 2017 13:11:23: start model_add_line... INFO @ Sat, 03 Jun 2017 13:11:24: #2 number of paired peaks: 1944 INFO @ Sat, 03 Jun 2017 13:11:24: start model_add_line... INFO @ Sat, 03 Jun 2017 13:11:24: #2 number of paired peaks: 1944 INFO @ Sat, 03 Jun 2017 13:11:24: start model_add_line... INFO @ Sat, 03 Jun 2017 13:11:37: start X-correlation... INFO @ Sat, 03 Jun 2017 13:11:37: end of X-cor INFO @ Sat, 03 Jun 2017 13:11:37: #2 finished! INFO @ Sat, 03 Jun 2017 13:11:37: #2 predicted fragment length is 78 bps INFO @ Sat, 03 Jun 2017 13:11:37: #2 alternative fragment length(s) may be 78 bps INFO @ Sat, 03 Jun 2017 13:11:37: #2.2 Generate R script for model : SRX1433398.20_model.r WARNING @ Sat, 03 Jun 2017 13:11:37: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:11:37: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sat, 03 Jun 2017 13:11:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 13:11:37: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:11:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:11:38: start X-correlation... INFO @ Sat, 03 Jun 2017 13:11:38: end of X-cor INFO @ Sat, 03 Jun 2017 13:11:38: #2 finished! INFO @ Sat, 03 Jun 2017 13:11:38: #2 predicted fragment length is 78 bps INFO @ Sat, 03 Jun 2017 13:11:38: #2 alternative fragment length(s) may be 78 bps INFO @ Sat, 03 Jun 2017 13:11:38: #2.2 Generate R script for model : SRX1433398.05_model.r WARNING @ Sat, 03 Jun 2017 13:11:38: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:11:38: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sat, 03 Jun 2017 13:11:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 13:11:38: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:11:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:11:38: start X-correlation... INFO @ Sat, 03 Jun 2017 13:11:38: end of X-cor INFO @ Sat, 03 Jun 2017 13:11:38: #2 finished! INFO @ Sat, 03 Jun 2017 13:11:38: #2 predicted fragment length is 78 bps INFO @ Sat, 03 Jun 2017 13:11:38: #2 alternative fragment length(s) may be 78 bps INFO @ Sat, 03 Jun 2017 13:11:38: #2.2 Generate R script for model : SRX1433398.10_model.r WARNING @ Sat, 03 Jun 2017 13:11:38: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:11:38: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sat, 03 Jun 2017 13:11:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 13:11:38: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:11:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:12:39: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:12:40: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:12:40: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:13:23: #4 Write output xls file... SRX1433398.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:13:23: #4 Write peak in narrowPeak format file... SRX1433398.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:13:24: #4 Write summits bed file... SRX1433398.10_summits.bed INFO @ Sat, 03 Jun 2017 13:13:24: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3118 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:13:25: #4 Write output xls file... SRX1433398.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:13:25: #4 Write peak in narrowPeak format file... SRX1433398.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:13:25: #4 Write summits bed file... SRX1433398.20_summits.bed INFO @ Sat, 03 Jun 2017 13:13:25: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1912 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:13:27: #4 Write output xls file... SRX1433398.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:13:27: #4 Write peak in narrowPeak format file... SRX1433398.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:13:27: #4 Write summits bed file... SRX1433398.05_summits.bed INFO @ Sat, 03 Jun 2017 13:13:27: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5179 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。