Job ID = 9157279 sra ファイルのダウンロード中... Completed: 508617K bytes transferred in 6 seconds (654365K 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 12237325 spots for /home/okishinya/chipatlas/results/ce10/SRX2350754/SRR5024063.sra Written 12237325 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: 00:03:05 12237325 reads; of these: 12237325 (100.00%) were unpaired; of these: 177875 (1.45%) aligned 0 times 10461296 (85.49%) aligned exactly 1 time 1598154 (13.06%) aligned >1 times 98.55% overall alignment rate Time searching: 00:03:05 Overall time: 00:03:05 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] 1479532 / 12059450 = 0.1227 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 11:24:13: # Command line: callpeak -t SRX2350754.bam -f BAM -g ce -n SRX2350754.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2350754.10 # format = BAM # ChIP-seq file = ['SRX2350754.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 11:24:13: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:24:13: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:24:13: # Command line: callpeak -t SRX2350754.bam -f BAM -g ce -n SRX2350754.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2350754.05 # format = BAM # ChIP-seq file = ['SRX2350754.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 11:24:13: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:24:13: # Command line: callpeak -t SRX2350754.bam -f BAM -g ce -n SRX2350754.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2350754.20 # format = BAM # ChIP-seq file = ['SRX2350754.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 11:24:13: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:24:13: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:24:13: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:24:20: 1000000 INFO @ Tue, 27 Jun 2017 11:24:20: 1000000 INFO @ Tue, 27 Jun 2017 11:24:20: 1000000 INFO @ Tue, 27 Jun 2017 11:24:26: 2000000 INFO @ Tue, 27 Jun 2017 11:24:27: 2000000 INFO @ Tue, 27 Jun 2017 11:24:27: 2000000 INFO @ Tue, 27 Jun 2017 11:24:33: 3000000 INFO @ Tue, 27 Jun 2017 11:24:33: 3000000 INFO @ Tue, 27 Jun 2017 11:24:34: 3000000 INFO @ Tue, 27 Jun 2017 11:24:39: 4000000 INFO @ Tue, 27 Jun 2017 11:24:40: 4000000 INFO @ Tue, 27 Jun 2017 11:24:40: 4000000 INFO @ Tue, 27 Jun 2017 11:24:46: 5000000 INFO @ Tue, 27 Jun 2017 11:24:47: 5000000 INFO @ Tue, 27 Jun 2017 11:24:47: 5000000 INFO @ Tue, 27 Jun 2017 11:24:52: 6000000 INFO @ Tue, 27 Jun 2017 11:24:54: 6000000 INFO @ Tue, 27 Jun 2017 11:24:55: 6000000 INFO @ Tue, 27 Jun 2017 11:24:59: 7000000 INFO @ Tue, 27 Jun 2017 11:25:01: 7000000 INFO @ Tue, 27 Jun 2017 11:25:02: 7000000 INFO @ Tue, 27 Jun 2017 11:25:05: 8000000 INFO @ Tue, 27 Jun 2017 11:25:08: 8000000 INFO @ Tue, 27 Jun 2017 11:25:09: 8000000 INFO @ Tue, 27 Jun 2017 11:25:12: 9000000 INFO @ Tue, 27 Jun 2017 11:25:15: 9000000 INFO @ Tue, 27 Jun 2017 11:25:16: 9000000 INFO @ Tue, 27 Jun 2017 11:25:18: 10000000 INFO @ Tue, 27 Jun 2017 11:25:22: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:25:22: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:25:22: #1 total tags in treatment: 10579918 INFO @ Tue, 27 Jun 2017 11:25:22: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:25:22: #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 11:25:23: 10000000 INFO @ Tue, 27 Jun 2017 11:25:23: #1 tags after filtering in treatment: 10579918 INFO @ Tue, 27 Jun 2017 11:25:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:25:23: #1 finished! INFO @ Tue, 27 Jun 2017 11:25:23: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:25:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:25:23: #2 number of paired peaks: 165 WARNING @ Tue, 27 Jun 2017 11:25:23: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Tue, 27 Jun 2017 11:25:23: start model_add_line... INFO @ Tue, 27 Jun 2017 11:25:23: start X-correlation... INFO @ Tue, 27 Jun 2017 11:25:23: end of X-cor INFO @ Tue, 27 Jun 2017 11:25:23: #2 finished! INFO @ Tue, 27 Jun 2017 11:25:23: #2 predicted fragment length is 53 bps INFO @ Tue, 27 Jun 2017 11:25:23: #2 alternative fragment length(s) may be 3,53,458,472,507,567,578 bps INFO @ Tue, 27 Jun 2017 11:25:23: #2.2 Generate R script for model : SRX2350754.10_model.r WARNING @ Tue, 27 Jun 2017 11:25:23: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:25:23: #2 You may need to consider one of the other alternative d(s): 3,53,458,472,507,567,578 WARNING @ Tue, 27 Jun 2017 11:25:23: #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 11:25:23: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:25:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:25:24: 10000000 INFO @ Tue, 27 Jun 2017 11:25:27: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:25:27: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:25:27: #1 total tags in treatment: 10579918 INFO @ Tue, 27 Jun 2017 11:25:27: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:25:27: #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 11:25:27: #1 tags after filtering in treatment: 10579918 INFO @ Tue, 27 Jun 2017 11:25:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:25:27: #1 finished! INFO @ Tue, 27 Jun 2017 11:25:27: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:25:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:25:28: #2 number of paired peaks: 165 WARNING @ Tue, 27 Jun 2017 11:25:28: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Tue, 27 Jun 2017 11:25:28: start model_add_line... INFO @ Tue, 27 Jun 2017 11:25:28: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:25:28: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:25:28: #1 total tags in treatment: 10579918 INFO @ Tue, 27 Jun 2017 11:25:28: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:25:28: #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 11:25:28: start X-correlation... INFO @ Tue, 27 Jun 2017 11:25:28: end of X-cor INFO @ Tue, 27 Jun 2017 11:25:28: #2 finished! INFO @ Tue, 27 Jun 2017 11:25:28: #2 predicted fragment length is 53 bps INFO @ Tue, 27 Jun 2017 11:25:28: #2 alternative fragment length(s) may be 3,53,458,472,507,567,578 bps INFO @ Tue, 27 Jun 2017 11:25:28: #2.2 Generate R script for model : SRX2350754.05_model.r WARNING @ Tue, 27 Jun 2017 11:25:28: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:25:28: #2 You may need to consider one of the other alternative d(s): 3,53,458,472,507,567,578 WARNING @ Tue, 27 Jun 2017 11:25:28: #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 11:25:28: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:25:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:25:28: #1 tags after filtering in treatment: 10579918 INFO @ Tue, 27 Jun 2017 11:25:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:25:28: #1 finished! INFO @ Tue, 27 Jun 2017 11:25:28: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:25:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:25:29: #2 number of paired peaks: 165 WARNING @ Tue, 27 Jun 2017 11:25:29: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Tue, 27 Jun 2017 11:25:29: start model_add_line... INFO @ Tue, 27 Jun 2017 11:25:29: start X-correlation... INFO @ Tue, 27 Jun 2017 11:25:29: end of X-cor INFO @ Tue, 27 Jun 2017 11:25:29: #2 finished! INFO @ Tue, 27 Jun 2017 11:25:29: #2 predicted fragment length is 53 bps INFO @ Tue, 27 Jun 2017 11:25:29: #2 alternative fragment length(s) may be 3,53,458,472,507,567,578 bps INFO @ Tue, 27 Jun 2017 11:25:29: #2.2 Generate R script for model : SRX2350754.20_model.r WARNING @ Tue, 27 Jun 2017 11:25:29: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:25:29: #2 You may need to consider one of the other alternative d(s): 3,53,458,472,507,567,578 WARNING @ Tue, 27 Jun 2017 11:25:29: #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 11:25:29: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:25:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:25:45: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:25:50: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:25:50: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:25:56: #4 Write output xls file... SRX2350754.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:25:56: #4 Write peak in narrowPeak format file... SRX2350754.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:25:56: #4 Write summits bed file... SRX2350754.10_summits.bed INFO @ Tue, 27 Jun 2017 11:25:56: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (244 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:26:02: #4 Write output xls file... SRX2350754.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:26:02: #4 Write peak in narrowPeak format file... SRX2350754.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:26:02: #4 Write summits bed file... SRX2350754.20_summits.bed INFO @ Tue, 27 Jun 2017 11:26:02: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (97 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:26:02: #4 Write output xls file... SRX2350754.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:26:02: #4 Write peak in narrowPeak format file... SRX2350754.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:26:02: #4 Write summits bed file... SRX2350754.05_summits.bed INFO @ Tue, 27 Jun 2017 11:26:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (636 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。