Job ID = 9157177 sra ファイルのダウンロード中... Completed: 272614K bytes transferred in 5 seconds (401415K 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 8168650 spots for /home/okishinya/chipatlas/results/ce10/SRX2228897/SRR4380353.sra Written 8168650 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: 00:02:09 8168650 reads; of these: 8168650 (100.00%) were unpaired; of these: 69167 (0.85%) aligned 0 times 6788473 (83.10%) aligned exactly 1 time 1311010 (16.05%) aligned >1 times 99.15% overall alignment rate Time searching: 00:02:09 Overall time: 00:02:09 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] 481111 / 8099483 = 0.0594 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 10:57:38: # Command line: callpeak -t SRX2228897.bam -f BAM -g ce -n SRX2228897.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228897.20 # format = BAM # ChIP-seq file = ['SRX2228897.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 10:57:38: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:57:38: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:57:38: # Command line: callpeak -t SRX2228897.bam -f BAM -g ce -n SRX2228897.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228897.10 # format = BAM # ChIP-seq file = ['SRX2228897.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 10:57:38: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:57:38: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:57:38: # Command line: callpeak -t SRX2228897.bam -f BAM -g ce -n SRX2228897.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228897.05 # format = BAM # ChIP-seq file = ['SRX2228897.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 10:57:38: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:57:38: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:57:45: 1000000 INFO @ Tue, 27 Jun 2017 10:57:45: 1000000 INFO @ Tue, 27 Jun 2017 10:57:45: 1000000 INFO @ Tue, 27 Jun 2017 10:57:52: 2000000 INFO @ Tue, 27 Jun 2017 10:57:52: 2000000 INFO @ Tue, 27 Jun 2017 10:57:52: 2000000 INFO @ Tue, 27 Jun 2017 10:57:58: 3000000 INFO @ Tue, 27 Jun 2017 10:58:00: 3000000 INFO @ Tue, 27 Jun 2017 10:58:00: 3000000 INFO @ Tue, 27 Jun 2017 10:58:05: 4000000 INFO @ Tue, 27 Jun 2017 10:58:07: 4000000 INFO @ Tue, 27 Jun 2017 10:58:07: 4000000 INFO @ Tue, 27 Jun 2017 10:58:12: 5000000 INFO @ Tue, 27 Jun 2017 10:58:14: 5000000 INFO @ Tue, 27 Jun 2017 10:58:14: 5000000 INFO @ Tue, 27 Jun 2017 10:58:19: 6000000 INFO @ Tue, 27 Jun 2017 10:58:21: 6000000 INFO @ Tue, 27 Jun 2017 10:58:21: 6000000 INFO @ Tue, 27 Jun 2017 10:58:25: 7000000 INFO @ Tue, 27 Jun 2017 10:58:28: 7000000 INFO @ Tue, 27 Jun 2017 10:58:28: 7000000 INFO @ Tue, 27 Jun 2017 10:58:29: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:58:29: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:58:29: #1 total tags in treatment: 7618372 INFO @ Tue, 27 Jun 2017 10:58:29: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:58:29: #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 10:58:30: #1 tags after filtering in treatment: 7618372 INFO @ Tue, 27 Jun 2017 10:58:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:58:30: #1 finished! INFO @ Tue, 27 Jun 2017 10:58:30: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:58:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:58:30: #2 number of paired peaks: 314 WARNING @ Tue, 27 Jun 2017 10:58:30: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Tue, 27 Jun 2017 10:58:30: start model_add_line... INFO @ Tue, 27 Jun 2017 10:58:30: start X-correlation... INFO @ Tue, 27 Jun 2017 10:58:30: end of X-cor INFO @ Tue, 27 Jun 2017 10:58:30: #2 finished! INFO @ Tue, 27 Jun 2017 10:58:30: #2 predicted fragment length is 48 bps INFO @ Tue, 27 Jun 2017 10:58:30: #2 alternative fragment length(s) may be 3,48 bps INFO @ Tue, 27 Jun 2017 10:58:30: #2.2 Generate R script for model : SRX2228897.10_model.r WARNING @ Tue, 27 Jun 2017 10:58:30: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 10:58:30: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Tue, 27 Jun 2017 10:58:30: #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 10:58:30: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:58:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:58:32: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:58:32: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:58:32: #1 total tags in treatment: 7618372 INFO @ Tue, 27 Jun 2017 10:58:32: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:58:32: #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 10:58:32: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:58:32: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:58:32: #1 total tags in treatment: 7618372 INFO @ Tue, 27 Jun 2017 10:58:32: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:58:32: #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 10:58:32: #1 tags after filtering in treatment: 7618372 INFO @ Tue, 27 Jun 2017 10:58:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:58:32: #1 finished! INFO @ Tue, 27 Jun 2017 10:58:32: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:58:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:58:32: #1 tags after filtering in treatment: 7618372 INFO @ Tue, 27 Jun 2017 10:58:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:58:32: #1 finished! INFO @ Tue, 27 Jun 2017 10:58:32: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:58:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:58:33: #2 number of paired peaks: 314 WARNING @ Tue, 27 Jun 2017 10:58:33: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Tue, 27 Jun 2017 10:58:33: start model_add_line... INFO @ Tue, 27 Jun 2017 10:58:33: #2 number of paired peaks: 314 WARNING @ Tue, 27 Jun 2017 10:58:33: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Tue, 27 Jun 2017 10:58:33: start model_add_line... INFO @ Tue, 27 Jun 2017 10:58:33: start X-correlation... INFO @ Tue, 27 Jun 2017 10:58:33: end of X-cor INFO @ Tue, 27 Jun 2017 10:58:33: #2 finished! INFO @ Tue, 27 Jun 2017 10:58:33: #2 predicted fragment length is 48 bps INFO @ Tue, 27 Jun 2017 10:58:33: #2 alternative fragment length(s) may be 3,48 bps INFO @ Tue, 27 Jun 2017 10:58:33: #2.2 Generate R script for model : SRX2228897.20_model.r WARNING @ Tue, 27 Jun 2017 10:58:33: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 10:58:33: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Tue, 27 Jun 2017 10:58:33: #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 10:58:33: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:58:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:58:33: start X-correlation... INFO @ Tue, 27 Jun 2017 10:58:33: end of X-cor INFO @ Tue, 27 Jun 2017 10:58:33: #2 finished! INFO @ Tue, 27 Jun 2017 10:58:33: #2 predicted fragment length is 48 bps INFO @ Tue, 27 Jun 2017 10:58:33: #2 alternative fragment length(s) may be 3,48 bps INFO @ Tue, 27 Jun 2017 10:58:33: #2.2 Generate R script for model : SRX2228897.05_model.r WARNING @ Tue, 27 Jun 2017 10:58:33: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 10:58:33: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Tue, 27 Jun 2017 10:58:33: #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 10:58:33: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:58:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:58:48: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:58:48: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:58:49: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:58:57: #4 Write output xls file... SRX2228897.05_peaks.xls INFO @ Tue, 27 Jun 2017 10:58:57: #4 Write peak in narrowPeak format file... SRX2228897.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:58:57: #4 Write summits bed file... SRX2228897.05_summits.bed INFO @ Tue, 27 Jun 2017 10:58:57: Done! INFO @ Tue, 27 Jun 2017 10:58:57: #4 Write output xls file... SRX2228897.10_peaks.xls INFO @ Tue, 27 Jun 2017 10:58:57: #4 Write peak in narrowPeak format file... SRX2228897.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:58:57: #4 Write summits bed file... SRX2228897.10_summits.bed INFO @ Tue, 27 Jun 2017 10:58:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (490 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (278 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:58:58: #4 Write output xls file... SRX2228897.20_peaks.xls INFO @ Tue, 27 Jun 2017 10:58:58: #4 Write peak in narrowPeak format file... SRX2228897.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:58:58: #4 Write summits bed file... SRX2228897.20_summits.bed INFO @ Tue, 27 Jun 2017 10:58:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (116 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。