Job ID = 9370019 sra ファイルのダウンロード中... Completed: 1566821K bytes transferred in 103 seconds (123965K 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 45384331 spots for /home/okishinya/chipatlas/results/ce10/SRX2710280/SRR5418734.sra Written 45384331 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: 00:31:42 45384331 reads; of these: 45384331 (100.00%) were unpaired; of these: 5984452 (13.19%) aligned 0 times 24192557 (53.31%) aligned exactly 1 time 15207322 (33.51%) aligned >1 times 86.81% overall alignment rate Time searching: 00:31:42 Overall time: 00:31:42 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 20 files... [bam_rmdupse_core] 18147601 / 39399879 = 0.4606 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 @ Fri, 04 Aug 2017 12:51:38: # Command line: callpeak -t SRX2710280.bam -f BAM -g ce -n SRX2710280.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2710280.20 # format = BAM # ChIP-seq file = ['SRX2710280.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 @ Fri, 04 Aug 2017 12:51:38: #1 read tag files... INFO @ Fri, 04 Aug 2017 12:51:38: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 12:51:38: # Command line: callpeak -t SRX2710280.bam -f BAM -g ce -n SRX2710280.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2710280.05 # format = BAM # ChIP-seq file = ['SRX2710280.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 @ Fri, 04 Aug 2017 12:51:38: #1 read tag files... INFO @ Fri, 04 Aug 2017 12:51:38: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 12:51:38: # Command line: callpeak -t SRX2710280.bam -f BAM -g ce -n SRX2710280.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2710280.10 # format = BAM # ChIP-seq file = ['SRX2710280.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 @ Fri, 04 Aug 2017 12:51:38: #1 read tag files... INFO @ Fri, 04 Aug 2017 12:51:38: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 12:51:51: 1000000 INFO @ Fri, 04 Aug 2017 12:51:56: 1000000 INFO @ Fri, 04 Aug 2017 12:51:58: 1000000 INFO @ Fri, 04 Aug 2017 12:52:02: 2000000 INFO @ Fri, 04 Aug 2017 12:52:11: 2000000 INFO @ Fri, 04 Aug 2017 12:52:16: 3000000 INFO @ Fri, 04 Aug 2017 12:52:21: 2000000 INFO @ Fri, 04 Aug 2017 12:52:28: 3000000 INFO @ Fri, 04 Aug 2017 12:52:30: 4000000 INFO @ Fri, 04 Aug 2017 12:52:41: 3000000 INFO @ Fri, 04 Aug 2017 12:52:43: 5000000 INFO @ Fri, 04 Aug 2017 12:52:44: 4000000 INFO @ Fri, 04 Aug 2017 12:52:56: 6000000 INFO @ Fri, 04 Aug 2017 12:52:57: 5000000 INFO @ Fri, 04 Aug 2017 12:53:03: 4000000 INFO @ Fri, 04 Aug 2017 12:53:08: 7000000 INFO @ Fri, 04 Aug 2017 12:53:15: 6000000 INFO @ Fri, 04 Aug 2017 12:53:20: 8000000 INFO @ Fri, 04 Aug 2017 12:53:28: 5000000 INFO @ Fri, 04 Aug 2017 12:53:31: 7000000 INFO @ Fri, 04 Aug 2017 12:53:32: 9000000 INFO @ Fri, 04 Aug 2017 12:53:44: 6000000 INFO @ Fri, 04 Aug 2017 12:53:44: 10000000 INFO @ Fri, 04 Aug 2017 12:53:48: 8000000 INFO @ Fri, 04 Aug 2017 12:53:54: 11000000 INFO @ Fri, 04 Aug 2017 12:53:57: 7000000 INFO @ Fri, 04 Aug 2017 12:54:05: 12000000 INFO @ Fri, 04 Aug 2017 12:54:06: 9000000 INFO @ Fri, 04 Aug 2017 12:54:17: 8000000 INFO @ Fri, 04 Aug 2017 12:54:17: 13000000 INFO @ Fri, 04 Aug 2017 12:54:26: 10000000 INFO @ Fri, 04 Aug 2017 12:54:28: 14000000 INFO @ Fri, 04 Aug 2017 12:54:30: 9000000 INFO @ Fri, 04 Aug 2017 12:54:41: 15000000 INFO @ Fri, 04 Aug 2017 12:54:45: 11000000 INFO @ Fri, 04 Aug 2017 12:54:45: 10000000 INFO @ Fri, 04 Aug 2017 12:54:54: 16000000 INFO @ Fri, 04 Aug 2017 12:55:01: 11000000 INFO @ Fri, 04 Aug 2017 12:55:02: 12000000 INFO @ Fri, 04 Aug 2017 12:55:07: 17000000 INFO @ Fri, 04 Aug 2017 12:55:15: 13000000 INFO @ Fri, 04 Aug 2017 12:55:18: 12000000 INFO @ Fri, 04 Aug 2017 12:55:19: 18000000 INFO @ Fri, 04 Aug 2017 12:55:29: 14000000 INFO @ Fri, 04 Aug 2017 12:55:30: 19000000 INFO @ Fri, 04 Aug 2017 12:55:33: 13000000 INFO @ Fri, 04 Aug 2017 12:55:42: 15000000 INFO @ Fri, 04 Aug 2017 12:55:43: 20000000 INFO @ Fri, 04 Aug 2017 12:55:46: 14000000 INFO @ Fri, 04 Aug 2017 12:55:56: 21000000 INFO @ Fri, 04 Aug 2017 12:56:00: 15000000 INFO @ Fri, 04 Aug 2017 12:56:01: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 12:56:01: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 12:56:01: #1 total tags in treatment: 21252278 INFO @ Fri, 04 Aug 2017 12:56:01: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 12:56:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 12:56:02: 16000000 INFO @ Fri, 04 Aug 2017 12:56:02: #1 tags after filtering in treatment: 21252278 INFO @ Fri, 04 Aug 2017 12:56:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 12:56:02: #1 finished! INFO @ Fri, 04 Aug 2017 12:56:02: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 12:56:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 12:56:05: #2 number of paired peaks: 591 WARNING @ Fri, 04 Aug 2017 12:56:05: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Fri, 04 Aug 2017 12:56:05: start model_add_line... INFO @ Fri, 04 Aug 2017 12:56:06: start X-correlation... INFO @ Fri, 04 Aug 2017 12:56:06: end of X-cor INFO @ Fri, 04 Aug 2017 12:56:06: #2 finished! INFO @ Fri, 04 Aug 2017 12:56:06: #2 predicted fragment length is 77 bps INFO @ Fri, 04 Aug 2017 12:56:06: #2 alternative fragment length(s) may be 2,77 bps INFO @ Fri, 04 Aug 2017 12:56:06: #2.2 Generate R script for model : SRX2710280.10_model.r WARNING @ Fri, 04 Aug 2017 12:56:06: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 12:56:06: #2 You may need to consider one of the other alternative d(s): 2,77 WARNING @ Fri, 04 Aug 2017 12:56:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 12:56:06: #3 Call peaks... INFO @ Fri, 04 Aug 2017 12:56:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 12:56:13: 16000000 INFO @ Fri, 04 Aug 2017 12:56:18: 17000000 INFO @ Fri, 04 Aug 2017 12:56:25: 17000000 INFO @ Fri, 04 Aug 2017 12:56:31: 18000000 INFO @ Fri, 04 Aug 2017 12:56:39: 18000000 INFO @ Fri, 04 Aug 2017 12:56:44: 19000000 INFO @ Fri, 04 Aug 2017 12:56:52: 19000000 INFO @ Fri, 04 Aug 2017 12:57:01: 20000000 INFO @ Fri, 04 Aug 2017 12:57:05: 20000000 INFO @ Fri, 04 Aug 2017 12:57:17: 21000000 INFO @ Fri, 04 Aug 2017 12:57:20: 21000000 INFO @ Fri, 04 Aug 2017 12:57:20: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 12:57:20: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 12:57:20: #1 total tags in treatment: 21252278 INFO @ Fri, 04 Aug 2017 12:57:20: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 12:57:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 12:57:21: #1 tags after filtering in treatment: 21252278 INFO @ Fri, 04 Aug 2017 12:57:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 12:57:21: #1 finished! INFO @ Fri, 04 Aug 2017 12:57:21: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 12:57:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 12:57:24: #2 number of paired peaks: 591 WARNING @ Fri, 04 Aug 2017 12:57:24: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Fri, 04 Aug 2017 12:57:24: start model_add_line... INFO @ Fri, 04 Aug 2017 12:57:24: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 12:57:24: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 12:57:24: #1 total tags in treatment: 21252278 INFO @ Fri, 04 Aug 2017 12:57:24: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 12:57:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 12:57:25: start X-correlation... INFO @ Fri, 04 Aug 2017 12:57:25: end of X-cor INFO @ Fri, 04 Aug 2017 12:57:25: #2 finished! INFO @ Fri, 04 Aug 2017 12:57:25: #2 predicted fragment length is 77 bps INFO @ Fri, 04 Aug 2017 12:57:25: #2 alternative fragment length(s) may be 2,77 bps INFO @ Fri, 04 Aug 2017 12:57:25: #2.2 Generate R script for model : SRX2710280.20_model.r WARNING @ Fri, 04 Aug 2017 12:57:25: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 12:57:25: #2 You may need to consider one of the other alternative d(s): 2,77 WARNING @ Fri, 04 Aug 2017 12:57:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 12:57:25: #3 Call peaks... INFO @ Fri, 04 Aug 2017 12:57:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 12:57:25: #1 tags after filtering in treatment: 21252278 INFO @ Fri, 04 Aug 2017 12:57:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 12:57:25: #1 finished! INFO @ Fri, 04 Aug 2017 12:57:25: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 12:57:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 12:57:29: #2 number of paired peaks: 591 WARNING @ Fri, 04 Aug 2017 12:57:29: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Fri, 04 Aug 2017 12:57:29: start model_add_line... INFO @ Fri, 04 Aug 2017 12:57:30: start X-correlation... INFO @ Fri, 04 Aug 2017 12:57:30: end of X-cor INFO @ Fri, 04 Aug 2017 12:57:30: #2 finished! INFO @ Fri, 04 Aug 2017 12:57:30: #2 predicted fragment length is 77 bps INFO @ Fri, 04 Aug 2017 12:57:30: #2 alternative fragment length(s) may be 2,77 bps INFO @ Fri, 04 Aug 2017 12:57:30: #2.2 Generate R script for model : SRX2710280.05_model.r WARNING @ Fri, 04 Aug 2017 12:57:30: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 12:57:30: #2 You may need to consider one of the other alternative d(s): 2,77 WARNING @ Fri, 04 Aug 2017 12:57:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 12:57:30: #3 Call peaks... INFO @ Fri, 04 Aug 2017 12:57:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 12:57:31: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 12:58:15: #4 Write output xls file... SRX2710280.10_peaks.xls INFO @ Fri, 04 Aug 2017 12:58:15: #4 Write peak in narrowPeak format file... SRX2710280.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 12:58:15: #4 Write summits bed file... SRX2710280.10_summits.bed INFO @ Fri, 04 Aug 2017 12:58:16: Done! pass1 - making usageList (7 chroms): 11 millis pass2 - checking and writing primary data (11792 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 12:58:47: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 12:58:51: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 12:59:29: #4 Write output xls file... SRX2710280.20_peaks.xls INFO @ Fri, 04 Aug 2017 12:59:29: #4 Write peak in narrowPeak format file... SRX2710280.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 12:59:29: #4 Write summits bed file... SRX2710280.20_summits.bed INFO @ Fri, 04 Aug 2017 12:59:29: Done! pass1 - making usageList (6 chroms): 5 millis pass2 - checking and writing primary data (4748 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 12:59:40: #4 Write output xls file... SRX2710280.05_peaks.xls INFO @ Fri, 04 Aug 2017 12:59:40: #4 Write peak in narrowPeak format file... SRX2710280.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 12:59:41: #4 Write summits bed file... SRX2710280.05_summits.bed INFO @ Fri, 04 Aug 2017 12:59:41: Done! pass1 - making usageList (7 chroms): 13 millis pass2 - checking and writing primary data (20237 records, 4 fields): 53 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。