Job ID = 9157253 sra ファイルのダウンロード中... Completed: 655666K bytes transferred in 8 seconds (629578K 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 15591993 spots for /home/okishinya/chipatlas/results/ce10/SRX2350737/SRR5024046.sra Written 15591993 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: 00:05:24 15591993 reads; of these: 15591993 (100.00%) were unpaired; of these: 771186 (4.95%) aligned 0 times 11733236 (75.25%) aligned exactly 1 time 3087571 (19.80%) aligned >1 times 95.05% overall alignment rate Time searching: 00:05:24 Overall time: 00:05:24 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] 2311858 / 14820807 = 0.1560 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 11:20:19: # Command line: callpeak -t SRX2350737.bam -f BAM -g ce -n SRX2350737.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2350737.10 # format = BAM # ChIP-seq file = ['SRX2350737.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 11:20:19: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:20:19: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:20:19: # Command line: callpeak -t SRX2350737.bam -f BAM -g ce -n SRX2350737.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2350737.20 # format = BAM # ChIP-seq file = ['SRX2350737.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 11:20:19: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:20:19: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:20:19: # Command line: callpeak -t SRX2350737.bam -f BAM -g ce -n SRX2350737.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2350737.05 # format = BAM # ChIP-seq file = ['SRX2350737.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 11:20:19: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:20:19: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:20:25: 1000000 INFO @ Tue, 27 Jun 2017 11:20:27: 1000000 INFO @ Tue, 27 Jun 2017 11:20:28: 1000000 INFO @ Tue, 27 Jun 2017 11:20:32: 2000000 INFO @ Tue, 27 Jun 2017 11:20:35: 2000000 INFO @ Tue, 27 Jun 2017 11:20:37: 2000000 INFO @ Tue, 27 Jun 2017 11:20:38: 3000000 INFO @ Tue, 27 Jun 2017 11:20:44: 3000000 INFO @ Tue, 27 Jun 2017 11:20:45: 4000000 INFO @ Tue, 27 Jun 2017 11:20:46: 3000000 INFO @ Tue, 27 Jun 2017 11:20:52: 5000000 INFO @ Tue, 27 Jun 2017 11:20:53: 4000000 INFO @ Tue, 27 Jun 2017 11:20:56: 4000000 INFO @ Tue, 27 Jun 2017 11:20:58: 6000000 INFO @ Tue, 27 Jun 2017 11:21:01: 5000000 INFO @ Tue, 27 Jun 2017 11:21:05: 7000000 INFO @ Tue, 27 Jun 2017 11:21:05: 5000000 INFO @ Tue, 27 Jun 2017 11:21:10: 6000000 INFO @ Tue, 27 Jun 2017 11:21:11: 8000000 INFO @ Tue, 27 Jun 2017 11:21:15: 6000000 INFO @ Tue, 27 Jun 2017 11:21:18: 9000000 INFO @ Tue, 27 Jun 2017 11:21:18: 7000000 INFO @ Tue, 27 Jun 2017 11:21:24: 7000000 INFO @ Tue, 27 Jun 2017 11:21:24: 10000000 INFO @ Tue, 27 Jun 2017 11:21:27: 8000000 INFO @ Tue, 27 Jun 2017 11:21:31: 11000000 INFO @ Tue, 27 Jun 2017 11:21:34: 8000000 INFO @ Tue, 27 Jun 2017 11:21:35: 9000000 INFO @ Tue, 27 Jun 2017 11:21:38: 12000000 INFO @ Tue, 27 Jun 2017 11:21:41: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:21:41: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:21:41: #1 total tags in treatment: 12508949 INFO @ Tue, 27 Jun 2017 11:21:41: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:21:41: #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 11:21:41: #1 tags after filtering in treatment: 12508949 INFO @ Tue, 27 Jun 2017 11:21:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:21:41: #1 finished! INFO @ Tue, 27 Jun 2017 11:21:41: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:21:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:21:42: #2 number of paired peaks: 362 WARNING @ Tue, 27 Jun 2017 11:21:42: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Tue, 27 Jun 2017 11:21:42: start model_add_line... INFO @ Tue, 27 Jun 2017 11:21:42: start X-correlation... INFO @ Tue, 27 Jun 2017 11:21:42: end of X-cor INFO @ Tue, 27 Jun 2017 11:21:42: #2 finished! INFO @ Tue, 27 Jun 2017 11:21:42: #2 predicted fragment length is 41 bps INFO @ Tue, 27 Jun 2017 11:21:42: #2 alternative fragment length(s) may be 3,41,537,541 bps INFO @ Tue, 27 Jun 2017 11:21:42: #2.2 Generate R script for model : SRX2350737.20_model.r WARNING @ Tue, 27 Jun 2017 11:21:42: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:21:42: #2 You may need to consider one of the other alternative d(s): 3,41,537,541 WARNING @ Tue, 27 Jun 2017 11:21:42: #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 11:21:42: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:21:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:21:43: 9000000 INFO @ Tue, 27 Jun 2017 11:21:44: 10000000 INFO @ Tue, 27 Jun 2017 11:21:52: 11000000 INFO @ Tue, 27 Jun 2017 11:21:53: 10000000 INFO @ Tue, 27 Jun 2017 11:22:01: 12000000 INFO @ Tue, 27 Jun 2017 11:22:02: 11000000 INFO @ Tue, 27 Jun 2017 11:22:05: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:22:05: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:22:05: #1 total tags in treatment: 12508949 INFO @ Tue, 27 Jun 2017 11:22:05: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:22:05: #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 11:22:05: #1 tags after filtering in treatment: 12508949 INFO @ Tue, 27 Jun 2017 11:22:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:22:05: #1 finished! INFO @ Tue, 27 Jun 2017 11:22:05: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:22:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:22:06: #2 number of paired peaks: 362 WARNING @ Tue, 27 Jun 2017 11:22:06: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Tue, 27 Jun 2017 11:22:06: start model_add_line... INFO @ Tue, 27 Jun 2017 11:22:06: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:22:06: start X-correlation... INFO @ Tue, 27 Jun 2017 11:22:06: end of X-cor INFO @ Tue, 27 Jun 2017 11:22:06: #2 finished! INFO @ Tue, 27 Jun 2017 11:22:06: #2 predicted fragment length is 41 bps INFO @ Tue, 27 Jun 2017 11:22:06: #2 alternative fragment length(s) may be 3,41,537,541 bps INFO @ Tue, 27 Jun 2017 11:22:06: #2.2 Generate R script for model : SRX2350737.05_model.r WARNING @ Tue, 27 Jun 2017 11:22:06: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:22:06: #2 You may need to consider one of the other alternative d(s): 3,41,537,541 WARNING @ Tue, 27 Jun 2017 11:22:06: #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 11:22:06: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:22:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:22:11: 12000000 INFO @ Tue, 27 Jun 2017 11:22:16: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:22:16: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:22:16: #1 total tags in treatment: 12508949 INFO @ Tue, 27 Jun 2017 11:22:16: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:22:16: #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 11:22:17: #1 tags after filtering in treatment: 12508949 INFO @ Tue, 27 Jun 2017 11:22:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:22:17: #1 finished! INFO @ Tue, 27 Jun 2017 11:22:17: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:22:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:22:17: #2 number of paired peaks: 362 WARNING @ Tue, 27 Jun 2017 11:22:17: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Tue, 27 Jun 2017 11:22:17: start model_add_line... INFO @ Tue, 27 Jun 2017 11:22:18: start X-correlation... INFO @ Tue, 27 Jun 2017 11:22:18: end of X-cor INFO @ Tue, 27 Jun 2017 11:22:18: #2 finished! INFO @ Tue, 27 Jun 2017 11:22:18: #2 predicted fragment length is 41 bps INFO @ Tue, 27 Jun 2017 11:22:18: #2 alternative fragment length(s) may be 3,41,537,541 bps INFO @ Tue, 27 Jun 2017 11:22:18: #2.2 Generate R script for model : SRX2350737.10_model.r WARNING @ Tue, 27 Jun 2017 11:22:18: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:22:18: #2 You may need to consider one of the other alternative d(s): 3,41,537,541 WARNING @ Tue, 27 Jun 2017 11:22:18: #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 11:22:18: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:22:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:22:21: #4 Write output xls file... SRX2350737.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:22:21: #4 Write peak in narrowPeak format file... SRX2350737.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:22:21: #4 Write summits bed file... SRX2350737.20_summits.bed INFO @ Tue, 27 Jun 2017 11:22:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (190 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:22:33: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:22:43: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:22:47: #4 Write output xls file... SRX2350737.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:22:47: #4 Write peak in narrowPeak format file... SRX2350737.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:22:47: #4 Write summits bed file... SRX2350737.05_summits.bed INFO @ Tue, 27 Jun 2017 11:22:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (872 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:22:58: #4 Write output xls file... SRX2350737.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:22:58: #4 Write peak in narrowPeak format file... SRX2350737.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:22:58: #4 Write summits bed file... SRX2350737.10_summits.bed INFO @ Tue, 27 Jun 2017 11:22:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (455 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。