Job ID = 9157182 sra ファイルのダウンロード中... Completed: 410852K bytes transferred in 6 seconds (515865K 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 19656452 spots for /home/okishinya/chipatlas/results/ce10/SRX2228901/SRR4380357.sra Written 19656452 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: 00:05:10 19656452 reads; of these: 19656452 (100.00%) were unpaired; of these: 164630 (0.84%) aligned 0 times 16235141 (82.59%) aligned exactly 1 time 3256681 (16.57%) aligned >1 times 99.16% overall alignment rate Time searching: 00:05:10 Overall time: 00:05:10 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] 1972367 / 19491822 = 0.1012 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 11:04:45: # Command line: callpeak -t SRX2228901.bam -f BAM -g ce -n SRX2228901.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228901.10 # format = BAM # ChIP-seq file = ['SRX2228901.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 11:04:45: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:04:45: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:04:45: # Command line: callpeak -t SRX2228901.bam -f BAM -g ce -n SRX2228901.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228901.20 # format = BAM # ChIP-seq file = ['SRX2228901.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 11:04:45: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:04:45: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:04:45: # Command line: callpeak -t SRX2228901.bam -f BAM -g ce -n SRX2228901.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228901.05 # format = BAM # ChIP-seq file = ['SRX2228901.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 11:04:45: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:04:45: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:04:52: 1000000 INFO @ Tue, 27 Jun 2017 11:04:52: 1000000 INFO @ Tue, 27 Jun 2017 11:04:53: 1000000 INFO @ Tue, 27 Jun 2017 11:04:58: 2000000 INFO @ Tue, 27 Jun 2017 11:04:59: 2000000 INFO @ Tue, 27 Jun 2017 11:05:00: 2000000 INFO @ Tue, 27 Jun 2017 11:05:05: 3000000 INFO @ Tue, 27 Jun 2017 11:05:06: 3000000 INFO @ Tue, 27 Jun 2017 11:05:07: 3000000 INFO @ Tue, 27 Jun 2017 11:05:12: 4000000 INFO @ Tue, 27 Jun 2017 11:05:13: 4000000 INFO @ Tue, 27 Jun 2017 11:05:15: 4000000 INFO @ Tue, 27 Jun 2017 11:05:18: 5000000 INFO @ Tue, 27 Jun 2017 11:05:20: 5000000 INFO @ Tue, 27 Jun 2017 11:05:22: 5000000 INFO @ Tue, 27 Jun 2017 11:05:25: 6000000 INFO @ Tue, 27 Jun 2017 11:05:27: 6000000 INFO @ Tue, 27 Jun 2017 11:05:30: 6000000 INFO @ Tue, 27 Jun 2017 11:05:32: 7000000 INFO @ Tue, 27 Jun 2017 11:05:34: 7000000 INFO @ Tue, 27 Jun 2017 11:05:37: 7000000 INFO @ Tue, 27 Jun 2017 11:05:38: 8000000 INFO @ Tue, 27 Jun 2017 11:05:41: 8000000 INFO @ Tue, 27 Jun 2017 11:05:44: 9000000 INFO @ Tue, 27 Jun 2017 11:05:45: 8000000 INFO @ Tue, 27 Jun 2017 11:05:47: 9000000 INFO @ Tue, 27 Jun 2017 11:05:50: 10000000 INFO @ Tue, 27 Jun 2017 11:05:52: 9000000 INFO @ Tue, 27 Jun 2017 11:05:53: 10000000 INFO @ Tue, 27 Jun 2017 11:05:56: 11000000 INFO @ Tue, 27 Jun 2017 11:06:00: 11000000 INFO @ Tue, 27 Jun 2017 11:06:00: 10000000 INFO @ Tue, 27 Jun 2017 11:06:03: 12000000 INFO @ Tue, 27 Jun 2017 11:06:07: 12000000 INFO @ Tue, 27 Jun 2017 11:06:08: 11000000 INFO @ Tue, 27 Jun 2017 11:06:09: 13000000 INFO @ Tue, 27 Jun 2017 11:06:13: 13000000 INFO @ Tue, 27 Jun 2017 11:06:15: 14000000 INFO @ Tue, 27 Jun 2017 11:06:16: 12000000 INFO @ Tue, 27 Jun 2017 11:06:20: 14000000 INFO @ Tue, 27 Jun 2017 11:06:22: 15000000 INFO @ Tue, 27 Jun 2017 11:06:24: 13000000 INFO @ Tue, 27 Jun 2017 11:06:27: 15000000 INFO @ Tue, 27 Jun 2017 11:06:28: 16000000 INFO @ Tue, 27 Jun 2017 11:06:32: 14000000 INFO @ Tue, 27 Jun 2017 11:06:33: 16000000 INFO @ Tue, 27 Jun 2017 11:06:34: 17000000 INFO @ Tue, 27 Jun 2017 11:06:37: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:06:37: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:06:37: #1 total tags in treatment: 17519455 INFO @ Tue, 27 Jun 2017 11:06:37: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:06:37: #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 11:06:38: #1 tags after filtering in treatment: 17519455 INFO @ Tue, 27 Jun 2017 11:06:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:06:38: #1 finished! INFO @ Tue, 27 Jun 2017 11:06:38: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:06:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:06:39: #2 number of paired peaks: 210 WARNING @ Tue, 27 Jun 2017 11:06:39: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Tue, 27 Jun 2017 11:06:39: start model_add_line... INFO @ Tue, 27 Jun 2017 11:06:39: start X-correlation... INFO @ Tue, 27 Jun 2017 11:06:39: end of X-cor INFO @ Tue, 27 Jun 2017 11:06:39: #2 finished! INFO @ Tue, 27 Jun 2017 11:06:39: #2 predicted fragment length is 50 bps INFO @ Tue, 27 Jun 2017 11:06:39: #2 alternative fragment length(s) may be 2,50 bps INFO @ Tue, 27 Jun 2017 11:06:39: #2.2 Generate R script for model : SRX2228901.10_model.r WARNING @ Tue, 27 Jun 2017 11:06:39: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:06:39: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Tue, 27 Jun 2017 11:06:39: #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 11:06:39: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:06:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:06:40: 17000000 INFO @ Tue, 27 Jun 2017 11:06:40: 15000000 INFO @ Tue, 27 Jun 2017 11:06:43: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:06:43: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:06:43: #1 total tags in treatment: 17519455 INFO @ Tue, 27 Jun 2017 11:06:43: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:06:43: #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 11:06:43: #1 tags after filtering in treatment: 17519455 INFO @ Tue, 27 Jun 2017 11:06:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:06:43: #1 finished! INFO @ Tue, 27 Jun 2017 11:06:43: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:06:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:06:45: #2 number of paired peaks: 210 WARNING @ Tue, 27 Jun 2017 11:06:45: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Tue, 27 Jun 2017 11:06:45: start model_add_line... INFO @ Tue, 27 Jun 2017 11:06:45: start X-correlation... INFO @ Tue, 27 Jun 2017 11:06:45: end of X-cor INFO @ Tue, 27 Jun 2017 11:06:45: #2 finished! INFO @ Tue, 27 Jun 2017 11:06:45: #2 predicted fragment length is 50 bps INFO @ Tue, 27 Jun 2017 11:06:45: #2 alternative fragment length(s) may be 2,50 bps INFO @ Tue, 27 Jun 2017 11:06:45: #2.2 Generate R script for model : SRX2228901.20_model.r WARNING @ Tue, 27 Jun 2017 11:06:45: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:06:45: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Tue, 27 Jun 2017 11:06:45: #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 11:06:45: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:06:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:06:48: 16000000 INFO @ Tue, 27 Jun 2017 11:06:56: 17000000 INFO @ Tue, 27 Jun 2017 11:07:01: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:07:01: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:07:01: #1 total tags in treatment: 17519455 INFO @ Tue, 27 Jun 2017 11:07:01: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:07:01: #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 11:07:01: #1 tags after filtering in treatment: 17519455 INFO @ Tue, 27 Jun 2017 11:07:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:07:01: #1 finished! INFO @ Tue, 27 Jun 2017 11:07:01: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:07:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:07:02: #2 number of paired peaks: 210 WARNING @ Tue, 27 Jun 2017 11:07:02: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Tue, 27 Jun 2017 11:07:02: start model_add_line... INFO @ Tue, 27 Jun 2017 11:07:02: start X-correlation... INFO @ Tue, 27 Jun 2017 11:07:02: end of X-cor INFO @ Tue, 27 Jun 2017 11:07:02: #2 finished! INFO @ Tue, 27 Jun 2017 11:07:02: #2 predicted fragment length is 50 bps INFO @ Tue, 27 Jun 2017 11:07:02: #2 alternative fragment length(s) may be 2,50 bps INFO @ Tue, 27 Jun 2017 11:07:02: #2.2 Generate R script for model : SRX2228901.05_model.r WARNING @ Tue, 27 Jun 2017 11:07:02: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:07:02: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Tue, 27 Jun 2017 11:07:02: #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 11:07:02: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:07:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:07:10: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:07:16: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:07:26: #4 Write output xls file... SRX2228901.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:07:26: #4 Write peak in narrowPeak format file... SRX2228901.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:07:26: #4 Write summits bed file... SRX2228901.10_summits.bed INFO @ Tue, 27 Jun 2017 11:07:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (433 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:07:33: #4 Write output xls file... SRX2228901.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:07:33: #4 Write peak in narrowPeak format file... SRX2228901.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:07:33: #4 Write summits bed file... SRX2228901.20_summits.bed INFO @ Tue, 27 Jun 2017 11:07:33: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (152 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:07:36: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:07:54: #4 Write output xls file... SRX2228901.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:07:54: #4 Write peak in narrowPeak format file... SRX2228901.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:07:54: #4 Write summits bed file... SRX2228901.05_summits.bed INFO @ Tue, 27 Jun 2017 11:07:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (699 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。