Job ID = 9157194 sra ファイルのダウンロード中... Completed: 275531K bytes transferred in 5 seconds (383289K 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 13551305 spots for /home/okishinya/chipatlas/results/ce10/SRX2228909/SRR4380365.sra Written 13551305 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: 00:03:32 13551305 reads; of these: 13551305 (100.00%) were unpaired; of these: 162945 (1.20%) aligned 0 times 11066761 (81.67%) aligned exactly 1 time 2321599 (17.13%) aligned >1 times 98.80% overall alignment rate Time searching: 00:03:32 Overall time: 00:03:32 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] 1166629 / 13388360 = 0.0871 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 11:03:40: # Command line: callpeak -t SRX2228909.bam -f BAM -g ce -n SRX2228909.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228909.20 # format = BAM # ChIP-seq file = ['SRX2228909.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 11:03:40: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:03:40: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:03:40: # Command line: callpeak -t SRX2228909.bam -f BAM -g ce -n SRX2228909.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228909.05 # format = BAM # ChIP-seq file = ['SRX2228909.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 11:03:40: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:03:40: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:03:40: # Command line: callpeak -t SRX2228909.bam -f BAM -g ce -n SRX2228909.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228909.10 # format = BAM # ChIP-seq file = ['SRX2228909.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 11:03:40: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:03:40: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:03:48: 1000000 INFO @ Tue, 27 Jun 2017 11:03:48: 1000000 INFO @ Tue, 27 Jun 2017 11:03:48: 1000000 INFO @ Tue, 27 Jun 2017 11:03:56: 2000000 INFO @ Tue, 27 Jun 2017 11:03:56: 2000000 INFO @ Tue, 27 Jun 2017 11:03:56: 2000000 INFO @ Tue, 27 Jun 2017 11:04:04: 3000000 INFO @ Tue, 27 Jun 2017 11:04:04: 3000000 INFO @ Tue, 27 Jun 2017 11:04:04: 3000000 INFO @ Tue, 27 Jun 2017 11:04:12: 4000000 INFO @ Tue, 27 Jun 2017 11:04:12: 4000000 INFO @ Tue, 27 Jun 2017 11:04:12: 4000000 INFO @ Tue, 27 Jun 2017 11:04:20: 5000000 INFO @ Tue, 27 Jun 2017 11:04:20: 5000000 INFO @ Tue, 27 Jun 2017 11:04:20: 5000000 INFO @ Tue, 27 Jun 2017 11:04:28: 6000000 INFO @ Tue, 27 Jun 2017 11:04:28: 6000000 INFO @ Tue, 27 Jun 2017 11:04:28: 6000000 INFO @ Tue, 27 Jun 2017 11:04:36: 7000000 INFO @ Tue, 27 Jun 2017 11:04:36: 7000000 INFO @ Tue, 27 Jun 2017 11:04:36: 7000000 INFO @ Tue, 27 Jun 2017 11:04:44: 8000000 INFO @ Tue, 27 Jun 2017 11:04:44: 8000000 INFO @ Tue, 27 Jun 2017 11:04:44: 8000000 INFO @ Tue, 27 Jun 2017 11:04:52: 9000000 INFO @ Tue, 27 Jun 2017 11:04:52: 9000000 INFO @ Tue, 27 Jun 2017 11:04:52: 9000000 INFO @ Tue, 27 Jun 2017 11:05:00: 10000000 INFO @ Tue, 27 Jun 2017 11:05:01: 10000000 INFO @ Tue, 27 Jun 2017 11:05:01: 10000000 INFO @ Tue, 27 Jun 2017 11:05:08: 11000000 INFO @ Tue, 27 Jun 2017 11:05:09: 11000000 INFO @ Tue, 27 Jun 2017 11:05:09: 11000000 INFO @ Tue, 27 Jun 2017 11:05:15: 12000000 INFO @ Tue, 27 Jun 2017 11:05:16: 12000000 INFO @ Tue, 27 Jun 2017 11:05:16: 12000000 INFO @ Tue, 27 Jun 2017 11:05:17: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:05:17: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:05:17: #1 total tags in treatment: 12221731 INFO @ Tue, 27 Jun 2017 11:05:17: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:05:17: #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 11:05:17: #1 tags after filtering in treatment: 12221731 INFO @ Tue, 27 Jun 2017 11:05:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:05:17: #1 finished! INFO @ Tue, 27 Jun 2017 11:05:17: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:05:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:05:18: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:05:18: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:05:18: #1 total tags in treatment: 12221731 INFO @ Tue, 27 Jun 2017 11:05:18: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:05:18: #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 11:05:18: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:05:18: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:05:18: #1 total tags in treatment: 12221731 INFO @ Tue, 27 Jun 2017 11:05:18: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:05:18: #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 11:05:18: #2 number of paired peaks: 299 WARNING @ Tue, 27 Jun 2017 11:05:18: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Tue, 27 Jun 2017 11:05:18: start model_add_line... INFO @ Tue, 27 Jun 2017 11:05:18: #1 tags after filtering in treatment: 12221731 INFO @ Tue, 27 Jun 2017 11:05:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:05:18: #1 finished! INFO @ Tue, 27 Jun 2017 11:05:18: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:05:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:05:18: start X-correlation... INFO @ Tue, 27 Jun 2017 11:05:18: end of X-cor INFO @ Tue, 27 Jun 2017 11:05:18: #2 finished! INFO @ Tue, 27 Jun 2017 11:05:18: #2 predicted fragment length is 52 bps INFO @ Tue, 27 Jun 2017 11:05:18: #2 alternative fragment length(s) may be 2,52,515,554 bps INFO @ Tue, 27 Jun 2017 11:05:18: #2.2 Generate R script for model : SRX2228909.20_model.r WARNING @ Tue, 27 Jun 2017 11:05:18: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:05:18: #2 You may need to consider one of the other alternative d(s): 2,52,515,554 WARNING @ Tue, 27 Jun 2017 11:05:18: #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 11:05:18: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:05:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:05:18: #1 tags after filtering in treatment: 12221731 INFO @ Tue, 27 Jun 2017 11:05:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:05:18: #1 finished! INFO @ Tue, 27 Jun 2017 11:05:18: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:05:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:05:19: #2 number of paired peaks: 299 WARNING @ Tue, 27 Jun 2017 11:05:19: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Tue, 27 Jun 2017 11:05:19: start model_add_line... INFO @ Tue, 27 Jun 2017 11:05:19: #2 number of paired peaks: 299 WARNING @ Tue, 27 Jun 2017 11:05:19: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Tue, 27 Jun 2017 11:05:19: start model_add_line... INFO @ Tue, 27 Jun 2017 11:05:19: start X-correlation... INFO @ Tue, 27 Jun 2017 11:05:19: end of X-cor INFO @ Tue, 27 Jun 2017 11:05:19: #2 finished! INFO @ Tue, 27 Jun 2017 11:05:19: #2 predicted fragment length is 52 bps INFO @ Tue, 27 Jun 2017 11:05:19: #2 alternative fragment length(s) may be 2,52,515,554 bps INFO @ Tue, 27 Jun 2017 11:05:19: #2.2 Generate R script for model : SRX2228909.05_model.r INFO @ Tue, 27 Jun 2017 11:05:19: start X-correlation... WARNING @ Tue, 27 Jun 2017 11:05:19: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:05:19: #2 You may need to consider one of the other alternative d(s): 2,52,515,554 WARNING @ Tue, 27 Jun 2017 11:05:19: #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 11:05:19: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:05:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:05:19: end of X-cor INFO @ Tue, 27 Jun 2017 11:05:19: #2 finished! INFO @ Tue, 27 Jun 2017 11:05:19: #2 predicted fragment length is 52 bps INFO @ Tue, 27 Jun 2017 11:05:19: #2 alternative fragment length(s) may be 2,52,515,554 bps INFO @ Tue, 27 Jun 2017 11:05:19: #2.2 Generate R script for model : SRX2228909.10_model.r WARNING @ Tue, 27 Jun 2017 11:05:19: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:05:19: #2 You may need to consider one of the other alternative d(s): 2,52,515,554 WARNING @ Tue, 27 Jun 2017 11:05:19: #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 11:05:19: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:05:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:05:42: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:05:44: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:05:44: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:05:56: #4 Write output xls file... SRX2228909.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:05:56: #4 Write peak in narrowPeak format file... SRX2228909.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:05:56: #4 Write summits bed file... SRX2228909.20_summits.bed INFO @ Tue, 27 Jun 2017 11:05:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (182 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:05:57: #4 Write output xls file... SRX2228909.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:05:57: #4 Write peak in narrowPeak format file... SRX2228909.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:05:57: #4 Write summits bed file... SRX2228909.05_summits.bed INFO @ Tue, 27 Jun 2017 11:05:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (617 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:06:02: #4 Write output xls file... SRX2228909.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:06:02: #4 Write peak in narrowPeak format file... SRX2228909.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:06:02: #4 Write summits bed file... SRX2228909.10_summits.bed INFO @ Tue, 27 Jun 2017 11:06:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (412 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。