Job ID = 9157276 sra ファイルのダウンロード中... Completed: 562997K bytes transferred in 6 seconds (707249K 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 12454882 spots for /home/okishinya/chipatlas/results/ce10/SRX2350752/SRR5024061.sra Written 12454882 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: 00:03:06 12454882 reads; of these: 12454882 (100.00%) were unpaired; of these: 161496 (1.30%) aligned 0 times 10796375 (86.68%) aligned exactly 1 time 1497011 (12.02%) aligned >1 times 98.70% overall alignment rate Time searching: 00:03:06 Overall time: 00:03:06 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] 1622704 / 12293386 = 0.1320 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 11:23:28: # Command line: callpeak -t SRX2350752.bam -f BAM -g ce -n SRX2350752.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2350752.10 # format = BAM # ChIP-seq file = ['SRX2350752.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 11:23:28: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:23:28: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:23:28: # Command line: callpeak -t SRX2350752.bam -f BAM -g ce -n SRX2350752.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2350752.20 # format = BAM # ChIP-seq file = ['SRX2350752.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 11:23:28: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:23:28: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:23:28: # Command line: callpeak -t SRX2350752.bam -f BAM -g ce -n SRX2350752.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2350752.05 # format = BAM # ChIP-seq file = ['SRX2350752.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 11:23:28: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:23:28: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:23:35: 1000000 INFO @ Tue, 27 Jun 2017 11:23:35: 1000000 INFO @ Tue, 27 Jun 2017 11:23:35: 1000000 INFO @ Tue, 27 Jun 2017 11:23:41: 2000000 INFO @ Tue, 27 Jun 2017 11:23:42: 2000000 INFO @ Tue, 27 Jun 2017 11:23:42: 2000000 INFO @ Tue, 27 Jun 2017 11:23:48: 3000000 INFO @ Tue, 27 Jun 2017 11:23:49: 3000000 INFO @ Tue, 27 Jun 2017 11:23:49: 3000000 INFO @ Tue, 27 Jun 2017 11:23:54: 4000000 INFO @ Tue, 27 Jun 2017 11:23:56: 4000000 INFO @ Tue, 27 Jun 2017 11:23:56: 4000000 INFO @ Tue, 27 Jun 2017 11:24:01: 5000000 INFO @ Tue, 27 Jun 2017 11:24:03: 5000000 INFO @ Tue, 27 Jun 2017 11:24:04: 5000000 INFO @ Tue, 27 Jun 2017 11:24:08: 6000000 INFO @ Tue, 27 Jun 2017 11:24:10: 6000000 INFO @ Tue, 27 Jun 2017 11:24:11: 6000000 INFO @ Tue, 27 Jun 2017 11:24:14: 7000000 INFO @ Tue, 27 Jun 2017 11:24:17: 7000000 INFO @ Tue, 27 Jun 2017 11:24:20: 7000000 INFO @ Tue, 27 Jun 2017 11:24:21: 8000000 INFO @ Tue, 27 Jun 2017 11:24:25: 8000000 INFO @ Tue, 27 Jun 2017 11:24:27: 8000000 INFO @ Tue, 27 Jun 2017 11:24:28: 9000000 INFO @ Tue, 27 Jun 2017 11:24:32: 9000000 INFO @ Tue, 27 Jun 2017 11:24:34: 9000000 INFO @ Tue, 27 Jun 2017 11:24:34: 10000000 INFO @ Tue, 27 Jun 2017 11:24:39: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:24:39: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:24:39: #1 total tags in treatment: 10670682 INFO @ Tue, 27 Jun 2017 11:24:39: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:24:39: #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 11:24:39: #1 tags after filtering in treatment: 10670682 INFO @ Tue, 27 Jun 2017 11:24:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:24:39: #1 finished! INFO @ Tue, 27 Jun 2017 11:24:39: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:24:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:24:39: 10000000 INFO @ Tue, 27 Jun 2017 11:24:40: #2 number of paired peaks: 161 WARNING @ Tue, 27 Jun 2017 11:24:40: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Tue, 27 Jun 2017 11:24:40: start model_add_line... INFO @ Tue, 27 Jun 2017 11:24:40: start X-correlation... INFO @ Tue, 27 Jun 2017 11:24:40: end of X-cor INFO @ Tue, 27 Jun 2017 11:24:40: #2 finished! INFO @ Tue, 27 Jun 2017 11:24:40: #2 predicted fragment length is 50 bps INFO @ Tue, 27 Jun 2017 11:24:40: #2 alternative fragment length(s) may be 3,50,148,181,239,257,404,486 bps INFO @ Tue, 27 Jun 2017 11:24:40: #2.2 Generate R script for model : SRX2350752.05_model.r WARNING @ Tue, 27 Jun 2017 11:24:40: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:24:40: #2 You may need to consider one of the other alternative d(s): 3,50,148,181,239,257,404,486 WARNING @ Tue, 27 Jun 2017 11:24:40: #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 11:24:40: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:24:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:24:41: 10000000 INFO @ Tue, 27 Jun 2017 11:24:44: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:24:44: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:24:44: #1 total tags in treatment: 10670682 INFO @ Tue, 27 Jun 2017 11:24:44: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:24:44: #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 11:24:44: #1 tags after filtering in treatment: 10670682 INFO @ Tue, 27 Jun 2017 11:24:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:24:44: #1 finished! INFO @ Tue, 27 Jun 2017 11:24:44: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:24:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:24:45: #2 number of paired peaks: 161 WARNING @ Tue, 27 Jun 2017 11:24:45: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Tue, 27 Jun 2017 11:24:45: start model_add_line... INFO @ Tue, 27 Jun 2017 11:24:45: start X-correlation... INFO @ Tue, 27 Jun 2017 11:24:45: end of X-cor INFO @ Tue, 27 Jun 2017 11:24:45: #2 finished! INFO @ Tue, 27 Jun 2017 11:24:45: #2 predicted fragment length is 50 bps INFO @ Tue, 27 Jun 2017 11:24:45: #2 alternative fragment length(s) may be 3,50,148,181,239,257,404,486 bps INFO @ Tue, 27 Jun 2017 11:24:45: #2.2 Generate R script for model : SRX2350752.10_model.r WARNING @ Tue, 27 Jun 2017 11:24:45: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:24:45: #2 You may need to consider one of the other alternative d(s): 3,50,148,181,239,257,404,486 WARNING @ Tue, 27 Jun 2017 11:24:45: #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 11:24:45: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:24:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:24:46: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:24:46: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:24:46: #1 total tags in treatment: 10670682 INFO @ Tue, 27 Jun 2017 11:24:46: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:24:46: #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 11:24:46: #1 tags after filtering in treatment: 10670682 INFO @ Tue, 27 Jun 2017 11:24:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:24:46: #1 finished! INFO @ Tue, 27 Jun 2017 11:24:46: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:24:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:24:47: #2 number of paired peaks: 161 WARNING @ Tue, 27 Jun 2017 11:24:47: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Tue, 27 Jun 2017 11:24:47: start model_add_line... INFO @ Tue, 27 Jun 2017 11:24:47: start X-correlation... INFO @ Tue, 27 Jun 2017 11:24:47: end of X-cor INFO @ Tue, 27 Jun 2017 11:24:47: #2 finished! INFO @ Tue, 27 Jun 2017 11:24:47: #2 predicted fragment length is 50 bps INFO @ Tue, 27 Jun 2017 11:24:47: #2 alternative fragment length(s) may be 3,50,148,181,239,257,404,486 bps INFO @ Tue, 27 Jun 2017 11:24:47: #2.2 Generate R script for model : SRX2350752.20_model.r WARNING @ Tue, 27 Jun 2017 11:24:47: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:24:47: #2 You may need to consider one of the other alternative d(s): 3,50,148,181,239,257,404,486 WARNING @ Tue, 27 Jun 2017 11:24:47: #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 11:24:47: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:24:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:25:01: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:25:06: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:25:08: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:25:12: #4 Write output xls file... SRX2350752.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:25:12: #4 Write peak in narrowPeak format file... SRX2350752.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:25:12: #4 Write summits bed file... SRX2350752.05_summits.bed INFO @ Tue, 27 Jun 2017 11:25:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (775 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:25:19: #4 Write output xls file... SRX2350752.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:25:19: #4 Write peak in narrowPeak format file... SRX2350752.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:25:19: #4 Write summits bed file... SRX2350752.10_summits.bed INFO @ Tue, 27 Jun 2017 11:25:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (203 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:25:22: #4 Write output xls file... SRX2350752.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:25:22: #4 Write peak in narrowPeak format file... SRX2350752.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:25:22: #4 Write summits bed file... SRX2350752.20_summits.bed INFO @ Tue, 27 Jun 2017 11:25:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (65 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。