Job ID = 9157981 sra ファイルのダウンロード中... Completed: 8109799K bytes transferred in 325 seconds (204218K 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 127170274 spots for /home/okishinya/chipatlas/results/dm3/SRX2788642/SRR5515262.sra Written 127170274 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: 00:58:56 127170274 reads; of these: 127170274 (100.00%) were unpaired; of these: 3215470 (2.53%) aligned 0 times 107407121 (84.46%) aligned exactly 1 time 16547683 (13.01%) aligned >1 times 97.47% overall alignment rate Time searching: 00:58:56 Overall time: 00:58:56 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 52 files... [bam_rmdupse_core] 109436627 / 123954804 = 0.8829 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 16:06:02: # Command line: callpeak -t SRX2788642.bam -f BAM -g dm -n SRX2788642.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2788642.10 # format = BAM # ChIP-seq file = ['SRX2788642.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 16:06:02: #1 read tag files... INFO @ Tue, 27 Jun 2017 16:06:02: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 16:06:02: # Command line: callpeak -t SRX2788642.bam -f BAM -g dm -n SRX2788642.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2788642.20 # format = BAM # ChIP-seq file = ['SRX2788642.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 16:06:02: #1 read tag files... INFO @ Tue, 27 Jun 2017 16:06:02: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 16:06:02: # Command line: callpeak -t SRX2788642.bam -f BAM -g dm -n SRX2788642.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2788642.05 # format = BAM # ChIP-seq file = ['SRX2788642.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 16:06:02: #1 read tag files... INFO @ Tue, 27 Jun 2017 16:06:02: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 16:06:10: 1000000 INFO @ Tue, 27 Jun 2017 16:06:10: 1000000 INFO @ Tue, 27 Jun 2017 16:06:10: 1000000 INFO @ Tue, 27 Jun 2017 16:06:19: 2000000 INFO @ Tue, 27 Jun 2017 16:06:19: 2000000 INFO @ Tue, 27 Jun 2017 16:06:19: 2000000 INFO @ Tue, 27 Jun 2017 16:06:27: 3000000 INFO @ Tue, 27 Jun 2017 16:06:27: 3000000 INFO @ Tue, 27 Jun 2017 16:06:28: 3000000 INFO @ Tue, 27 Jun 2017 16:06:36: 4000000 INFO @ Tue, 27 Jun 2017 16:06:36: 4000000 INFO @ Tue, 27 Jun 2017 16:06:36: 4000000 INFO @ Tue, 27 Jun 2017 16:06:44: 5000000 INFO @ Tue, 27 Jun 2017 16:06:45: 5000000 INFO @ Tue, 27 Jun 2017 16:06:45: 5000000 INFO @ Tue, 27 Jun 2017 16:06:52: 6000000 INFO @ Tue, 27 Jun 2017 16:06:53: 6000000 INFO @ Tue, 27 Jun 2017 16:06:53: 6000000 INFO @ Tue, 27 Jun 2017 16:07:01: 7000000 INFO @ Tue, 27 Jun 2017 16:07:02: 7000000 INFO @ Tue, 27 Jun 2017 16:07:02: 7000000 INFO @ Tue, 27 Jun 2017 16:07:09: 8000000 INFO @ Tue, 27 Jun 2017 16:07:10: 8000000 INFO @ Tue, 27 Jun 2017 16:07:10: 8000000 INFO @ Tue, 27 Jun 2017 16:07:17: 9000000 INFO @ Tue, 27 Jun 2017 16:07:18: 9000000 INFO @ Tue, 27 Jun 2017 16:07:18: 9000000 INFO @ Tue, 27 Jun 2017 16:07:25: 10000000 INFO @ Tue, 27 Jun 2017 16:07:27: 10000000 INFO @ Tue, 27 Jun 2017 16:07:27: 10000000 INFO @ Tue, 27 Jun 2017 16:07:33: 11000000 INFO @ Tue, 27 Jun 2017 16:07:35: 11000000 INFO @ Tue, 27 Jun 2017 16:07:35: 11000000 INFO @ Tue, 27 Jun 2017 16:07:41: 12000000 INFO @ Tue, 27 Jun 2017 16:07:44: 12000000 INFO @ Tue, 27 Jun 2017 16:07:44: 12000000 INFO @ Tue, 27 Jun 2017 16:07:49: 13000000 INFO @ Tue, 27 Jun 2017 16:07:53: 13000000 INFO @ Tue, 27 Jun 2017 16:07:53: 13000000 INFO @ Tue, 27 Jun 2017 16:07:57: 14000000 INFO @ Tue, 27 Jun 2017 16:08:01: #1 tag size is determined as 94 bps INFO @ Tue, 27 Jun 2017 16:08:01: #1 tag size = 94 INFO @ Tue, 27 Jun 2017 16:08:01: #1 total tags in treatment: 14518177 INFO @ Tue, 27 Jun 2017 16:08:01: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 16:08:01: #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 16:08:02: 14000000 INFO @ Tue, 27 Jun 2017 16:08:02: 14000000 INFO @ Tue, 27 Jun 2017 16:08:02: #1 tags after filtering in treatment: 14518177 INFO @ Tue, 27 Jun 2017 16:08:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 16:08:02: #1 finished! INFO @ Tue, 27 Jun 2017 16:08:02: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 16:08:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 16:08:03: #2 number of paired peaks: 5994 INFO @ Tue, 27 Jun 2017 16:08:03: start model_add_line... INFO @ Tue, 27 Jun 2017 16:08:04: start X-correlation... INFO @ Tue, 27 Jun 2017 16:08:04: end of X-cor INFO @ Tue, 27 Jun 2017 16:08:04: #2 finished! INFO @ Tue, 27 Jun 2017 16:08:04: #2 predicted fragment length is 119 bps INFO @ Tue, 27 Jun 2017 16:08:04: #2 alternative fragment length(s) may be 119 bps INFO @ Tue, 27 Jun 2017 16:08:04: #2.2 Generate R script for model : SRX2788642.20_model.r WARNING @ Tue, 27 Jun 2017 16:08:04: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 16:08:04: #2 You may need to consider one of the other alternative d(s): 119 WARNING @ Tue, 27 Jun 2017 16:08:04: #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 16:08:04: #3 Call peaks... INFO @ Tue, 27 Jun 2017 16:08:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 16:08:06: #1 tag size is determined as 94 bps INFO @ Tue, 27 Jun 2017 16:08:06: #1 tag size = 94 INFO @ Tue, 27 Jun 2017 16:08:06: #1 total tags in treatment: 14518177 INFO @ Tue, 27 Jun 2017 16:08:06: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 16:08:06: #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 16:08:06: #1 tag size is determined as 94 bps INFO @ Tue, 27 Jun 2017 16:08:06: #1 tag size = 94 INFO @ Tue, 27 Jun 2017 16:08:06: #1 total tags in treatment: 14518177 INFO @ Tue, 27 Jun 2017 16:08:06: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 16:08:06: #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 16:08:07: #1 tags after filtering in treatment: 14518177 INFO @ Tue, 27 Jun 2017 16:08:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 16:08:07: #1 finished! INFO @ Tue, 27 Jun 2017 16:08:07: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 16:08:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 16:08:07: #1 tags after filtering in treatment: 14518177 INFO @ Tue, 27 Jun 2017 16:08:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 16:08:07: #1 finished! INFO @ Tue, 27 Jun 2017 16:08:07: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 16:08:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 16:08:08: #2 number of paired peaks: 5994 INFO @ Tue, 27 Jun 2017 16:08:08: start model_add_line... INFO @ Tue, 27 Jun 2017 16:08:08: #2 number of paired peaks: 5994 INFO @ Tue, 27 Jun 2017 16:08:08: start model_add_line... INFO @ Tue, 27 Jun 2017 16:08:09: start X-correlation... INFO @ Tue, 27 Jun 2017 16:08:09: start X-correlation... INFO @ Tue, 27 Jun 2017 16:08:09: end of X-cor INFO @ Tue, 27 Jun 2017 16:08:09: end of X-cor INFO @ Tue, 27 Jun 2017 16:08:09: #2 finished! INFO @ Tue, 27 Jun 2017 16:08:09: #2 finished! INFO @ Tue, 27 Jun 2017 16:08:09: #2 predicted fragment length is 119 bps INFO @ Tue, 27 Jun 2017 16:08:09: #2 predicted fragment length is 119 bps INFO @ Tue, 27 Jun 2017 16:08:09: #2 alternative fragment length(s) may be 119 bps INFO @ Tue, 27 Jun 2017 16:08:09: #2 alternative fragment length(s) may be 119 bps INFO @ Tue, 27 Jun 2017 16:08:09: #2.2 Generate R script for model : SRX2788642.10_model.r INFO @ Tue, 27 Jun 2017 16:08:09: #2.2 Generate R script for model : SRX2788642.05_model.r WARNING @ Tue, 27 Jun 2017 16:08:09: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 16:08:09: #2 You may need to consider one of the other alternative d(s): 119 WARNING @ Tue, 27 Jun 2017 16:08:09: #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 16:08:09: #3 Call peaks... WARNING @ Tue, 27 Jun 2017 16:08:09: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! INFO @ Tue, 27 Jun 2017 16:08:09: #3 Pre-compute pvalue-qvalue table... WARNING @ Tue, 27 Jun 2017 16:08:09: #2 You may need to consider one of the other alternative d(s): 119 WARNING @ Tue, 27 Jun 2017 16:08:09: #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 16:08:09: #3 Call peaks... INFO @ Tue, 27 Jun 2017 16:08:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 16:08:45: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 16:08:49: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 16:08:50: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 16:09:05: #4 Write output xls file... SRX2788642.20_peaks.xls INFO @ Tue, 27 Jun 2017 16:09:05: #4 Write peak in narrowPeak format file... SRX2788642.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 16:09:05: #4 Write summits bed file... SRX2788642.20_summits.bed INFO @ Tue, 27 Jun 2017 16:09:05: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8081 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 16:09:09: #4 Write output xls file... SRX2788642.05_peaks.xls INFO @ Tue, 27 Jun 2017 16:09:09: #4 Write peak in narrowPeak format file... SRX2788642.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 16:09:09: #4 Write summits bed file... SRX2788642.05_summits.bed INFO @ Tue, 27 Jun 2017 16:09:09: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (12947 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 16:09:10: #4 Write output xls file... SRX2788642.10_peaks.xls INFO @ Tue, 27 Jun 2017 16:09:10: #4 Write peak in narrowPeak format file... SRX2788642.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 16:09:10: #4 Write summits bed file... SRX2788642.10_summits.bed INFO @ Tue, 27 Jun 2017 16:09:10: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10368 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。