Job ID = 11598013 sra ファイルのダウンロード中... Completed: 418455K bytes transferred in 9 seconds (348254K bits/sec), in 1 file. 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... Read 17747472 spots for /home/okishinya/chipatlas/results/dm3/SRX4664668/SRR7813095.sra Written 17747472 spots for /home/okishinya/chipatlas/results/dm3/SRX4664668/SRR7813095.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:00:01 Multiseed full-index search: 00:07:03 17747472 reads; of these: 17747472 (100.00%) were unpaired; of these: 800715 (4.51%) aligned 0 times 11894767 (67.02%) aligned exactly 1 time 5051990 (28.47%) aligned >1 times 95.49% overall alignment rate Time searching: 00:07:04 Overall time: 00:07:04 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] 1923171 / 16946757 = 0.1135 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 @ Wed, 30 Jan 2019 17:08:30: # Command line: callpeak -t SRX4664668.bam -f BAM -g dm -n SRX4664668.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4664668.10 # format = BAM # ChIP-seq file = ['SRX4664668.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 @ Wed, 30 Jan 2019 17:08:30: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:08:30: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:08:30: # Command line: callpeak -t SRX4664668.bam -f BAM -g dm -n SRX4664668.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4664668.20 # format = BAM # ChIP-seq file = ['SRX4664668.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 @ Wed, 30 Jan 2019 17:08:30: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:08:30: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:08:30: # Command line: callpeak -t SRX4664668.bam -f BAM -g dm -n SRX4664668.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4664668.05 # format = BAM # ChIP-seq file = ['SRX4664668.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 @ Wed, 30 Jan 2019 17:08:30: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:08:30: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:08:36: 1000000 INFO @ Wed, 30 Jan 2019 17:08:36: 1000000 INFO @ Wed, 30 Jan 2019 17:08:36: 1000000 INFO @ Wed, 30 Jan 2019 17:08:42: 2000000 INFO @ Wed, 30 Jan 2019 17:08:42: 2000000 INFO @ Wed, 30 Jan 2019 17:08:42: 2000000 INFO @ Wed, 30 Jan 2019 17:08:48: 3000000 INFO @ Wed, 30 Jan 2019 17:08:48: 3000000 INFO @ Wed, 30 Jan 2019 17:08:49: 3000000 INFO @ Wed, 30 Jan 2019 17:08:54: 4000000 INFO @ Wed, 30 Jan 2019 17:08:55: 4000000 INFO @ Wed, 30 Jan 2019 17:08:55: 4000000 INFO @ Wed, 30 Jan 2019 17:09:00: 5000000 INFO @ Wed, 30 Jan 2019 17:09:01: 5000000 INFO @ Wed, 30 Jan 2019 17:09:01: 5000000 INFO @ Wed, 30 Jan 2019 17:09:06: 6000000 INFO @ Wed, 30 Jan 2019 17:09:07: 6000000 INFO @ Wed, 30 Jan 2019 17:09:07: 6000000 INFO @ Wed, 30 Jan 2019 17:09:12: 7000000 INFO @ Wed, 30 Jan 2019 17:09:13: 7000000 INFO @ Wed, 30 Jan 2019 17:09:13: 7000000 INFO @ Wed, 30 Jan 2019 17:09:18: 8000000 INFO @ Wed, 30 Jan 2019 17:09:19: 8000000 INFO @ Wed, 30 Jan 2019 17:09:20: 8000000 INFO @ Wed, 30 Jan 2019 17:09:24: 9000000 INFO @ Wed, 30 Jan 2019 17:09:25: 9000000 INFO @ Wed, 30 Jan 2019 17:09:26: 9000000 INFO @ Wed, 30 Jan 2019 17:09:30: 10000000 INFO @ Wed, 30 Jan 2019 17:09:32: 10000000 INFO @ Wed, 30 Jan 2019 17:09:32: 10000000 INFO @ Wed, 30 Jan 2019 17:09:36: 11000000 INFO @ Wed, 30 Jan 2019 17:09:38: 11000000 INFO @ Wed, 30 Jan 2019 17:09:39: 11000000 INFO @ Wed, 30 Jan 2019 17:09:42: 12000000 INFO @ Wed, 30 Jan 2019 17:09:44: 12000000 INFO @ Wed, 30 Jan 2019 17:09:45: 12000000 INFO @ Wed, 30 Jan 2019 17:09:48: 13000000 INFO @ Wed, 30 Jan 2019 17:09:50: 13000000 INFO @ Wed, 30 Jan 2019 17:09:52: 13000000 INFO @ Wed, 30 Jan 2019 17:09:53: 14000000 INFO @ Wed, 30 Jan 2019 17:09:57: 14000000 INFO @ Wed, 30 Jan 2019 17:09:58: 14000000 INFO @ Wed, 30 Jan 2019 17:09:59: 15000000 INFO @ Wed, 30 Jan 2019 17:10:00: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:10:00: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:10:00: #1 total tags in treatment: 15023586 INFO @ Wed, 30 Jan 2019 17:10:00: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:10:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 17:10:00: #1 tags after filtering in treatment: 15023586 INFO @ Wed, 30 Jan 2019 17:10:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:10:00: #1 finished! INFO @ Wed, 30 Jan 2019 17:10:00: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:10:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:10:01: #2 number of paired peaks: 703 WARNING @ Wed, 30 Jan 2019 17:10:01: Fewer paired peaks (703) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 703 pairs to build model! INFO @ Wed, 30 Jan 2019 17:10:01: start model_add_line... INFO @ Wed, 30 Jan 2019 17:10:01: start X-correlation... INFO @ Wed, 30 Jan 2019 17:10:01: end of X-cor INFO @ Wed, 30 Jan 2019 17:10:01: #2 finished! INFO @ Wed, 30 Jan 2019 17:10:01: #2 predicted fragment length is 79 bps INFO @ Wed, 30 Jan 2019 17:10:01: #2 alternative fragment length(s) may be 79 bps INFO @ Wed, 30 Jan 2019 17:10:01: #2.2 Generate R script for model : SRX4664668.20_model.r WARNING @ Wed, 30 Jan 2019 17:10:01: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 17:10:01: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Wed, 30 Jan 2019 17:10:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 17:10:01: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:10:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:10:03: 15000000 INFO @ Wed, 30 Jan 2019 17:10:03: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:10:03: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:10:03: #1 total tags in treatment: 15023586 INFO @ Wed, 30 Jan 2019 17:10:03: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:10:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 17:10:04: #1 tags after filtering in treatment: 15023586 INFO @ Wed, 30 Jan 2019 17:10:04: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:10:04: #1 finished! INFO @ Wed, 30 Jan 2019 17:10:04: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:10:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:10:04: 15000000 INFO @ Wed, 30 Jan 2019 17:10:04: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:10:04: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:10:04: #1 total tags in treatment: 15023586 INFO @ Wed, 30 Jan 2019 17:10:04: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:10:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 17:10:05: #2 number of paired peaks: 703 WARNING @ Wed, 30 Jan 2019 17:10:05: Fewer paired peaks (703) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 703 pairs to build model! INFO @ Wed, 30 Jan 2019 17:10:05: start model_add_line... INFO @ Wed, 30 Jan 2019 17:10:05: #1 tags after filtering in treatment: 15023586 INFO @ Wed, 30 Jan 2019 17:10:05: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:10:05: #1 finished! INFO @ Wed, 30 Jan 2019 17:10:05: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:10:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:10:05: start X-correlation... INFO @ Wed, 30 Jan 2019 17:10:05: end of X-cor INFO @ Wed, 30 Jan 2019 17:10:05: #2 finished! INFO @ Wed, 30 Jan 2019 17:10:05: #2 predicted fragment length is 79 bps INFO @ Wed, 30 Jan 2019 17:10:05: #2 alternative fragment length(s) may be 79 bps INFO @ Wed, 30 Jan 2019 17:10:05: #2.2 Generate R script for model : SRX4664668.05_model.r WARNING @ Wed, 30 Jan 2019 17:10:05: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 17:10:05: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Wed, 30 Jan 2019 17:10:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 17:10:05: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:10:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:10:06: #2 number of paired peaks: 703 WARNING @ Wed, 30 Jan 2019 17:10:06: Fewer paired peaks (703) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 703 pairs to build model! INFO @ Wed, 30 Jan 2019 17:10:06: start model_add_line... INFO @ Wed, 30 Jan 2019 17:10:06: start X-correlation... INFO @ Wed, 30 Jan 2019 17:10:06: end of X-cor INFO @ Wed, 30 Jan 2019 17:10:06: #2 finished! INFO @ Wed, 30 Jan 2019 17:10:06: #2 predicted fragment length is 79 bps INFO @ Wed, 30 Jan 2019 17:10:06: #2 alternative fragment length(s) may be 79 bps INFO @ Wed, 30 Jan 2019 17:10:06: #2.2 Generate R script for model : SRX4664668.10_model.r WARNING @ Wed, 30 Jan 2019 17:10:06: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 17:10:06: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Wed, 30 Jan 2019 17:10:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 17:10:06: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:10:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:10:34: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:10:37: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:10:38: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:10:51: #4 Write output xls file... SRX4664668.20_peaks.xls INFO @ Wed, 30 Jan 2019 17:10:51: #4 Write peak in narrowPeak format file... SRX4664668.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:10:51: #4 Write summits bed file... SRX4664668.20_summits.bed INFO @ Wed, 30 Jan 2019 17:10:51: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1938 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 17:10:55: #4 Write output xls file... SRX4664668.10_peaks.xls INFO @ Wed, 30 Jan 2019 17:10:55: #4 Write peak in narrowPeak format file... SRX4664668.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:10:55: #4 Write summits bed file... SRX4664668.10_summits.bed INFO @ Wed, 30 Jan 2019 17:10:55: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3261 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 17:10:57: #4 Write output xls file... SRX4664668.05_peaks.xls INFO @ Wed, 30 Jan 2019 17:10:57: #4 Write peak in narrowPeak format file... SRX4664668.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:10:57: #4 Write summits bed file... SRX4664668.05_summits.bed INFO @ Wed, 30 Jan 2019 17:10:58: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5253 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。