Job ID = 9157278 sra ファイルのダウンロード中... Completed: 414187K bytes transferred in 6 seconds (535195K 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 9953156 spots for /home/okishinya/chipatlas/results/ce10/SRX2350753/SRR5024062.sra Written 9953156 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: 00:02:34 9953156 reads; of these: 9953156 (100.00%) were unpaired; of these: 93123 (0.94%) aligned 0 times 8640833 (86.82%) aligned exactly 1 time 1219200 (12.25%) aligned >1 times 99.06% overall alignment rate Time searching: 00:02:34 Overall time: 00:02:34 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] 1189662 / 9860033 = 0.1207 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 11:22:16: # Command line: callpeak -t SRX2350753.bam -f BAM -g ce -n SRX2350753.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2350753.10 # format = BAM # ChIP-seq file = ['SRX2350753.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 11:22:16: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:22:16: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:22:16: # Command line: callpeak -t SRX2350753.bam -f BAM -g ce -n SRX2350753.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2350753.20 # format = BAM # ChIP-seq file = ['SRX2350753.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 11:22:16: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:22:16: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:22:16: # Command line: callpeak -t SRX2350753.bam -f BAM -g ce -n SRX2350753.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2350753.05 # format = BAM # ChIP-seq file = ['SRX2350753.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 11:22:16: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:22:16: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:22:22: 1000000 INFO @ Tue, 27 Jun 2017 11:22:22: 1000000 INFO @ Tue, 27 Jun 2017 11:22:22: 1000000 INFO @ Tue, 27 Jun 2017 11:22:28: 2000000 INFO @ Tue, 27 Jun 2017 11:22:28: 2000000 INFO @ Tue, 27 Jun 2017 11:22:29: 2000000 INFO @ Tue, 27 Jun 2017 11:22:34: 3000000 INFO @ Tue, 27 Jun 2017 11:22:34: 3000000 INFO @ Tue, 27 Jun 2017 11:22:35: 3000000 INFO @ Tue, 27 Jun 2017 11:22:40: 4000000 INFO @ Tue, 27 Jun 2017 11:22:40: 4000000 INFO @ Tue, 27 Jun 2017 11:22:41: 4000000 INFO @ Tue, 27 Jun 2017 11:22:46: 5000000 INFO @ Tue, 27 Jun 2017 11:22:47: 5000000 INFO @ Tue, 27 Jun 2017 11:22:47: 5000000 INFO @ Tue, 27 Jun 2017 11:22:52: 6000000 INFO @ Tue, 27 Jun 2017 11:22:53: 6000000 INFO @ Tue, 27 Jun 2017 11:22:53: 6000000 INFO @ Tue, 27 Jun 2017 11:22:58: 7000000 INFO @ Tue, 27 Jun 2017 11:22:59: 7000000 INFO @ Tue, 27 Jun 2017 11:22:59: 7000000 INFO @ Tue, 27 Jun 2017 11:23:05: 8000000 INFO @ Tue, 27 Jun 2017 11:23:05: 8000000 INFO @ Tue, 27 Jun 2017 11:23:06: 8000000 INFO @ Tue, 27 Jun 2017 11:23:09: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:23:09: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:23:09: #1 total tags in treatment: 8670371 INFO @ Tue, 27 Jun 2017 11:23:09: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:23:09: #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 11:23:09: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:23:09: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:23:09: #1 total tags in treatment: 8670371 INFO @ Tue, 27 Jun 2017 11:23:09: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:23:09: #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 11:23:09: #1 tags after filtering in treatment: 8670371 INFO @ Tue, 27 Jun 2017 11:23:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:23:09: #1 finished! INFO @ Tue, 27 Jun 2017 11:23:09: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:23:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:23:09: #1 tags after filtering in treatment: 8670371 INFO @ Tue, 27 Jun 2017 11:23:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:23:09: #1 finished! INFO @ Tue, 27 Jun 2017 11:23:09: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:23:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:23:10: #2 number of paired peaks: 161 WARNING @ Tue, 27 Jun 2017 11:23:10: 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 11:23:10: start model_add_line... INFO @ Tue, 27 Jun 2017 11:23:10: start X-correlation... INFO @ Tue, 27 Jun 2017 11:23:10: end of X-cor INFO @ Tue, 27 Jun 2017 11:23:10: #2 finished! INFO @ Tue, 27 Jun 2017 11:23:10: #2 predicted fragment length is 53 bps INFO @ Tue, 27 Jun 2017 11:23:10: #2 alternative fragment length(s) may be 3,53,220,528,574 bps INFO @ Tue, 27 Jun 2017 11:23:10: #2.2 Generate R script for model : SRX2350753.05_model.r WARNING @ Tue, 27 Jun 2017 11:23:10: #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 11:23:10: #2 You may need to consider one of the other alternative d(s): 3,53,220,528,574 WARNING @ Tue, 27 Jun 2017 11:23:10: #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 11:23:10: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:23:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:23:10: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:23:10: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:23:10: #1 total tags in treatment: 8670371 INFO @ Tue, 27 Jun 2017 11:23:10: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:23:10: #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 11:23:10: #2 number of paired peaks: 161 WARNING @ Tue, 27 Jun 2017 11:23:10: 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 11:23:10: start model_add_line... INFO @ Tue, 27 Jun 2017 11:23:10: start X-correlation... INFO @ Tue, 27 Jun 2017 11:23:10: end of X-cor INFO @ Tue, 27 Jun 2017 11:23:10: #2 finished! INFO @ Tue, 27 Jun 2017 11:23:10: #2 predicted fragment length is 53 bps INFO @ Tue, 27 Jun 2017 11:23:10: #2 alternative fragment length(s) may be 3,53,220,528,574 bps INFO @ Tue, 27 Jun 2017 11:23:10: #2.2 Generate R script for model : SRX2350753.20_model.r WARNING @ Tue, 27 Jun 2017 11:23:10: #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 11:23:10: #2 You may need to consider one of the other alternative d(s): 3,53,220,528,574 WARNING @ Tue, 27 Jun 2017 11:23:10: #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 11:23:10: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:23:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:23:10: #1 tags after filtering in treatment: 8670371 INFO @ Tue, 27 Jun 2017 11:23:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:23:10: #1 finished! INFO @ Tue, 27 Jun 2017 11:23:10: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:23:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:23:11: #2 number of paired peaks: 161 WARNING @ Tue, 27 Jun 2017 11:23:11: 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 11:23:11: start model_add_line... INFO @ Tue, 27 Jun 2017 11:23:11: start X-correlation... INFO @ Tue, 27 Jun 2017 11:23:11: end of X-cor INFO @ Tue, 27 Jun 2017 11:23:11: #2 finished! INFO @ Tue, 27 Jun 2017 11:23:11: #2 predicted fragment length is 53 bps INFO @ Tue, 27 Jun 2017 11:23:11: #2 alternative fragment length(s) may be 3,53,220,528,574 bps INFO @ Tue, 27 Jun 2017 11:23:11: #2.2 Generate R script for model : SRX2350753.10_model.r WARNING @ Tue, 27 Jun 2017 11:23:11: #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 11:23:11: #2 You may need to consider one of the other alternative d(s): 3,53,220,528,574 WARNING @ Tue, 27 Jun 2017 11:23:11: #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 11:23:11: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:23:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:23:27: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:23:27: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:23:27: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:23:37: #4 Write output xls file... SRX2350753.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:23:37: #4 Write peak in narrowPeak format file... SRX2350753.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:23:37: #4 Write summits bed file... SRX2350753.10_summits.bed INFO @ Tue, 27 Jun 2017 11:23:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (168 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:23:37: #4 Write output xls file... SRX2350753.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:23:37: #4 Write peak in narrowPeak format file... SRX2350753.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:23:37: #4 Write summits bed file... SRX2350753.20_summits.bed INFO @ Tue, 27 Jun 2017 11:23:37: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (59 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:23:38: #4 Write output xls file... SRX2350753.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:23:38: #4 Write peak in narrowPeak format file... SRX2350753.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:23:38: #4 Write summits bed file... SRX2350753.05_summits.bed INFO @ Tue, 27 Jun 2017 11:23:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (599 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。