Job ID = 9157513 sra ファイルのダウンロード中... Completed: 446785K bytes transferred in 7 seconds (498771K 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 17988956 spots for /home/okishinya/chipatlas/results/ce10/SRX245913/SRR765970.sra Written 17988956 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: 00:03:54 17988956 reads; of these: 17988956 (100.00%) were unpaired; of these: 4787031 (26.61%) aligned 0 times 10994384 (61.12%) aligned exactly 1 time 2207541 (12.27%) aligned >1 times 73.39% overall alignment rate Time searching: 00:03:54 Overall time: 00:03:54 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_rmdupse_core] 1013014 / 13201925 = 0.0767 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 12:09:44: # Command line: callpeak -t SRX245913.bam -f BAM -g ce -n SRX245913.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX245913.05 # format = BAM # ChIP-seq file = ['SRX245913.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 12:09:44: #1 read tag files... INFO @ Tue, 27 Jun 2017 12:09:44: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 12:09:44: # Command line: callpeak -t SRX245913.bam -f BAM -g ce -n SRX245913.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX245913.10 # format = BAM # ChIP-seq file = ['SRX245913.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 12:09:44: #1 read tag files... INFO @ Tue, 27 Jun 2017 12:09:44: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 12:09:44: # Command line: callpeak -t SRX245913.bam -f BAM -g ce -n SRX245913.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX245913.20 # format = BAM # ChIP-seq file = ['SRX245913.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 12:09:44: #1 read tag files... INFO @ Tue, 27 Jun 2017 12:09:44: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 12:09:52: 1000000 INFO @ Tue, 27 Jun 2017 12:09:52: 1000000 INFO @ Tue, 27 Jun 2017 12:09:53: 1000000 INFO @ Tue, 27 Jun 2017 12:10:00: 2000000 INFO @ Tue, 27 Jun 2017 12:10:00: 2000000 INFO @ Tue, 27 Jun 2017 12:10:01: 2000000 INFO @ Tue, 27 Jun 2017 12:10:08: 3000000 INFO @ Tue, 27 Jun 2017 12:10:08: 3000000 INFO @ Tue, 27 Jun 2017 12:10:09: 3000000 INFO @ Tue, 27 Jun 2017 12:10:16: 4000000 INFO @ Tue, 27 Jun 2017 12:10:16: 4000000 INFO @ Tue, 27 Jun 2017 12:10:18: 4000000 INFO @ Tue, 27 Jun 2017 12:10:23: 5000000 INFO @ Tue, 27 Jun 2017 12:10:23: 5000000 INFO @ Tue, 27 Jun 2017 12:10:26: 5000000 INFO @ Tue, 27 Jun 2017 12:10:31: 6000000 INFO @ Tue, 27 Jun 2017 12:10:31: 6000000 INFO @ Tue, 27 Jun 2017 12:10:34: 6000000 INFO @ Tue, 27 Jun 2017 12:10:39: 7000000 INFO @ Tue, 27 Jun 2017 12:10:39: 7000000 INFO @ Tue, 27 Jun 2017 12:10:43: 7000000 INFO @ Tue, 27 Jun 2017 12:10:47: 8000000 INFO @ Tue, 27 Jun 2017 12:10:47: 8000000 INFO @ Tue, 27 Jun 2017 12:10:51: 8000000 INFO @ Tue, 27 Jun 2017 12:10:54: 9000000 INFO @ Tue, 27 Jun 2017 12:10:54: 9000000 INFO @ Tue, 27 Jun 2017 12:10:59: 9000000 INFO @ Tue, 27 Jun 2017 12:11:01: 10000000 INFO @ Tue, 27 Jun 2017 12:11:01: 10000000 INFO @ Tue, 27 Jun 2017 12:11:06: 10000000 INFO @ Tue, 27 Jun 2017 12:11:08: 11000000 INFO @ Tue, 27 Jun 2017 12:11:08: 11000000 INFO @ Tue, 27 Jun 2017 12:11:13: 11000000 INFO @ Tue, 27 Jun 2017 12:11:15: 12000000 INFO @ Tue, 27 Jun 2017 12:11:15: 12000000 INFO @ Tue, 27 Jun 2017 12:11:17: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 12:11:17: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 12:11:17: #1 total tags in treatment: 12188911 INFO @ Tue, 27 Jun 2017 12:11:17: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:11:17: #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 12:11:17: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 12:11:17: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 12:11:17: #1 total tags in treatment: 12188911 INFO @ Tue, 27 Jun 2017 12:11:17: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:11:17: #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 12:11:17: #1 tags after filtering in treatment: 12188911 INFO @ Tue, 27 Jun 2017 12:11:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 12:11:17: #1 finished! INFO @ Tue, 27 Jun 2017 12:11:17: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:11:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:11:17: #1 tags after filtering in treatment: 12188911 INFO @ Tue, 27 Jun 2017 12:11:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 12:11:17: #1 finished! INFO @ Tue, 27 Jun 2017 12:11:17: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:11:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:11:18: #2 number of paired peaks: 288 WARNING @ Tue, 27 Jun 2017 12:11:18: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Tue, 27 Jun 2017 12:11:18: start model_add_line... INFO @ Tue, 27 Jun 2017 12:11:18: #2 number of paired peaks: 288 WARNING @ Tue, 27 Jun 2017 12:11:18: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Tue, 27 Jun 2017 12:11:18: start model_add_line... INFO @ Tue, 27 Jun 2017 12:11:18: start X-correlation... INFO @ Tue, 27 Jun 2017 12:11:18: end of X-cor INFO @ Tue, 27 Jun 2017 12:11:18: #2 finished! INFO @ Tue, 27 Jun 2017 12:11:18: #2 predicted fragment length is 32 bps INFO @ Tue, 27 Jun 2017 12:11:18: #2 alternative fragment length(s) may be 2,32,541 bps INFO @ Tue, 27 Jun 2017 12:11:18: #2.2 Generate R script for model : SRX245913.05_model.r WARNING @ Tue, 27 Jun 2017 12:11:18: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! INFO @ Tue, 27 Jun 2017 12:11:18: start X-correlation... WARNING @ Tue, 27 Jun 2017 12:11:18: #2 You may need to consider one of the other alternative d(s): 2,32,541 WARNING @ Tue, 27 Jun 2017 12:11:18: #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 12:11:18: #3 Call peaks... INFO @ Tue, 27 Jun 2017 12:11:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:11:18: end of X-cor INFO @ Tue, 27 Jun 2017 12:11:18: #2 finished! INFO @ Tue, 27 Jun 2017 12:11:18: #2 predicted fragment length is 32 bps INFO @ Tue, 27 Jun 2017 12:11:18: #2 alternative fragment length(s) may be 2,32,541 bps INFO @ Tue, 27 Jun 2017 12:11:18: #2.2 Generate R script for model : SRX245913.10_model.r WARNING @ Tue, 27 Jun 2017 12:11:18: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 12:11:18: #2 You may need to consider one of the other alternative d(s): 2,32,541 WARNING @ Tue, 27 Jun 2017 12:11:18: #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 12:11:18: #3 Call peaks... INFO @ Tue, 27 Jun 2017 12:11:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:11:21: 12000000 INFO @ Tue, 27 Jun 2017 12:11:22: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 12:11:22: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 12:11:22: #1 total tags in treatment: 12188911 INFO @ Tue, 27 Jun 2017 12:11:22: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:11:22: #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 12:11:22: #1 tags after filtering in treatment: 12188911 INFO @ Tue, 27 Jun 2017 12:11:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 12:11:22: #1 finished! INFO @ Tue, 27 Jun 2017 12:11:22: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:11:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:11:23: #2 number of paired peaks: 288 WARNING @ Tue, 27 Jun 2017 12:11:23: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Tue, 27 Jun 2017 12:11:23: start model_add_line... INFO @ Tue, 27 Jun 2017 12:11:23: start X-correlation... INFO @ Tue, 27 Jun 2017 12:11:23: end of X-cor INFO @ Tue, 27 Jun 2017 12:11:23: #2 finished! INFO @ Tue, 27 Jun 2017 12:11:23: #2 predicted fragment length is 32 bps INFO @ Tue, 27 Jun 2017 12:11:23: #2 alternative fragment length(s) may be 2,32,541 bps INFO @ Tue, 27 Jun 2017 12:11:23: #2.2 Generate R script for model : SRX245913.20_model.r WARNING @ Tue, 27 Jun 2017 12:11:23: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 12:11:23: #2 You may need to consider one of the other alternative d(s): 2,32,541 WARNING @ Tue, 27 Jun 2017 12:11:23: #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 12:11:23: #3 Call peaks... INFO @ Tue, 27 Jun 2017 12:11:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:11:42: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:11:44: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:11:47: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:11:55: #4 Write output xls file... SRX245913.05_peaks.xls INFO @ Tue, 27 Jun 2017 12:11:55: #4 Write peak in narrowPeak format file... SRX245913.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:11:55: #4 Write summits bed file... SRX245913.05_summits.bed INFO @ Tue, 27 Jun 2017 12:11:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (936 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 12:11:57: #4 Write output xls file... SRX245913.10_peaks.xls INFO @ Tue, 27 Jun 2017 12:11:57: #4 Write peak in narrowPeak format file... SRX245913.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:11:57: #4 Write summits bed file... SRX245913.10_summits.bed INFO @ Tue, 27 Jun 2017 12:11:57: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (393 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 12:12:00: #4 Write output xls file... SRX245913.20_peaks.xls INFO @ Tue, 27 Jun 2017 12:12:00: #4 Write peak in narrowPeak format file... SRX245913.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:12:00: #4 Write summits bed file... SRX245913.20_summits.bed INFO @ Tue, 27 Jun 2017 12:12:00: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (95 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。