Job ID = 9040949 sra ファイルのダウンロード中... Completed: 647253K bytes transferred in 6 seconds (787776K 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 1073 0 --:--:-- 0:00:07 --:--:-- 9495 100 32453 0 32453 0 0 4072 0 --:--:-- 0:00:07 --:--:-- 19824 100 90373 0 90373 0 0 10082 0 --:--:-- 0:00:08 --:--:-- 34336 100 146k 0 146k 0 0 15539 0 --:--:-- 0:00:09 --:--:-- 45392 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 8989038 spots for /home/okishinya/chipatlas/results/dm3/SRX1158167/SRR2173466.sra Written 8989038 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: 00:02:33 8989038 reads; of these: 8989038 (100.00%) were unpaired; of these: 2342543 (26.06%) aligned 0 times 4898194 (54.49%) aligned exactly 1 time 1748301 (19.45%) aligned >1 times 73.94% overall alignment rate Time searching: 00:02:33 Overall time: 00:02:33 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] 2278072 / 6646495 = 0.3427 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 @ Mon, 05 Jun 2017 00:21:19: # Command line: callpeak -t SRX1158167.bam -f BAM -g dm -n SRX1158167.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1158167.20 # format = BAM # ChIP-seq file = ['SRX1158167.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 @ Mon, 05 Jun 2017 00:21:19: #1 read tag files... INFO @ Mon, 05 Jun 2017 00:21:19: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 00:21:19: # Command line: callpeak -t SRX1158167.bam -f BAM -g dm -n SRX1158167.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1158167.05 # format = BAM # ChIP-seq file = ['SRX1158167.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 @ Mon, 05 Jun 2017 00:21:19: #1 read tag files... INFO @ Mon, 05 Jun 2017 00:21:19: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 00:21:19: # Command line: callpeak -t SRX1158167.bam -f BAM -g dm -n SRX1158167.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1158167.10 # format = BAM # ChIP-seq file = ['SRX1158167.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 @ Mon, 05 Jun 2017 00:21:19: #1 read tag files... INFO @ Mon, 05 Jun 2017 00:21:19: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 00:21:27: 1000000 INFO @ Mon, 05 Jun 2017 00:21:27: 1000000 INFO @ Mon, 05 Jun 2017 00:21:28: 1000000 INFO @ Mon, 05 Jun 2017 00:21:35: 2000000 INFO @ Mon, 05 Jun 2017 00:21:36: 2000000 INFO @ Mon, 05 Jun 2017 00:21:38: 2000000 INFO @ Mon, 05 Jun 2017 00:21:43: 3000000 INFO @ Mon, 05 Jun 2017 00:21:44: 3000000 INFO @ Mon, 05 Jun 2017 00:21:47: 3000000 INFO @ Mon, 05 Jun 2017 00:21:51: 4000000 INFO @ Mon, 05 Jun 2017 00:21:52: 4000000 INFO @ Mon, 05 Jun 2017 00:21:54: #1 tag size is determined as 101 bps INFO @ Mon, 05 Jun 2017 00:21:54: #1 tag size = 101 INFO @ Mon, 05 Jun 2017 00:21:54: #1 total tags in treatment: 4368423 INFO @ Mon, 05 Jun 2017 00:21:54: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 00:21:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 00:21:55: #1 tag size is determined as 101 bps INFO @ Mon, 05 Jun 2017 00:21:55: #1 tag size = 101 INFO @ Mon, 05 Jun 2017 00:21:55: #1 total tags in treatment: 4368423 INFO @ Mon, 05 Jun 2017 00:21:55: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 00:21:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 00:21:55: #1 tags after filtering in treatment: 4364622 INFO @ Mon, 05 Jun 2017 00:21:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 00:21:55: #1 finished! INFO @ Mon, 05 Jun 2017 00:21:55: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 00:21:56: #1 tags after filtering in treatment: 4364622 INFO @ Mon, 05 Jun 2017 00:21:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 00:21:56: #1 finished! INFO @ Mon, 05 Jun 2017 00:21:56: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 00:21:56: 4000000 INFO @ Mon, 05 Jun 2017 00:21:56: #2 number of paired peaks: 2849 INFO @ Mon, 05 Jun 2017 00:21:56: start model_add_line... INFO @ Mon, 05 Jun 2017 00:21:57: #2 number of paired peaks: 2849 INFO @ Mon, 05 Jun 2017 00:21:57: start model_add_line... INFO @ Mon, 05 Jun 2017 00:21:59: #1 tag size is determined as 101 bps INFO @ Mon, 05 Jun 2017 00:21:59: #1 tag size = 101 INFO @ Mon, 05 Jun 2017 00:21:59: #1 total tags in treatment: 4368423 INFO @ Mon, 05 Jun 2017 00:21:59: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 00:21:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 00:22:00: #1 tags after filtering in treatment: 4364622 INFO @ Mon, 05 Jun 2017 00:22:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 00:22:00: #1 finished! INFO @ Mon, 05 Jun 2017 00:22:00: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 00:22:01: #2 number of paired peaks: 2849 INFO @ Mon, 05 Jun 2017 00:22:01: start model_add_line... INFO @ Mon, 05 Jun 2017 00:22:05: start X-correlation... INFO @ Mon, 05 Jun 2017 00:22:05: end of X-cor INFO @ Mon, 05 Jun 2017 00:22:05: #2 finished! INFO @ Mon, 05 Jun 2017 00:22:05: #2 predicted fragment length is 141 bps INFO @ Mon, 05 Jun 2017 00:22:05: #2 alternative fragment length(s) may be 141 bps INFO @ Mon, 05 Jun 2017 00:22:05: #2.2 Generate R script for model : SRX1158167.05_model.r WARNING @ Mon, 05 Jun 2017 00:22:05: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 00:22:05: #2 You may need to consider one of the other alternative d(s): 141 WARNING @ Mon, 05 Jun 2017 00:22:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 05 Jun 2017 00:22:05: #3 Call peaks... INFO @ Mon, 05 Jun 2017 00:22:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 00:22:06: start X-correlation... INFO @ Mon, 05 Jun 2017 00:22:06: end of X-cor INFO @ Mon, 05 Jun 2017 00:22:06: #2 finished! INFO @ Mon, 05 Jun 2017 00:22:06: #2 predicted fragment length is 141 bps INFO @ Mon, 05 Jun 2017 00:22:06: #2 alternative fragment length(s) may be 141 bps INFO @ Mon, 05 Jun 2017 00:22:06: #2.2 Generate R script for model : SRX1158167.20_model.r WARNING @ Mon, 05 Jun 2017 00:22:06: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 00:22:06: #2 You may need to consider one of the other alternative d(s): 141 WARNING @ Mon, 05 Jun 2017 00:22:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 05 Jun 2017 00:22:06: #3 Call peaks... INFO @ Mon, 05 Jun 2017 00:22:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 00:22:10: start X-correlation... INFO @ Mon, 05 Jun 2017 00:22:10: end of X-cor INFO @ Mon, 05 Jun 2017 00:22:10: #2 finished! INFO @ Mon, 05 Jun 2017 00:22:10: #2 predicted fragment length is 141 bps INFO @ Mon, 05 Jun 2017 00:22:10: #2 alternative fragment length(s) may be 141 bps INFO @ Mon, 05 Jun 2017 00:22:10: #2.2 Generate R script for model : SRX1158167.10_model.r WARNING @ Mon, 05 Jun 2017 00:22:10: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 00:22:10: #2 You may need to consider one of the other alternative d(s): 141 WARNING @ Mon, 05 Jun 2017 00:22:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 05 Jun 2017 00:22:10: #3 Call peaks... INFO @ Mon, 05 Jun 2017 00:22:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 00:22:32: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 00:22:34: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 00:22:36: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 00:22:52: #4 Write output xls file... SRX1158167.20_peaks.xls INFO @ Mon, 05 Jun 2017 00:22:52: #4 Write peak in narrowPeak format file... SRX1158167.20_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 00:22:52: #4 Write summits bed file... SRX1158167.20_summits.bed INFO @ Mon, 05 Jun 2017 00:22:52: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (590 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 00:22:55: #4 Write output xls file... SRX1158167.05_peaks.xls INFO @ Mon, 05 Jun 2017 00:22:55: #4 Write peak in narrowPeak format file... SRX1158167.05_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 00:22:55: #4 Write summits bed file... SRX1158167.05_summits.bed INFO @ Mon, 05 Jun 2017 00:22:55: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4965 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 00:22:56: #4 Write output xls file... SRX1158167.10_peaks.xls INFO @ Mon, 05 Jun 2017 00:22:56: #4 Write peak in narrowPeak format file... SRX1158167.10_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 00:22:56: #4 Write summits bed file... SRX1158167.10_summits.bed INFO @ Mon, 05 Jun 2017 00:22:56: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (2102 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。