Job ID = 9157125 sra ファイルのダウンロード中... Completed: 305658K bytes transferred in 5 seconds (427834K 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 10064622 spots for /home/okishinya/chipatlas/results/ce10/SRX2228864/SRR4380320.sra Written 10064622 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: 00:02:22 10064622 reads; of these: 10064622 (100.00%) were unpaired; of these: 2079861 (20.67%) aligned 0 times 6652996 (66.10%) aligned exactly 1 time 1331765 (13.23%) aligned >1 times 79.33% overall alignment rate Time searching: 00:02:22 Overall time: 00:02:22 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_rmdupse_core] 1051535 / 7984761 = 0.1317 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 10:39:45: # Command line: callpeak -t SRX2228864.bam -f BAM -g ce -n SRX2228864.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228864.05 # format = BAM # ChIP-seq file = ['SRX2228864.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 10:39:45: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:39:45: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:39:45: # Command line: callpeak -t SRX2228864.bam -f BAM -g ce -n SRX2228864.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228864.20 # format = BAM # ChIP-seq file = ['SRX2228864.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 10:39:45: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:39:45: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:39:45: # Command line: callpeak -t SRX2228864.bam -f BAM -g ce -n SRX2228864.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228864.10 # format = BAM # ChIP-seq file = ['SRX2228864.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 10:39:45: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:39:45: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:39:51: 1000000 INFO @ Tue, 27 Jun 2017 10:39:52: 1000000 INFO @ Tue, 27 Jun 2017 10:39:52: 1000000 INFO @ Tue, 27 Jun 2017 10:39:57: 2000000 INFO @ Tue, 27 Jun 2017 10:39:59: 2000000 INFO @ Tue, 27 Jun 2017 10:39:59: 2000000 INFO @ Tue, 27 Jun 2017 10:40:04: 3000000 INFO @ Tue, 27 Jun 2017 10:40:06: 3000000 INFO @ Tue, 27 Jun 2017 10:40:06: 3000000 INFO @ Tue, 27 Jun 2017 10:40:10: 4000000 INFO @ Tue, 27 Jun 2017 10:40:13: 4000000 INFO @ Tue, 27 Jun 2017 10:40:13: 4000000 INFO @ Tue, 27 Jun 2017 10:40:16: 5000000 INFO @ Tue, 27 Jun 2017 10:40:20: 5000000 INFO @ Tue, 27 Jun 2017 10:40:20: 5000000 INFO @ Tue, 27 Jun 2017 10:40:22: 6000000 INFO @ Tue, 27 Jun 2017 10:40:27: 6000000 INFO @ Tue, 27 Jun 2017 10:40:27: 6000000 INFO @ Tue, 27 Jun 2017 10:40:28: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:40:28: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:40:28: #1 total tags in treatment: 6933226 INFO @ Tue, 27 Jun 2017 10:40:28: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:40:28: #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 10:40:28: #1 tags after filtering in treatment: 6933226 INFO @ Tue, 27 Jun 2017 10:40:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:40:28: #1 finished! INFO @ Tue, 27 Jun 2017 10:40:28: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:40:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:40:28: #2 number of paired peaks: 704 WARNING @ Tue, 27 Jun 2017 10:40:28: Fewer paired peaks (704) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 704 pairs to build model! INFO @ Tue, 27 Jun 2017 10:40:28: start model_add_line... INFO @ Tue, 27 Jun 2017 10:40:29: start X-correlation... INFO @ Tue, 27 Jun 2017 10:40:29: end of X-cor INFO @ Tue, 27 Jun 2017 10:40:29: #2 finished! INFO @ Tue, 27 Jun 2017 10:40:29: #2 predicted fragment length is 113 bps INFO @ Tue, 27 Jun 2017 10:40:29: #2 alternative fragment length(s) may be 113 bps INFO @ Tue, 27 Jun 2017 10:40:29: #2.2 Generate R script for model : SRX2228864.05_model.r INFO @ Tue, 27 Jun 2017 10:40:29: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:40:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:40:33: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:40:33: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:40:33: #1 total tags in treatment: 6933226 INFO @ Tue, 27 Jun 2017 10:40:33: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:40:33: #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 10:40:33: #1 tags after filtering in treatment: 6933226 INFO @ Tue, 27 Jun 2017 10:40:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:40:33: #1 finished! INFO @ Tue, 27 Jun 2017 10:40:33: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:40:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:40:34: #2 number of paired peaks: 704 WARNING @ Tue, 27 Jun 2017 10:40:34: Fewer paired peaks (704) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 704 pairs to build model! INFO @ Tue, 27 Jun 2017 10:40:34: start model_add_line... INFO @ Tue, 27 Jun 2017 10:40:34: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:40:34: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:40:34: #1 total tags in treatment: 6933226 INFO @ Tue, 27 Jun 2017 10:40:34: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:40:34: #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 10:40:34: start X-correlation... INFO @ Tue, 27 Jun 2017 10:40:34: end of X-cor INFO @ Tue, 27 Jun 2017 10:40:34: #2 finished! INFO @ Tue, 27 Jun 2017 10:40:34: #2 predicted fragment length is 113 bps INFO @ Tue, 27 Jun 2017 10:40:34: #2 alternative fragment length(s) may be 113 bps INFO @ Tue, 27 Jun 2017 10:40:34: #2.2 Generate R script for model : SRX2228864.10_model.r INFO @ Tue, 27 Jun 2017 10:40:34: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:40:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:40:34: #1 tags after filtering in treatment: 6933226 INFO @ Tue, 27 Jun 2017 10:40:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:40:34: #1 finished! INFO @ Tue, 27 Jun 2017 10:40:34: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:40:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:40:35: #2 number of paired peaks: 704 WARNING @ Tue, 27 Jun 2017 10:40:35: Fewer paired peaks (704) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 704 pairs to build model! INFO @ Tue, 27 Jun 2017 10:40:35: start model_add_line... INFO @ Tue, 27 Jun 2017 10:40:35: start X-correlation... INFO @ Tue, 27 Jun 2017 10:40:35: end of X-cor INFO @ Tue, 27 Jun 2017 10:40:35: #2 finished! INFO @ Tue, 27 Jun 2017 10:40:35: #2 predicted fragment length is 113 bps INFO @ Tue, 27 Jun 2017 10:40:35: #2 alternative fragment length(s) may be 113 bps INFO @ Tue, 27 Jun 2017 10:40:35: #2.2 Generate R script for model : SRX2228864.20_model.r INFO @ Tue, 27 Jun 2017 10:40:35: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:40:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:40:45: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:40:51: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:40:52: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:40:54: #4 Write output xls file... SRX2228864.05_peaks.xls INFO @ Tue, 27 Jun 2017 10:40:54: #4 Write peak in narrowPeak format file... SRX2228864.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:40:54: #4 Write summits bed file... SRX2228864.05_summits.bed INFO @ Tue, 27 Jun 2017 10:40:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1749 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:41:00: #4 Write output xls file... SRX2228864.10_peaks.xls INFO @ Tue, 27 Jun 2017 10:41:00: #4 Write peak in narrowPeak format file... SRX2228864.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:41:00: #4 Write summits bed file... SRX2228864.10_summits.bed INFO @ Tue, 27 Jun 2017 10:41:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1095 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:41:00: #4 Write output xls file... SRX2228864.20_peaks.xls INFO @ Tue, 27 Jun 2017 10:41:00: #4 Write peak in narrowPeak format file... SRX2228864.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:41:00: #4 Write summits bed file... SRX2228864.20_summits.bed INFO @ Tue, 27 Jun 2017 10:41:00: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (630 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。