Job ID = 9157236 sra ファイルのダウンロード中... Completed: 650377K bytes transferred in 8 seconds (647575K 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 15570342 spots for /home/okishinya/chipatlas/results/ce10/SRX2350735/SRR5024044.sra Written 15570342 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: 00:04:25 15570342 reads; of these: 15570342 (100.00%) were unpaired; of these: 298266 (1.92%) aligned 0 times 12069873 (77.52%) aligned exactly 1 time 3202203 (20.57%) aligned >1 times 98.08% overall alignment rate Time searching: 00:04:25 Overall time: 00:04:25 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2207880 / 15272076 = 0.1446 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 11:17:45: # Command line: callpeak -t SRX2350735.bam -f BAM -g ce -n SRX2350735.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2350735.05 # format = BAM # ChIP-seq file = ['SRX2350735.bam'] # control file = None # effective genome size = 9.00e+07 # 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 11:17:45: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:17:45: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:17:45: # Command line: callpeak -t SRX2350735.bam -f BAM -g ce -n SRX2350735.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2350735.10 # format = BAM # ChIP-seq file = ['SRX2350735.bam'] # control file = None # effective genome size = 9.00e+07 # 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 11:17:45: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:17:45: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:17:45: # Command line: callpeak -t SRX2350735.bam -f BAM -g ce -n SRX2350735.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2350735.20 # format = BAM # ChIP-seq file = ['SRX2350735.bam'] # control file = None # effective genome size = 9.00e+07 # 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 11:17:45: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:17:45: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:17:52: 1000000 INFO @ Tue, 27 Jun 2017 11:17:52: 1000000 INFO @ Tue, 27 Jun 2017 11:17:53: 1000000 INFO @ Tue, 27 Jun 2017 11:18:00: 2000000 INFO @ Tue, 27 Jun 2017 11:18:00: 2000000 INFO @ Tue, 27 Jun 2017 11:18:00: 2000000 INFO @ Tue, 27 Jun 2017 11:18:07: 3000000 INFO @ Tue, 27 Jun 2017 11:18:07: 3000000 INFO @ Tue, 27 Jun 2017 11:18:08: 3000000 INFO @ Tue, 27 Jun 2017 11:18:14: 4000000 INFO @ Tue, 27 Jun 2017 11:18:15: 4000000 INFO @ Tue, 27 Jun 2017 11:18:16: 4000000 INFO @ Tue, 27 Jun 2017 11:18:22: 5000000 INFO @ Tue, 27 Jun 2017 11:18:22: 5000000 INFO @ Tue, 27 Jun 2017 11:18:24: 5000000 INFO @ Tue, 27 Jun 2017 11:18:30: 6000000 INFO @ Tue, 27 Jun 2017 11:18:30: 6000000 INFO @ Tue, 27 Jun 2017 11:18:32: 6000000 INFO @ Tue, 27 Jun 2017 11:18:37: 7000000 INFO @ Tue, 27 Jun 2017 11:18:37: 7000000 INFO @ Tue, 27 Jun 2017 11:18:40: 7000000 INFO @ Tue, 27 Jun 2017 11:18:45: 8000000 INFO @ Tue, 27 Jun 2017 11:18:45: 8000000 INFO @ Tue, 27 Jun 2017 11:18:48: 8000000 INFO @ Tue, 27 Jun 2017 11:18:52: 9000000 INFO @ Tue, 27 Jun 2017 11:18:53: 9000000 INFO @ Tue, 27 Jun 2017 11:18:56: 9000000 INFO @ Tue, 27 Jun 2017 11:19:00: 10000000 INFO @ Tue, 27 Jun 2017 11:19:00: 10000000 INFO @ Tue, 27 Jun 2017 11:19:04: 10000000 INFO @ Tue, 27 Jun 2017 11:19:08: 11000000 INFO @ Tue, 27 Jun 2017 11:19:08: 11000000 INFO @ Tue, 27 Jun 2017 11:19:12: 11000000 INFO @ Tue, 27 Jun 2017 11:19:15: 12000000 INFO @ Tue, 27 Jun 2017 11:19:16: 12000000 INFO @ Tue, 27 Jun 2017 11:19:20: 12000000 INFO @ Tue, 27 Jun 2017 11:19:23: 13000000 INFO @ Tue, 27 Jun 2017 11:19:24: 13000000 INFO @ Tue, 27 Jun 2017 11:19:24: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:19:24: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:19:24: #1 total tags in treatment: 13064196 INFO @ Tue, 27 Jun 2017 11:19:24: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:19:24: #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 11:19:24: #1 tags after filtering in treatment: 13064196 INFO @ Tue, 27 Jun 2017 11:19:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:19:24: #1 finished! INFO @ Tue, 27 Jun 2017 11:19:24: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:19:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:19:24: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:19:24: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:19:24: #1 total tags in treatment: 13064196 INFO @ Tue, 27 Jun 2017 11:19:24: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:19:24: #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 11:19:24: #1 tags after filtering in treatment: 13064196 INFO @ Tue, 27 Jun 2017 11:19:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:19:24: #1 finished! INFO @ Tue, 27 Jun 2017 11:19:24: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:19:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:19:25: #2 number of paired peaks: 361 WARNING @ Tue, 27 Jun 2017 11:19:25: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Tue, 27 Jun 2017 11:19:25: start model_add_line... INFO @ Tue, 27 Jun 2017 11:19:25: start X-correlation... INFO @ Tue, 27 Jun 2017 11:19:25: end of X-cor INFO @ Tue, 27 Jun 2017 11:19:25: #2 finished! INFO @ Tue, 27 Jun 2017 11:19:25: #2 predicted fragment length is 46 bps INFO @ Tue, 27 Jun 2017 11:19:25: #2 alternative fragment length(s) may be 2,46 bps INFO @ Tue, 27 Jun 2017 11:19:25: #2.2 Generate R script for model : SRX2350735.10_model.r WARNING @ Tue, 27 Jun 2017 11:19:25: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:19:25: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Tue, 27 Jun 2017 11:19:25: #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 11:19:25: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:19:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:19:25: #2 number of paired peaks: 361 WARNING @ Tue, 27 Jun 2017 11:19:25: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Tue, 27 Jun 2017 11:19:25: start model_add_line... INFO @ Tue, 27 Jun 2017 11:19:25: start X-correlation... INFO @ Tue, 27 Jun 2017 11:19:25: end of X-cor INFO @ Tue, 27 Jun 2017 11:19:25: #2 finished! INFO @ Tue, 27 Jun 2017 11:19:25: #2 predicted fragment length is 46 bps INFO @ Tue, 27 Jun 2017 11:19:25: #2 alternative fragment length(s) may be 2,46 bps INFO @ Tue, 27 Jun 2017 11:19:25: #2.2 Generate R script for model : SRX2350735.05_model.r WARNING @ Tue, 27 Jun 2017 11:19:25: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:19:25: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Tue, 27 Jun 2017 11:19:25: #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 11:19:25: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:19:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:19:27: 13000000 INFO @ Tue, 27 Jun 2017 11:19:28: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:19:28: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:19:28: #1 total tags in treatment: 13064196 INFO @ Tue, 27 Jun 2017 11:19:28: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:19:28: #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 11:19:28: #1 tags after filtering in treatment: 13064196 INFO @ Tue, 27 Jun 2017 11:19:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:19:28: #1 finished! INFO @ Tue, 27 Jun 2017 11:19:28: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:19:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:19:29: #2 number of paired peaks: 361 WARNING @ Tue, 27 Jun 2017 11:19:29: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Tue, 27 Jun 2017 11:19:29: start model_add_line... INFO @ Tue, 27 Jun 2017 11:19:29: start X-correlation... INFO @ Tue, 27 Jun 2017 11:19:29: end of X-cor INFO @ Tue, 27 Jun 2017 11:19:29: #2 finished! INFO @ Tue, 27 Jun 2017 11:19:29: #2 predicted fragment length is 46 bps INFO @ Tue, 27 Jun 2017 11:19:29: #2 alternative fragment length(s) may be 2,46 bps INFO @ Tue, 27 Jun 2017 11:19:29: #2.2 Generate R script for model : SRX2350735.20_model.r WARNING @ Tue, 27 Jun 2017 11:19:29: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:19:29: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Tue, 27 Jun 2017 11:19:29: #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 11:19:29: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:19:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:19:52: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:19:52: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:19:55: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:20:05: #4 Write output xls file... SRX2350735.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:20:05: #4 Write peak in narrowPeak format file... SRX2350735.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:20:05: #4 Write summits bed file... SRX2350735.10_summits.bed INFO @ Tue, 27 Jun 2017 11:20:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (471 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:20:06: #4 Write output xls file... SRX2350735.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:20:06: #4 Write peak in narrowPeak format file... SRX2350735.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:20:06: #4 Write summits bed file... SRX2350735.05_summits.bed INFO @ Tue, 27 Jun 2017 11:20:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (795 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:20:10: #4 Write output xls file... SRX2350735.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:20:10: #4 Write peak in narrowPeak format file... SRX2350735.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:20:10: #4 Write summits bed file... SRX2350735.20_summits.bed INFO @ Tue, 27 Jun 2017 11:20:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (212 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。