Job ID = 9157975 sra ファイルのダウンロード中... Completed: 4238009K bytes transferred in 162 seconds (213038K bits/sec), in 1 file, 2 directories. 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 67934521 spots for /home/okishinya/chipatlas/results/dm3/SRX2788638/SRR5515258.sra Written 67934521 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: 00:25:41 67934521 reads; of these: 67934521 (100.00%) were unpaired; of these: 28193032 (41.50%) aligned 0 times 34994181 (51.51%) aligned exactly 1 time 4747308 (6.99%) aligned >1 times 58.50% overall alignment rate Time searching: 00:25:41 Overall time: 00:25:41 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 20 files... [bam_rmdupse_core] 35003310 / 39741489 = 0.8808 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, 27 Jun 2017 15:01:39: # Command line: callpeak -t SRX2788638.bam -f BAM -g dm -n SRX2788638.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2788638.05 # format = BAM # ChIP-seq file = ['SRX2788638.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 # Paired-End mode is off INFO @ Tue, 27 Jun 2017 15:01:39: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:01:39: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:01:39: # Command line: callpeak -t SRX2788638.bam -f BAM -g dm -n SRX2788638.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2788638.10 # format = BAM # ChIP-seq file = ['SRX2788638.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 # Paired-End mode is off INFO @ Tue, 27 Jun 2017 15:01:39: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:01:39: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:01:39: # Command line: callpeak -t SRX2788638.bam -f BAM -g dm -n SRX2788638.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2788638.20 # format = BAM # ChIP-seq file = ['SRX2788638.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 # Paired-End mode is off INFO @ Tue, 27 Jun 2017 15:01:39: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:01:39: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:01:48: 1000000 INFO @ Tue, 27 Jun 2017 15:01:49: 1000000 INFO @ Tue, 27 Jun 2017 15:01:49: 1000000 INFO @ Tue, 27 Jun 2017 15:01:58: 2000000 INFO @ Tue, 27 Jun 2017 15:01:58: 2000000 INFO @ Tue, 27 Jun 2017 15:01:58: 2000000 INFO @ Tue, 27 Jun 2017 15:02:07: 3000000 INFO @ Tue, 27 Jun 2017 15:02:08: 3000000 INFO @ Tue, 27 Jun 2017 15:02:08: 3000000 INFO @ Tue, 27 Jun 2017 15:02:16: 4000000 INFO @ Tue, 27 Jun 2017 15:02:17: 4000000 INFO @ Tue, 27 Jun 2017 15:02:17: 4000000 INFO @ Tue, 27 Jun 2017 15:02:23: #1 tag size is determined as 100 bps INFO @ Tue, 27 Jun 2017 15:02:23: #1 tag size = 100 INFO @ Tue, 27 Jun 2017 15:02:23: #1 total tags in treatment: 4738179 INFO @ Tue, 27 Jun 2017 15:02:23: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:02:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 15:02:23: #1 tags after filtering in treatment: 4738179 INFO @ Tue, 27 Jun 2017 15:02:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 15:02:23: #1 finished! INFO @ Tue, 27 Jun 2017 15:02:23: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:02:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:02:23: #1 tag size is determined as 100 bps INFO @ Tue, 27 Jun 2017 15:02:23: #1 tag size = 100 INFO @ Tue, 27 Jun 2017 15:02:23: #1 total tags in treatment: 4738179 INFO @ Tue, 27 Jun 2017 15:02:23: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:02:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 15:02:23: #1 tag size is determined as 100 bps INFO @ Tue, 27 Jun 2017 15:02:23: #1 tag size = 100 INFO @ Tue, 27 Jun 2017 15:02:23: #1 total tags in treatment: 4738179 INFO @ Tue, 27 Jun 2017 15:02:23: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:02:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 15:02:23: #1 tags after filtering in treatment: 4738179 INFO @ Tue, 27 Jun 2017 15:02:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 15:02:23: #1 finished! INFO @ Tue, 27 Jun 2017 15:02:23: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:02:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:02:23: #1 tags after filtering in treatment: 4738179 INFO @ Tue, 27 Jun 2017 15:02:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 15:02:23: #1 finished! INFO @ Tue, 27 Jun 2017 15:02:23: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:02:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:02:24: #2 number of paired peaks: 1696 INFO @ Tue, 27 Jun 2017 15:02:24: start model_add_line... INFO @ Tue, 27 Jun 2017 15:02:24: start X-correlation... INFO @ Tue, 27 Jun 2017 15:02:24: end of X-cor INFO @ Tue, 27 Jun 2017 15:02:24: #2 finished! INFO @ Tue, 27 Jun 2017 15:02:24: #2 predicted fragment length is 115 bps INFO @ Tue, 27 Jun 2017 15:02:24: #2 alternative fragment length(s) may be 115 bps INFO @ Tue, 27 Jun 2017 15:02:24: #2.2 Generate R script for model : SRX2788638.10_model.r WARNING @ Tue, 27 Jun 2017 15:02:24: #2 Since the d (115) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 15:02:24: #2 You may need to consider one of the other alternative d(s): 115 WARNING @ Tue, 27 Jun 2017 15:02:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 15:02:24: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:02:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:02:24: #2 number of paired peaks: 1696 INFO @ Tue, 27 Jun 2017 15:02:24: start model_add_line... INFO @ Tue, 27 Jun 2017 15:02:24: #2 number of paired peaks: 1696 INFO @ Tue, 27 Jun 2017 15:02:24: start model_add_line... INFO @ Tue, 27 Jun 2017 15:02:24: start X-correlation... INFO @ Tue, 27 Jun 2017 15:02:24: end of X-cor INFO @ Tue, 27 Jun 2017 15:02:24: #2 finished! INFO @ Tue, 27 Jun 2017 15:02:24: #2 predicted fragment length is 115 bps INFO @ Tue, 27 Jun 2017 15:02:24: #2 alternative fragment length(s) may be 115 bps INFO @ Tue, 27 Jun 2017 15:02:24: #2.2 Generate R script for model : SRX2788638.05_model.r WARNING @ Tue, 27 Jun 2017 15:02:24: #2 Since the d (115) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 15:02:24: #2 You may need to consider one of the other alternative d(s): 115 WARNING @ Tue, 27 Jun 2017 15:02:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 15:02:24: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:02:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:02:24: start X-correlation... INFO @ Tue, 27 Jun 2017 15:02:24: end of X-cor INFO @ Tue, 27 Jun 2017 15:02:24: #2 finished! INFO @ Tue, 27 Jun 2017 15:02:24: #2 predicted fragment length is 115 bps INFO @ Tue, 27 Jun 2017 15:02:24: #2 alternative fragment length(s) may be 115 bps INFO @ Tue, 27 Jun 2017 15:02:24: #2.2 Generate R script for model : SRX2788638.20_model.r WARNING @ Tue, 27 Jun 2017 15:02:24: #2 Since the d (115) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 15:02:24: #2 You may need to consider one of the other alternative d(s): 115 WARNING @ Tue, 27 Jun 2017 15:02:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 15:02:24: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:02:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:02:35: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:02:35: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:02:36: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:02:42: #4 Write output xls file... SRX2788638.20_peaks.xls INFO @ Tue, 27 Jun 2017 15:02:42: #4 Write peak in narrowPeak format file... SRX2788638.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:02:42: #4 Write summits bed file... SRX2788638.20_summits.bed INFO @ Tue, 27 Jun 2017 15:02:42: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1180 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 15:02:42: #4 Write output xls file... SRX2788638.10_peaks.xls INFO @ Tue, 27 Jun 2017 15:02:42: #4 Write peak in narrowPeak format file... SRX2788638.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:02:42: #4 Write summits bed file... SRX2788638.10_summits.bed INFO @ Tue, 27 Jun 2017 15:02:42: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2804 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 15:02:43: #4 Write output xls file... SRX2788638.05_peaks.xls INFO @ Tue, 27 Jun 2017 15:02:43: #4 Write peak in narrowPeak format file... SRX2788638.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:02:43: #4 Write summits bed file... SRX2788638.05_summits.bed INFO @ Tue, 27 Jun 2017 15:02:43: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6550 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。