Job ID = 9730463 sra ファイルのダウンロード中... Completed: 531738K bytes transferred in 41 seconds (105711K 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 16060245 spots for /home/okishinya/chipatlas/results/dm3/SRX2829102/SRR5569912.sra Written 16060245 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:05 16060245 reads; of these: 16060245 (100.00%) were unpaired; of these: 747392 (4.65%) aligned 0 times 10254144 (63.85%) aligned exactly 1 time 5058709 (31.50%) aligned >1 times 95.35% overall alignment rate Time searching: 00:07:06 Overall time: 00:07:06 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 8 files... [bam_rmdupse_core] 10065470 / 15312853 = 0.6573 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 @ Sun, 03 Sep 2017 01:06:24: # Command line: callpeak -t SRX2829102.bam -f BAM -g dm -n SRX2829102.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2829102.20 # format = BAM # ChIP-seq file = ['SRX2829102.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 @ Sun, 03 Sep 2017 01:06:24: # Command line: callpeak -t SRX2829102.bam -f BAM -g dm -n SRX2829102.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2829102.10 # format = BAM # ChIP-seq file = ['SRX2829102.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 @ Sun, 03 Sep 2017 01:06:24: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:06:24: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:06:24: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:06:24: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:06:24: # Command line: callpeak -t SRX2829102.bam -f BAM -g dm -n SRX2829102.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2829102.05 # format = BAM # ChIP-seq file = ['SRX2829102.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 @ Sun, 03 Sep 2017 01:06:24: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:06:24: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:06:33: 1000000 INFO @ Sun, 03 Sep 2017 01:06:34: 1000000 INFO @ Sun, 03 Sep 2017 01:06:34: 1000000 INFO @ Sun, 03 Sep 2017 01:06:41: 2000000 INFO @ Sun, 03 Sep 2017 01:06:45: 2000000 INFO @ Sun, 03 Sep 2017 01:06:45: 2000000 INFO @ Sun, 03 Sep 2017 01:06:49: 3000000 INFO @ Sun, 03 Sep 2017 01:06:54: 3000000 INFO @ Sun, 03 Sep 2017 01:06:54: 3000000 INFO @ Sun, 03 Sep 2017 01:06:57: 4000000 INFO @ Sun, 03 Sep 2017 01:07:04: 4000000 INFO @ Sun, 03 Sep 2017 01:07:04: 4000000 INFO @ Sun, 03 Sep 2017 01:07:05: 5000000 INFO @ Sun, 03 Sep 2017 01:07:07: #1 tag size is determined as 51 bps INFO @ Sun, 03 Sep 2017 01:07:07: #1 tag size = 51 INFO @ Sun, 03 Sep 2017 01:07:07: #1 total tags in treatment: 5247383 INFO @ Sun, 03 Sep 2017 01:07:07: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:07:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:07:07: #1 tags after filtering in treatment: 5247383 INFO @ Sun, 03 Sep 2017 01:07:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:07:07: #1 finished! INFO @ Sun, 03 Sep 2017 01:07:07: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:07:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:07:08: #2 number of paired peaks: 699 WARNING @ Sun, 03 Sep 2017 01:07:08: Fewer paired peaks (699) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 699 pairs to build model! INFO @ Sun, 03 Sep 2017 01:07:08: start model_add_line... INFO @ Sun, 03 Sep 2017 01:07:08: start X-correlation... INFO @ Sun, 03 Sep 2017 01:07:08: end of X-cor INFO @ Sun, 03 Sep 2017 01:07:08: #2 finished! INFO @ Sun, 03 Sep 2017 01:07:08: #2 predicted fragment length is 50 bps INFO @ Sun, 03 Sep 2017 01:07:08: #2 alternative fragment length(s) may be 50 bps INFO @ Sun, 03 Sep 2017 01:07:08: #2.2 Generate R script for model : SRX2829102.10_model.r WARNING @ Sun, 03 Sep 2017 01:07:08: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:07:08: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sun, 03 Sep 2017 01:07:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Sep 2017 01:07:08: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:07:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:07:14: 5000000 INFO @ Sun, 03 Sep 2017 01:07:14: 5000000 INFO @ Sun, 03 Sep 2017 01:07:16: #1 tag size is determined as 51 bps INFO @ Sun, 03 Sep 2017 01:07:16: #1 tag size = 51 INFO @ Sun, 03 Sep 2017 01:07:16: #1 total tags in treatment: 5247383 INFO @ Sun, 03 Sep 2017 01:07:16: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:07:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:07:16: #1 tags after filtering in treatment: 5247383 INFO @ Sun, 03 Sep 2017 01:07:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:07:16: #1 finished! INFO @ Sun, 03 Sep 2017 01:07:16: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:07:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:07:16: #2 number of paired peaks: 699 WARNING @ Sun, 03 Sep 2017 01:07:16: Fewer paired peaks (699) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 699 pairs to build model! INFO @ Sun, 03 Sep 2017 01:07:16: start model_add_line... INFO @ Sun, 03 Sep 2017 01:07:16: start X-correlation... INFO @ Sun, 03 Sep 2017 01:07:16: end of X-cor INFO @ Sun, 03 Sep 2017 01:07:16: #2 finished! INFO @ Sun, 03 Sep 2017 01:07:16: #2 predicted fragment length is 50 bps INFO @ Sun, 03 Sep 2017 01:07:16: #2 alternative fragment length(s) may be 50 bps INFO @ Sun, 03 Sep 2017 01:07:16: #2.2 Generate R script for model : SRX2829102.05_model.r WARNING @ Sun, 03 Sep 2017 01:07:16: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:07:16: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sun, 03 Sep 2017 01:07:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Sep 2017 01:07:16: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:07:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:07:17: #1 tag size is determined as 51 bps INFO @ Sun, 03 Sep 2017 01:07:17: #1 tag size = 51 INFO @ Sun, 03 Sep 2017 01:07:17: #1 total tags in treatment: 5247383 INFO @ Sun, 03 Sep 2017 01:07:17: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:07:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:07:17: #1 tags after filtering in treatment: 5247383 INFO @ Sun, 03 Sep 2017 01:07:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:07:17: #1 finished! INFO @ Sun, 03 Sep 2017 01:07:17: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:07:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:07:17: #2 number of paired peaks: 699 WARNING @ Sun, 03 Sep 2017 01:07:17: Fewer paired peaks (699) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 699 pairs to build model! INFO @ Sun, 03 Sep 2017 01:07:17: start model_add_line... INFO @ Sun, 03 Sep 2017 01:07:17: start X-correlation... INFO @ Sun, 03 Sep 2017 01:07:17: end of X-cor INFO @ Sun, 03 Sep 2017 01:07:17: #2 finished! INFO @ Sun, 03 Sep 2017 01:07:17: #2 predicted fragment length is 50 bps INFO @ Sun, 03 Sep 2017 01:07:17: #2 alternative fragment length(s) may be 50 bps INFO @ Sun, 03 Sep 2017 01:07:17: #2.2 Generate R script for model : SRX2829102.20_model.r WARNING @ Sun, 03 Sep 2017 01:07:17: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:07:17: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sun, 03 Sep 2017 01:07:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Sep 2017 01:07:17: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:07:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:07:21: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:07:29: #4 Write output xls file... SRX2829102.10_peaks.xls INFO @ Sun, 03 Sep 2017 01:07:29: #4 Write peak in narrowPeak format file... SRX2829102.10_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:07:29: #4 Write summits bed file... SRX2829102.10_summits.bed INFO @ Sun, 03 Sep 2017 01:07:29: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1289 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:07:29: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:07:29: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:07:36: #4 Write output xls file... SRX2829102.05_peaks.xls INFO @ Sun, 03 Sep 2017 01:07:36: #4 Write peak in narrowPeak format file... SRX2829102.05_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:07:36: #4 Write summits bed file... SRX2829102.05_summits.bed INFO @ Sun, 03 Sep 2017 01:07:36: Done! pass1 - making usageList (13 chroms): 10 millis pass2 - checking and writing primary data (1927 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:07:36: #4 Write output xls file... SRX2829102.20_peaks.xls INFO @ Sun, 03 Sep 2017 01:07:36: #4 Write peak in narrowPeak format file... SRX2829102.20_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:07:36: #4 Write summits bed file... SRX2829102.20_summits.bed INFO @ Sun, 03 Sep 2017 01:07:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (869 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。