Job ID = 2162423 sra ファイルのダウンロード中... Completed: 786920K bytes transferred in 9 seconds (664169K 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 13456 0 13456 0 0 24433 0 --:--:-- --:--:-- --:--:-- 37377 100 36867 0 36867 0 0 49806 0 --:--:-- --:--:-- --:--:-- 67153 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 34331163 spots for /home/okishinya/chipatlas/results/dm3/SRX097615/SRR345566.sra Written 34331163 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: 00:14:06 34331163 reads; of these: 34331163 (100.00%) were unpaired; of these: 1309066 (3.81%) aligned 0 times 22470902 (65.45%) aligned exactly 1 time 10551195 (30.73%) aligned >1 times 96.19% overall alignment rate Time searching: 00:14:06 Overall time: 00:14:06 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] 21981742 / 33022097 = 0.6657 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 14:14:43: # Command line: callpeak -t SRX097615.bam -f BAM -g dm -n SRX097615.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX097615.10 # format = BAM # ChIP-seq file = ['SRX097615.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 14:14:43: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:14:43: # Command line: callpeak -t SRX097615.bam -f BAM -g dm -n SRX097615.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX097615.20 # format = BAM # ChIP-seq file = ['SRX097615.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 14:14:43: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:14:43: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:14:43: # Command line: callpeak -t SRX097615.bam -f BAM -g dm -n SRX097615.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX097615.05 # format = BAM # ChIP-seq file = ['SRX097615.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 14:14:43: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:14:43: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:14:43: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:14:49: 1000000 INFO @ Tue, 21 Apr 2015 14:14:49: 1000000 INFO @ Tue, 21 Apr 2015 14:14:49: 1000000 INFO @ Tue, 21 Apr 2015 14:14:55: 2000000 INFO @ Tue, 21 Apr 2015 14:14:55: 2000000 INFO @ Tue, 21 Apr 2015 14:14:55: 2000000 INFO @ Tue, 21 Apr 2015 14:15:01: 3000000 INFO @ Tue, 21 Apr 2015 14:15:01: 3000000 INFO @ Tue, 21 Apr 2015 14:15:01: 3000000 INFO @ Tue, 21 Apr 2015 14:15:07: 4000000 INFO @ Tue, 21 Apr 2015 14:15:07: 4000000 INFO @ Tue, 21 Apr 2015 14:15:08: 4000000 INFO @ Tue, 21 Apr 2015 14:15:13: 5000000 INFO @ Tue, 21 Apr 2015 14:15:14: 5000000 INFO @ Tue, 21 Apr 2015 14:15:14: 5000000 INFO @ Tue, 21 Apr 2015 14:15:19: 6000000 INFO @ Tue, 21 Apr 2015 14:15:20: 6000000 INFO @ Tue, 21 Apr 2015 14:15:21: 6000000 INFO @ Tue, 21 Apr 2015 14:15:25: 7000000 INFO @ Tue, 21 Apr 2015 14:15:26: 7000000 INFO @ Tue, 21 Apr 2015 14:15:27: 7000000 INFO @ Tue, 21 Apr 2015 14:15:30: 8000000 INFO @ Tue, 21 Apr 2015 14:15:33: 8000000 INFO @ Tue, 21 Apr 2015 14:15:35: 8000000 INFO @ Tue, 21 Apr 2015 14:15:37: 9000000 INFO @ Tue, 21 Apr 2015 14:15:40: 9000000 INFO @ Tue, 21 Apr 2015 14:15:42: 9000000 INFO @ Tue, 21 Apr 2015 14:15:43: 10000000 INFO @ Tue, 21 Apr 2015 14:15:46: 10000000 INFO @ Tue, 21 Apr 2015 14:15:48: 10000000 INFO @ Tue, 21 Apr 2015 14:15:48: 11000000 INFO @ Tue, 21 Apr 2015 14:15:49: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 14:15:49: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 14:15:49: #1 total tags in treatment: 11040355 INFO @ Tue, 21 Apr 2015 14:15:49: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:15:49: #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 14:15:51: #1 tags after filtering in treatment: 11037873 INFO @ Tue, 21 Apr 2015 14:15:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:15:51: #1 finished! INFO @ Tue, 21 Apr 2015 14:15:51: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:15:53: 11000000 INFO @ Tue, 21 Apr 2015 14:15:53: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 14:15:53: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 14:15:53: #1 total tags in treatment: 11040355 INFO @ Tue, 21 Apr 2015 14:15:53: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:15:53: #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 14:15:53: #2 number of paired peaks: 4777 INFO @ Tue, 21 Apr 2015 14:15:53: start model_add_line... INFO @ Tue, 21 Apr 2015 14:15:54: 11000000 INFO @ Tue, 21 Apr 2015 14:15:55: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 14:15:55: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 14:15:55: #1 total tags in treatment: 11040355 INFO @ Tue, 21 Apr 2015 14:15:55: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:15:55: #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 14:15:56: #1 tags after filtering in treatment: 11037873 INFO @ Tue, 21 Apr 2015 14:15:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:15:56: #1 finished! INFO @ Tue, 21 Apr 2015 14:15:56: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:15:57: #1 tags after filtering in treatment: 11037873 INFO @ Tue, 21 Apr 2015 14:15:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:15:57: #1 finished! INFO @ Tue, 21 Apr 2015 14:15:57: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:15:59: #2 number of paired peaks: 4777 INFO @ Tue, 21 Apr 2015 14:15:59: start model_add_line... INFO @ Tue, 21 Apr 2015 14:15:59: #2 number of paired peaks: 4777 INFO @ Tue, 21 Apr 2015 14:15:59: start model_add_line... INFO @ Tue, 21 Apr 2015 14:16:27: start X-correlation... INFO @ Tue, 21 Apr 2015 14:16:27: end of X-cor INFO @ Tue, 21 Apr 2015 14:16:27: #2 finished! INFO @ Tue, 21 Apr 2015 14:16:27: #2 predicted fragment length is 71 bps INFO @ Tue, 21 Apr 2015 14:16:27: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 21 Apr 2015 14:16:27: #2.2 Generate R script for model : SRX097615.20_model.r WARNING @ Tue, 21 Apr 2015 14:16:27: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 14:16:27: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 21 Apr 2015 14:16:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 14:16:27: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:16:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:16:33: start X-correlation... INFO @ Tue, 21 Apr 2015 14:16:33: end of X-cor INFO @ Tue, 21 Apr 2015 14:16:33: #2 finished! INFO @ Tue, 21 Apr 2015 14:16:33: #2 predicted fragment length is 71 bps INFO @ Tue, 21 Apr 2015 14:16:33: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 21 Apr 2015 14:16:33: #2.2 Generate R script for model : SRX097615.10_model.r WARNING @ Tue, 21 Apr 2015 14:16:33: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 14:16:33: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 21 Apr 2015 14:16:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 14:16:33: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:16:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:16:34: start X-correlation... INFO @ Tue, 21 Apr 2015 14:16:34: end of X-cor INFO @ Tue, 21 Apr 2015 14:16:34: #2 finished! INFO @ Tue, 21 Apr 2015 14:16:34: #2 predicted fragment length is 71 bps INFO @ Tue, 21 Apr 2015 14:16:34: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 21 Apr 2015 14:16:34: #2.2 Generate R script for model : SRX097615.05_model.r WARNING @ Tue, 21 Apr 2015 14:16:34: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 14:16:34: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 21 Apr 2015 14:16:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 14:16:34: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:16:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:17:27: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:17:32: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:17:34: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:18:15: #4 Write output xls file... SRX097615.20_peaks.xls INFO @ Tue, 21 Apr 2015 14:18:15: #4 Write peak in narrowPeak format file... SRX097615.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:18:15: #4 Write summits bed file... SRX097615.20_summits.bed INFO @ Tue, 21 Apr 2015 14:18:15: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9243 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 21 Apr 2015 14:18:27: #4 Write output xls file... SRX097615.10_peaks.xls INFO @ Tue, 21 Apr 2015 14:18:27: #4 Write peak in narrowPeak format file... SRX097615.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:18:27: #4 Write summits bed file... SRX097615.10_summits.bed INFO @ Tue, 21 Apr 2015 14:18:28: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (13363 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:18:33: #4 Write output xls file... SRX097615.05_peaks.xls INFO @ Tue, 21 Apr 2015 14:18:33: #4 Write peak in narrowPeak format file... SRX097615.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:18:33: #4 Write summits bed file... SRX097615.05_summits.bed INFO @ Tue, 21 Apr 2015 14:18:33: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (16829 records, 4 fields): 21 millis CompletedMACS2peakCalling BigWig に変換しました。