Job ID = 9157205 sra ファイルのダウンロード中... Completed: 424861K bytes transferred in 5 seconds (593843K 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 20952107 spots for /home/okishinya/chipatlas/results/ce10/SRX2228918/SRR4380374.sra Written 20952107 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: 00:03:56 20952107 reads; of these: 20952107 (100.00%) were unpaired; of these: 616219 (2.94%) aligned 0 times 16788213 (80.13%) aligned exactly 1 time 3547675 (16.93%) aligned >1 times 97.06% overall alignment rate Time searching: 00:03:56 Overall time: 00:03:56 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2048221 / 20335888 = 0.1007 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 11:09:37: # Command line: callpeak -t SRX2228918.bam -f BAM -g ce -n SRX2228918.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228918.10 # format = BAM # ChIP-seq file = ['SRX2228918.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 11:09:37: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:09:37: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:09:37: # Command line: callpeak -t SRX2228918.bam -f BAM -g ce -n SRX2228918.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228918.05 # format = BAM # ChIP-seq file = ['SRX2228918.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 11:09:37: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:09:37: # Command line: callpeak -t SRX2228918.bam -f BAM -g ce -n SRX2228918.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228918.20 # format = BAM # ChIP-seq file = ['SRX2228918.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 11:09:37: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:09:37: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:09:37: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:09:43: 1000000 INFO @ Tue, 27 Jun 2017 11:09:44: 1000000 INFO @ Tue, 27 Jun 2017 11:09:44: 1000000 INFO @ Tue, 27 Jun 2017 11:09:49: 2000000 INFO @ Tue, 27 Jun 2017 11:09:50: 2000000 INFO @ Tue, 27 Jun 2017 11:09:50: 2000000 INFO @ Tue, 27 Jun 2017 11:09:55: 3000000 INFO @ Tue, 27 Jun 2017 11:09:56: 3000000 INFO @ Tue, 27 Jun 2017 11:09:56: 3000000 INFO @ Tue, 27 Jun 2017 11:10:01: 4000000 INFO @ Tue, 27 Jun 2017 11:10:02: 4000000 INFO @ Tue, 27 Jun 2017 11:10:02: 4000000 INFO @ Tue, 27 Jun 2017 11:10:06: 5000000 INFO @ Tue, 27 Jun 2017 11:10:09: 5000000 INFO @ Tue, 27 Jun 2017 11:10:09: 5000000 INFO @ Tue, 27 Jun 2017 11:10:12: 6000000 INFO @ Tue, 27 Jun 2017 11:10:15: 6000000 INFO @ Tue, 27 Jun 2017 11:10:15: 6000000 INFO @ Tue, 27 Jun 2017 11:10:18: 7000000 INFO @ Tue, 27 Jun 2017 11:10:21: 7000000 INFO @ Tue, 27 Jun 2017 11:10:21: 7000000 INFO @ Tue, 27 Jun 2017 11:10:24: 8000000 INFO @ Tue, 27 Jun 2017 11:10:28: 8000000 INFO @ Tue, 27 Jun 2017 11:10:28: 8000000 INFO @ Tue, 27 Jun 2017 11:10:30: 9000000 INFO @ Tue, 27 Jun 2017 11:10:34: 9000000 INFO @ Tue, 27 Jun 2017 11:10:34: 9000000 INFO @ Tue, 27 Jun 2017 11:10:35: 10000000 INFO @ Tue, 27 Jun 2017 11:10:40: 10000000 INFO @ Tue, 27 Jun 2017 11:10:40: 10000000 INFO @ Tue, 27 Jun 2017 11:10:41: 11000000 INFO @ Tue, 27 Jun 2017 11:10:47: 11000000 INFO @ Tue, 27 Jun 2017 11:10:47: 11000000 INFO @ Tue, 27 Jun 2017 11:10:47: 12000000 INFO @ Tue, 27 Jun 2017 11:10:53: 13000000 INFO @ Tue, 27 Jun 2017 11:10:53: 12000000 INFO @ Tue, 27 Jun 2017 11:10:53: 12000000 INFO @ Tue, 27 Jun 2017 11:10:58: 14000000 INFO @ Tue, 27 Jun 2017 11:10:59: 13000000 INFO @ Tue, 27 Jun 2017 11:10:59: 13000000 INFO @ Tue, 27 Jun 2017 11:11:04: 15000000 INFO @ Tue, 27 Jun 2017 11:11:05: 14000000 INFO @ Tue, 27 Jun 2017 11:11:05: 14000000 INFO @ Tue, 27 Jun 2017 11:11:10: 16000000 INFO @ Tue, 27 Jun 2017 11:11:12: 15000000 INFO @ Tue, 27 Jun 2017 11:11:12: 15000000 INFO @ Tue, 27 Jun 2017 11:11:16: 17000000 INFO @ Tue, 27 Jun 2017 11:11:18: 16000000 INFO @ Tue, 27 Jun 2017 11:11:18: 16000000 INFO @ Tue, 27 Jun 2017 11:11:22: 18000000 INFO @ Tue, 27 Jun 2017 11:11:23: #1 tag size is determined as 35 bps INFO @ Tue, 27 Jun 2017 11:11:23: #1 tag size = 35 INFO @ Tue, 27 Jun 2017 11:11:23: #1 total tags in treatment: 18287667 INFO @ Tue, 27 Jun 2017 11:11:23: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:11:23: #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 11:11:24: #1 tags after filtering in treatment: 18287667 INFO @ Tue, 27 Jun 2017 11:11:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:11:24: #1 finished! INFO @ Tue, 27 Jun 2017 11:11:24: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:11:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:11:24: 17000000 INFO @ Tue, 27 Jun 2017 11:11:24: 17000000 INFO @ Tue, 27 Jun 2017 11:11:25: #2 number of paired peaks: 236 WARNING @ Tue, 27 Jun 2017 11:11:25: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Tue, 27 Jun 2017 11:11:25: start model_add_line... INFO @ Tue, 27 Jun 2017 11:11:25: start X-correlation... INFO @ Tue, 27 Jun 2017 11:11:25: end of X-cor INFO @ Tue, 27 Jun 2017 11:11:25: #2 finished! INFO @ Tue, 27 Jun 2017 11:11:25: #2 predicted fragment length is 31 bps INFO @ Tue, 27 Jun 2017 11:11:25: #2 alternative fragment length(s) may be 1,31,86,514,553,574 bps INFO @ Tue, 27 Jun 2017 11:11:25: #2.2 Generate R script for model : SRX2228918.10_model.r WARNING @ Tue, 27 Jun 2017 11:11:25: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:11:25: #2 You may need to consider one of the other alternative d(s): 1,31,86,514,553,574 WARNING @ Tue, 27 Jun 2017 11:11:25: #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 11:11:25: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:11:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:11:30: 18000000 INFO @ Tue, 27 Jun 2017 11:11:30: 18000000 INFO @ Tue, 27 Jun 2017 11:11:32: #1 tag size is determined as 35 bps INFO @ Tue, 27 Jun 2017 11:11:32: #1 tag size = 35 INFO @ Tue, 27 Jun 2017 11:11:32: #1 total tags in treatment: 18287667 INFO @ Tue, 27 Jun 2017 11:11:32: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:11:32: #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 11:11:32: #1 tag size is determined as 35 bps INFO @ Tue, 27 Jun 2017 11:11:32: #1 tag size = 35 INFO @ Tue, 27 Jun 2017 11:11:32: #1 total tags in treatment: 18287667 INFO @ Tue, 27 Jun 2017 11:11:32: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:11:32: #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 11:11:33: #1 tags after filtering in treatment: 18287667 INFO @ Tue, 27 Jun 2017 11:11:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:11:33: #1 finished! INFO @ Tue, 27 Jun 2017 11:11:33: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:11:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:11:33: #1 tags after filtering in treatment: 18287667 INFO @ Tue, 27 Jun 2017 11:11:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:11:33: #1 finished! INFO @ Tue, 27 Jun 2017 11:11:33: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:11:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:11:34: #2 number of paired peaks: 236 WARNING @ Tue, 27 Jun 2017 11:11:34: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Tue, 27 Jun 2017 11:11:34: start model_add_line... INFO @ Tue, 27 Jun 2017 11:11:34: #2 number of paired peaks: 236 WARNING @ Tue, 27 Jun 2017 11:11:34: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Tue, 27 Jun 2017 11:11:34: start model_add_line... INFO @ Tue, 27 Jun 2017 11:11:34: start X-correlation... INFO @ Tue, 27 Jun 2017 11:11:34: end of X-cor INFO @ Tue, 27 Jun 2017 11:11:34: #2 finished! INFO @ Tue, 27 Jun 2017 11:11:34: #2 predicted fragment length is 31 bps INFO @ Tue, 27 Jun 2017 11:11:34: #2 alternative fragment length(s) may be 1,31,86,514,553,574 bps INFO @ Tue, 27 Jun 2017 11:11:34: #2.2 Generate R script for model : SRX2228918.20_model.r WARNING @ Tue, 27 Jun 2017 11:11:34: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:11:34: #2 You may need to consider one of the other alternative d(s): 1,31,86,514,553,574 WARNING @ Tue, 27 Jun 2017 11:11:34: #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 11:11:34: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:11:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:11:34: start X-correlation... INFO @ Tue, 27 Jun 2017 11:11:34: end of X-cor INFO @ Tue, 27 Jun 2017 11:11:34: #2 finished! INFO @ Tue, 27 Jun 2017 11:11:34: #2 predicted fragment length is 31 bps INFO @ Tue, 27 Jun 2017 11:11:34: #2 alternative fragment length(s) may be 1,31,86,514,553,574 bps INFO @ Tue, 27 Jun 2017 11:11:34: #2.2 Generate R script for model : SRX2228918.05_model.r WARNING @ Tue, 27 Jun 2017 11:11:34: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:11:34: #2 You may need to consider one of the other alternative d(s): 1,31,86,514,553,574 WARNING @ Tue, 27 Jun 2017 11:11:34: #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 11:11:34: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:11:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:11:57: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:12:05: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:12:09: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:12:15: #4 Write output xls file... SRX2228918.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:12:15: #4 Write peak in narrowPeak format file... SRX2228918.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:12:15: #4 Write summits bed file... SRX2228918.10_summits.bed INFO @ Tue, 27 Jun 2017 11:12:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (280 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:12:23: #4 Write output xls file... SRX2228918.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:12:23: #4 Write peak in narrowPeak format file... SRX2228918.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:12:23: #4 Write summits bed file... SRX2228918.20_summits.bed INFO @ Tue, 27 Jun 2017 11:12:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (62 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:12:26: #4 Write output xls file... SRX2228918.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:12:26: #4 Write peak in narrowPeak format file... SRX2228918.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:12:26: #4 Write summits bed file... SRX2228918.05_summits.bed INFO @ Tue, 27 Jun 2017 11:12:26: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (654 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。