Job ID = 9157201 sra ファイルのダウンロード中... Completed: 261604K bytes transferred in 5 seconds (396333K 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 10075319 spots for /home/okishinya/chipatlas/results/ce10/SRX2228914/SRR4380370.sra Written 10075319 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: 00:01:59 10075319 reads; of these: 10075319 (100.00%) were unpaired; of these: 1468389 (14.57%) aligned 0 times 6958891 (69.07%) aligned exactly 1 time 1648039 (16.36%) aligned >1 times 85.43% overall alignment rate Time searching: 00:02:00 Overall time: 00:02:00 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] 1384611 / 8606930 = 0.1609 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 11:03:05: # Command line: callpeak -t SRX2228914.bam -f BAM -g ce -n SRX2228914.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228914.20 # format = BAM # ChIP-seq file = ['SRX2228914.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 11:03:05: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:03:05: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:03:05: # Command line: callpeak -t SRX2228914.bam -f BAM -g ce -n SRX2228914.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228914.05 # format = BAM # ChIP-seq file = ['SRX2228914.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 11:03:05: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:03:05: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:03:05: # Command line: callpeak -t SRX2228914.bam -f BAM -g ce -n SRX2228914.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228914.10 # format = BAM # ChIP-seq file = ['SRX2228914.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 11:03:05: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:03:05: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:03:12: 1000000 INFO @ Tue, 27 Jun 2017 11:03:13: 1000000 INFO @ Tue, 27 Jun 2017 11:03:13: 1000000 INFO @ Tue, 27 Jun 2017 11:03:19: 2000000 INFO @ Tue, 27 Jun 2017 11:03:20: 2000000 INFO @ Tue, 27 Jun 2017 11:03:20: 2000000 INFO @ Tue, 27 Jun 2017 11:03:26: 3000000 INFO @ Tue, 27 Jun 2017 11:03:28: 3000000 INFO @ Tue, 27 Jun 2017 11:03:28: 3000000 INFO @ Tue, 27 Jun 2017 11:03:33: 4000000 INFO @ Tue, 27 Jun 2017 11:03:36: 4000000 INFO @ Tue, 27 Jun 2017 11:03:36: 4000000 INFO @ Tue, 27 Jun 2017 11:03:40: 5000000 INFO @ Tue, 27 Jun 2017 11:03:44: 5000000 INFO @ Tue, 27 Jun 2017 11:03:44: 5000000 INFO @ Tue, 27 Jun 2017 11:03:47: 6000000 INFO @ Tue, 27 Jun 2017 11:03:52: 6000000 INFO @ Tue, 27 Jun 2017 11:03:52: 6000000 INFO @ Tue, 27 Jun 2017 11:03:55: 7000000 INFO @ Tue, 27 Jun 2017 11:03:56: #1 tag size is determined as 42 bps INFO @ Tue, 27 Jun 2017 11:03:56: #1 tag size = 42 INFO @ Tue, 27 Jun 2017 11:03:56: #1 total tags in treatment: 7222319 INFO @ Tue, 27 Jun 2017 11:03:56: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:03:56: #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 11:03:56: #1 tags after filtering in treatment: 7222319 INFO @ Tue, 27 Jun 2017 11:03:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:03:56: #1 finished! INFO @ Tue, 27 Jun 2017 11:03:56: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:03:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:03:57: #2 number of paired peaks: 550 WARNING @ Tue, 27 Jun 2017 11:03:57: Fewer paired peaks (550) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 550 pairs to build model! INFO @ Tue, 27 Jun 2017 11:03:57: start model_add_line... INFO @ Tue, 27 Jun 2017 11:03:57: start X-correlation... INFO @ Tue, 27 Jun 2017 11:03:57: end of X-cor INFO @ Tue, 27 Jun 2017 11:03:57: #2 finished! INFO @ Tue, 27 Jun 2017 11:03:57: #2 predicted fragment length is 74 bps INFO @ Tue, 27 Jun 2017 11:03:57: #2 alternative fragment length(s) may be 4,63,74 bps INFO @ Tue, 27 Jun 2017 11:03:57: #2.2 Generate R script for model : SRX2228914.20_model.r WARNING @ Tue, 27 Jun 2017 11:03:57: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:03:57: #2 You may need to consider one of the other alternative d(s): 4,63,74 WARNING @ Tue, 27 Jun 2017 11:03:57: #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 11:03:57: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:03:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:04:00: 7000000 INFO @ Tue, 27 Jun 2017 11:04:00: 7000000 INFO @ Tue, 27 Jun 2017 11:04:01: #1 tag size is determined as 42 bps INFO @ Tue, 27 Jun 2017 11:04:01: #1 tag size = 42 INFO @ Tue, 27 Jun 2017 11:04:01: #1 total tags in treatment: 7222319 INFO @ Tue, 27 Jun 2017 11:04:01: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:04:01: #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 11:04:02: #1 tag size is determined as 42 bps INFO @ Tue, 27 Jun 2017 11:04:02: #1 tag size = 42 INFO @ Tue, 27 Jun 2017 11:04:02: #1 total tags in treatment: 7222319 INFO @ Tue, 27 Jun 2017 11:04:02: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:04:02: #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 11:04:02: #1 tags after filtering in treatment: 7222319 INFO @ Tue, 27 Jun 2017 11:04:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:04:02: #1 finished! INFO @ Tue, 27 Jun 2017 11:04:02: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:04:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:04:02: #1 tags after filtering in treatment: 7222319 INFO @ Tue, 27 Jun 2017 11:04:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:04:02: #1 finished! INFO @ Tue, 27 Jun 2017 11:04:02: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:04:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:04:02: #2 number of paired peaks: 550 WARNING @ Tue, 27 Jun 2017 11:04:02: Fewer paired peaks (550) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 550 pairs to build model! INFO @ Tue, 27 Jun 2017 11:04:02: start model_add_line... INFO @ Tue, 27 Jun 2017 11:04:02: #2 number of paired peaks: 550 WARNING @ Tue, 27 Jun 2017 11:04:02: Fewer paired peaks (550) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 550 pairs to build model! INFO @ Tue, 27 Jun 2017 11:04:02: start model_add_line... INFO @ Tue, 27 Jun 2017 11:04:02: start X-correlation... INFO @ Tue, 27 Jun 2017 11:04:02: end of X-cor INFO @ Tue, 27 Jun 2017 11:04:02: #2 finished! INFO @ Tue, 27 Jun 2017 11:04:02: #2 predicted fragment length is 74 bps INFO @ Tue, 27 Jun 2017 11:04:02: #2 alternative fragment length(s) may be 4,63,74 bps INFO @ Tue, 27 Jun 2017 11:04:02: #2.2 Generate R script for model : SRX2228914.05_model.r WARNING @ Tue, 27 Jun 2017 11:04:02: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:04:02: #2 You may need to consider one of the other alternative d(s): 4,63,74 WARNING @ Tue, 27 Jun 2017 11:04:02: #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 11:04:02: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:04:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:04:02: start X-correlation... INFO @ Tue, 27 Jun 2017 11:04:02: end of X-cor INFO @ Tue, 27 Jun 2017 11:04:02: #2 finished! INFO @ Tue, 27 Jun 2017 11:04:02: #2 predicted fragment length is 74 bps INFO @ Tue, 27 Jun 2017 11:04:02: #2 alternative fragment length(s) may be 4,63,74 bps INFO @ Tue, 27 Jun 2017 11:04:02: #2.2 Generate R script for model : SRX2228914.10_model.r WARNING @ Tue, 27 Jun 2017 11:04:02: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:04:02: #2 You may need to consider one of the other alternative d(s): 4,63,74 WARNING @ Tue, 27 Jun 2017 11:04:02: #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 11:04:02: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:04:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:04:13: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:04:20: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:04:20: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:04:22: #4 Write output xls file... SRX2228914.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:04:22: #4 Write peak in narrowPeak format file... SRX2228914.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:04:22: #4 Write summits bed file... SRX2228914.20_summits.bed INFO @ Tue, 27 Jun 2017 11:04:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (240 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:04:28: #4 Write output xls file... SRX2228914.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:04:28: #4 Write peak in narrowPeak format file... SRX2228914.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:04:28: #4 Write summits bed file... SRX2228914.05_summits.bed INFO @ Tue, 27 Jun 2017 11:04:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2122 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:04:29: #4 Write output xls file... SRX2228914.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:04:29: #4 Write peak in narrowPeak format file... SRX2228914.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:04:29: #4 Write summits bed file... SRX2228914.10_summits.bed INFO @ Tue, 27 Jun 2017 11:04:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (662 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。