Job ID = 9730419 sra ファイルのダウンロード中... Completed: 627015K bytes transferred in 9 seconds (556566K bits/sec), in 2 files, 3 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 14865800 spots for /home/okishinya/chipatlas/results/ce10/SRX2582953/SRR5279130.sra Written 14865800 spots total Written 15065068 spots for /home/okishinya/chipatlas/results/ce10/SRX2582953/SRR5279129.sra Written 15065068 spots total 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: 00:07:00 29930868 reads; of these: 29930868 (100.00%) were unpaired; of these: 5849429 (19.54%) aligned 0 times 20133805 (67.27%) aligned exactly 1 time 3947634 (13.19%) aligned >1 times 80.46% overall alignment rate Time searching: 00:07:00 Overall time: 00:07:00 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_sort_core] merging from 12 files... [bam_rmdupse_core] 6915325 / 24081439 = 0.2872 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 @ Sun, 03 Sep 2017 01:07:25: # Command line: callpeak -t SRX2582953.bam -f BAM -g ce -n SRX2582953.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2582953.10 # format = BAM # ChIP-seq file = ['SRX2582953.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 @ Sun, 03 Sep 2017 01:07:25: # Command line: callpeak -t SRX2582953.bam -f BAM -g ce -n SRX2582953.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2582953.20 # format = BAM # ChIP-seq file = ['SRX2582953.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 @ Sun, 03 Sep 2017 01:07:25: # Command line: callpeak -t SRX2582953.bam -f BAM -g ce -n SRX2582953.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2582953.05 # format = BAM # ChIP-seq file = ['SRX2582953.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 @ Sun, 03 Sep 2017 01:07:25: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:07:25: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:07:25: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:07:25: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:07:25: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:07:25: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:07:31: 1000000 INFO @ Sun, 03 Sep 2017 01:07:31: 1000000 INFO @ Sun, 03 Sep 2017 01:07:31: 1000000 INFO @ Sun, 03 Sep 2017 01:07:37: 2000000 INFO @ Sun, 03 Sep 2017 01:07:37: 2000000 INFO @ Sun, 03 Sep 2017 01:07:37: 2000000 INFO @ Sun, 03 Sep 2017 01:07:43: 3000000 INFO @ Sun, 03 Sep 2017 01:07:43: 3000000 INFO @ Sun, 03 Sep 2017 01:07:43: 3000000 INFO @ Sun, 03 Sep 2017 01:07:49: 4000000 INFO @ Sun, 03 Sep 2017 01:07:49: 4000000 INFO @ Sun, 03 Sep 2017 01:07:49: 4000000 INFO @ Sun, 03 Sep 2017 01:07:55: 5000000 INFO @ Sun, 03 Sep 2017 01:07:55: 5000000 INFO @ Sun, 03 Sep 2017 01:07:55: 5000000 INFO @ Sun, 03 Sep 2017 01:08:01: 6000000 INFO @ Sun, 03 Sep 2017 01:08:01: 6000000 INFO @ Sun, 03 Sep 2017 01:08:01: 6000000 INFO @ Sun, 03 Sep 2017 01:08:06: 7000000 INFO @ Sun, 03 Sep 2017 01:08:07: 7000000 INFO @ Sun, 03 Sep 2017 01:08:07: 7000000 INFO @ Sun, 03 Sep 2017 01:08:12: 8000000 INFO @ Sun, 03 Sep 2017 01:08:13: 8000000 INFO @ Sun, 03 Sep 2017 01:08:13: 8000000 INFO @ Sun, 03 Sep 2017 01:08:18: 9000000 INFO @ Sun, 03 Sep 2017 01:08:19: 9000000 INFO @ Sun, 03 Sep 2017 01:08:20: 9000000 INFO @ Sun, 03 Sep 2017 01:08:24: 10000000 INFO @ Sun, 03 Sep 2017 01:08:25: 10000000 INFO @ Sun, 03 Sep 2017 01:08:26: 10000000 INFO @ Sun, 03 Sep 2017 01:08:31: 11000000 INFO @ Sun, 03 Sep 2017 01:08:32: 11000000 INFO @ Sun, 03 Sep 2017 01:08:33: 11000000 INFO @ Sun, 03 Sep 2017 01:08:38: 12000000 INFO @ Sun, 03 Sep 2017 01:08:38: 12000000 INFO @ Sun, 03 Sep 2017 01:08:40: 12000000 INFO @ Sun, 03 Sep 2017 01:08:44: 13000000 INFO @ Sun, 03 Sep 2017 01:08:45: 13000000 INFO @ Sun, 03 Sep 2017 01:08:47: 13000000 INFO @ Sun, 03 Sep 2017 01:08:51: 14000000 INFO @ Sun, 03 Sep 2017 01:08:51: 14000000 INFO @ Sun, 03 Sep 2017 01:08:53: 14000000 INFO @ Sun, 03 Sep 2017 01:08:57: 15000000 INFO @ Sun, 03 Sep 2017 01:08:58: 15000000 INFO @ Sun, 03 Sep 2017 01:09:00: 15000000 INFO @ Sun, 03 Sep 2017 01:09:04: 16000000 INFO @ Sun, 03 Sep 2017 01:09:04: 16000000 INFO @ Sun, 03 Sep 2017 01:09:07: 16000000 INFO @ Sun, 03 Sep 2017 01:09:10: 17000000 INFO @ Sun, 03 Sep 2017 01:09:11: 17000000 INFO @ Sun, 03 Sep 2017 01:09:12: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:09:12: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:09:12: #1 total tags in treatment: 17166114 INFO @ Sun, 03 Sep 2017 01:09:12: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:09:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:09:12: #1 tags after filtering in treatment: 17166114 INFO @ Sun, 03 Sep 2017 01:09:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:09:12: #1 finished! INFO @ Sun, 03 Sep 2017 01:09:12: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:09:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:09:12: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:09:12: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:09:12: #1 total tags in treatment: 17166114 INFO @ Sun, 03 Sep 2017 01:09:12: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:09:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:09:12: #1 tags after filtering in treatment: 17166114 INFO @ Sun, 03 Sep 2017 01:09:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:09:12: #1 finished! INFO @ Sun, 03 Sep 2017 01:09:12: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:09:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:09:13: #2 number of paired peaks: 263 WARNING @ Sun, 03 Sep 2017 01:09:13: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Sun, 03 Sep 2017 01:09:13: start model_add_line... INFO @ Sun, 03 Sep 2017 01:09:13: start X-correlation... INFO @ Sun, 03 Sep 2017 01:09:13: 17000000 INFO @ Sun, 03 Sep 2017 01:09:13: end of X-cor INFO @ Sun, 03 Sep 2017 01:09:13: #2 finished! INFO @ Sun, 03 Sep 2017 01:09:13: #2 predicted fragment length is 47 bps INFO @ Sun, 03 Sep 2017 01:09:13: #2 alternative fragment length(s) may be 2,47,598 bps INFO @ Sun, 03 Sep 2017 01:09:13: #2.2 Generate R script for model : SRX2582953.20_model.r WARNING @ Sun, 03 Sep 2017 01:09:13: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:09:13: #2 You may need to consider one of the other alternative d(s): 2,47,598 WARNING @ Sun, 03 Sep 2017 01:09:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Sep 2017 01:09:13: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:09:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:09:14: #2 number of paired peaks: 263 WARNING @ Sun, 03 Sep 2017 01:09:14: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Sun, 03 Sep 2017 01:09:14: start model_add_line... INFO @ Sun, 03 Sep 2017 01:09:14: start X-correlation... INFO @ Sun, 03 Sep 2017 01:09:14: end of X-cor INFO @ Sun, 03 Sep 2017 01:09:14: #2 finished! INFO @ Sun, 03 Sep 2017 01:09:14: #2 predicted fragment length is 47 bps INFO @ Sun, 03 Sep 2017 01:09:14: #2 alternative fragment length(s) may be 2,47,598 bps INFO @ Sun, 03 Sep 2017 01:09:14: #2.2 Generate R script for model : SRX2582953.05_model.r WARNING @ Sun, 03 Sep 2017 01:09:14: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:09:14: #2 You may need to consider one of the other alternative d(s): 2,47,598 WARNING @ Sun, 03 Sep 2017 01:09:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Sep 2017 01:09:14: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:09:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:09:14: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:09:14: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:09:14: #1 total tags in treatment: 17166114 INFO @ Sun, 03 Sep 2017 01:09:14: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:09:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:09:15: #1 tags after filtering in treatment: 17166114 INFO @ Sun, 03 Sep 2017 01:09:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:09:15: #1 finished! INFO @ Sun, 03 Sep 2017 01:09:15: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:09:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:09:16: #2 number of paired peaks: 263 WARNING @ Sun, 03 Sep 2017 01:09:16: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Sun, 03 Sep 2017 01:09:16: start model_add_line... INFO @ Sun, 03 Sep 2017 01:09:16: start X-correlation... INFO @ Sun, 03 Sep 2017 01:09:16: end of X-cor INFO @ Sun, 03 Sep 2017 01:09:16: #2 finished! INFO @ Sun, 03 Sep 2017 01:09:16: #2 predicted fragment length is 47 bps INFO @ Sun, 03 Sep 2017 01:09:16: #2 alternative fragment length(s) may be 2,47,598 bps INFO @ Sun, 03 Sep 2017 01:09:16: #2.2 Generate R script for model : SRX2582953.10_model.r WARNING @ Sun, 03 Sep 2017 01:09:16: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:09:16: #2 You may need to consider one of the other alternative d(s): 2,47,598 WARNING @ Sun, 03 Sep 2017 01:09:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Sep 2017 01:09:16: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:09:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:09:46: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:09:47: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:09:50: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:10:03: #4 Write output xls file... SRX2582953.05_peaks.xls INFO @ Sun, 03 Sep 2017 01:10:03: #4 Write peak in narrowPeak format file... SRX2582953.05_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:10:03: #4 Write summits bed file... SRX2582953.05_summits.bed INFO @ Sun, 03 Sep 2017 01:10:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1848 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:10:03: #4 Write output xls file... SRX2582953.20_peaks.xls INFO @ Sun, 03 Sep 2017 01:10:03: #4 Write peak in narrowPeak format file... SRX2582953.20_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:10:03: #4 Write summits bed file... SRX2582953.20_summits.bed INFO @ Sun, 03 Sep 2017 01:10:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (358 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:10:06: #4 Write output xls file... SRX2582953.10_peaks.xls INFO @ Sun, 03 Sep 2017 01:10:06: #4 Write peak in narrowPeak format file... SRX2582953.10_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:10:06: #4 Write summits bed file... SRX2582953.10_summits.bed INFO @ Sun, 03 Sep 2017 01:10:06: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (950 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。