Job ID = 10714569 sra ファイルのダウンロード中... Completed: 368981K bytes transferred in 5 seconds (536084K bits/sec), in 1 file. 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... Read 24856300 spots for /home/okishinya/chipatlas/results/dm3/SRX4053303/SRR7132410.sra Written 24856300 spots for /home/okishinya/chipatlas/results/dm3/SRX4053303/SRR7132410.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:10:22 24856300 reads; of these: 24856300 (100.00%) were unpaired; of these: 2519959 (10.14%) aligned 0 times 15617539 (62.83%) aligned exactly 1 time 6718802 (27.03%) aligned >1 times 89.86% overall alignment rate Time searching: 00:10:22 Overall time: 00:10:22 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4239920 / 22336341 = 0.1898 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 @ Sun, 03 Jun 2018 13:45:19: # Command line: callpeak -t SRX4053303.bam -f BAM -g dm -n SRX4053303.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4053303.05 # format = BAM # ChIP-seq file = ['SRX4053303.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 03 Jun 2018 13:45:19: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:45:19: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:45:19: # Command line: callpeak -t SRX4053303.bam -f BAM -g dm -n SRX4053303.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4053303.20 # format = BAM # ChIP-seq file = ['SRX4053303.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 03 Jun 2018 13:45:19: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:45:19: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:45:19: # Command line: callpeak -t SRX4053303.bam -f BAM -g dm -n SRX4053303.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4053303.10 # format = BAM # ChIP-seq file = ['SRX4053303.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 03 Jun 2018 13:45:19: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:45:19: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:45:25: 1000000 INFO @ Sun, 03 Jun 2018 13:45:25: 1000000 INFO @ Sun, 03 Jun 2018 13:45:25: 1000000 INFO @ Sun, 03 Jun 2018 13:45:31: 2000000 INFO @ Sun, 03 Jun 2018 13:45:32: 2000000 INFO @ Sun, 03 Jun 2018 13:45:32: 2000000 INFO @ Sun, 03 Jun 2018 13:45:38: 3000000 INFO @ Sun, 03 Jun 2018 13:45:38: 3000000 INFO @ Sun, 03 Jun 2018 13:45:38: 3000000 INFO @ Sun, 03 Jun 2018 13:45:44: 4000000 INFO @ Sun, 03 Jun 2018 13:45:44: 4000000 INFO @ Sun, 03 Jun 2018 13:45:44: 4000000 INFO @ Sun, 03 Jun 2018 13:45:50: 5000000 INFO @ Sun, 03 Jun 2018 13:45:50: 5000000 INFO @ Sun, 03 Jun 2018 13:45:50: 5000000 INFO @ Sun, 03 Jun 2018 13:45:56: 6000000 INFO @ Sun, 03 Jun 2018 13:45:56: 6000000 INFO @ Sun, 03 Jun 2018 13:45:57: 6000000 INFO @ Sun, 03 Jun 2018 13:46:03: 7000000 INFO @ Sun, 03 Jun 2018 13:46:03: 7000000 INFO @ Sun, 03 Jun 2018 13:46:03: 7000000 INFO @ Sun, 03 Jun 2018 13:46:09: 8000000 INFO @ Sun, 03 Jun 2018 13:46:09: 8000000 INFO @ Sun, 03 Jun 2018 13:46:09: 8000000 INFO @ Sun, 03 Jun 2018 13:46:15: 9000000 INFO @ Sun, 03 Jun 2018 13:46:15: 9000000 INFO @ Sun, 03 Jun 2018 13:46:15: 9000000 INFO @ Sun, 03 Jun 2018 13:46:21: 10000000 INFO @ Sun, 03 Jun 2018 13:46:21: 10000000 INFO @ Sun, 03 Jun 2018 13:46:22: 10000000 INFO @ Sun, 03 Jun 2018 13:46:28: 11000000 INFO @ Sun, 03 Jun 2018 13:46:28: 11000000 INFO @ Sun, 03 Jun 2018 13:46:28: 11000000 INFO @ Sun, 03 Jun 2018 13:46:34: 12000000 INFO @ Sun, 03 Jun 2018 13:46:34: 12000000 INFO @ Sun, 03 Jun 2018 13:46:34: 12000000 INFO @ Sun, 03 Jun 2018 13:46:40: 13000000 INFO @ Sun, 03 Jun 2018 13:46:40: 13000000 INFO @ Sun, 03 Jun 2018 13:46:40: 13000000 INFO @ Sun, 03 Jun 2018 13:46:46: 14000000 INFO @ Sun, 03 Jun 2018 13:46:46: 14000000 INFO @ Sun, 03 Jun 2018 13:46:47: 14000000 INFO @ Sun, 03 Jun 2018 13:46:52: 15000000 INFO @ Sun, 03 Jun 2018 13:46:53: 15000000 INFO @ Sun, 03 Jun 2018 13:46:53: 15000000 INFO @ Sun, 03 Jun 2018 13:46:59: 16000000 INFO @ Sun, 03 Jun 2018 13:46:59: 16000000 INFO @ Sun, 03 Jun 2018 13:47:00: 16000000 INFO @ Sun, 03 Jun 2018 13:47:06: 17000000 INFO @ Sun, 03 Jun 2018 13:47:06: 17000000 INFO @ Sun, 03 Jun 2018 13:47:07: 17000000 INFO @ Sun, 03 Jun 2018 13:47:12: 18000000 INFO @ Sun, 03 Jun 2018 13:47:13: 18000000 INFO @ Sun, 03 Jun 2018 13:47:13: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:47:13: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:47:13: #1 total tags in treatment: 18096421 INFO @ Sun, 03 Jun 2018 13:47:13: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:47:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:47:14: #1 tags after filtering in treatment: 18096421 INFO @ Sun, 03 Jun 2018 13:47:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:47:14: #1 finished! INFO @ Sun, 03 Jun 2018 13:47:14: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:47:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:47:14: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:47:14: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:47:14: #1 total tags in treatment: 18096421 INFO @ Sun, 03 Jun 2018 13:47:14: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:47:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:47:14: 18000000 INFO @ Sun, 03 Jun 2018 13:47:14: #1 tags after filtering in treatment: 18096421 INFO @ Sun, 03 Jun 2018 13:47:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:47:14: #1 finished! INFO @ Sun, 03 Jun 2018 13:47:14: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:47:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:47:15: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:47:15: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:47:15: #1 total tags in treatment: 18096421 INFO @ Sun, 03 Jun 2018 13:47:15: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:47:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:47:15: #2 number of paired peaks: 109 WARNING @ Sun, 03 Jun 2018 13:47:15: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Sun, 03 Jun 2018 13:47:15: start model_add_line... INFO @ Sun, 03 Jun 2018 13:47:15: start X-correlation... INFO @ Sun, 03 Jun 2018 13:47:15: end of X-cor INFO @ Sun, 03 Jun 2018 13:47:15: #2 finished! INFO @ Sun, 03 Jun 2018 13:47:15: #2 predicted fragment length is 45 bps INFO @ Sun, 03 Jun 2018 13:47:15: #2 alternative fragment length(s) may be 4,45 bps INFO @ Sun, 03 Jun 2018 13:47:15: #2.2 Generate R script for model : SRX4053303.10_model.r WARNING @ Sun, 03 Jun 2018 13:47:15: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:47:15: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Sun, 03 Jun 2018 13:47:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:47:15: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:47:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:47:15: #1 tags after filtering in treatment: 18096421 INFO @ Sun, 03 Jun 2018 13:47:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:47:15: #1 finished! INFO @ Sun, 03 Jun 2018 13:47:15: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:47:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:47:16: #2 number of paired peaks: 109 WARNING @ Sun, 03 Jun 2018 13:47:16: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Sun, 03 Jun 2018 13:47:16: start model_add_line... INFO @ Sun, 03 Jun 2018 13:47:16: start X-correlation... INFO @ Sun, 03 Jun 2018 13:47:16: end of X-cor INFO @ Sun, 03 Jun 2018 13:47:16: #2 finished! INFO @ Sun, 03 Jun 2018 13:47:16: #2 predicted fragment length is 45 bps INFO @ Sun, 03 Jun 2018 13:47:16: #2 alternative fragment length(s) may be 4,45 bps INFO @ Sun, 03 Jun 2018 13:47:16: #2.2 Generate R script for model : SRX4053303.20_model.r WARNING @ Sun, 03 Jun 2018 13:47:16: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:47:16: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Sun, 03 Jun 2018 13:47:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:47:16: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:47:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:47:16: #2 number of paired peaks: 109 WARNING @ Sun, 03 Jun 2018 13:47:16: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Sun, 03 Jun 2018 13:47:16: start model_add_line... INFO @ Sun, 03 Jun 2018 13:47:16: start X-correlation... INFO @ Sun, 03 Jun 2018 13:47:16: end of X-cor INFO @ Sun, 03 Jun 2018 13:47:16: #2 finished! INFO @ Sun, 03 Jun 2018 13:47:16: #2 predicted fragment length is 45 bps INFO @ Sun, 03 Jun 2018 13:47:16: #2 alternative fragment length(s) may be 4,45 bps INFO @ Sun, 03 Jun 2018 13:47:16: #2.2 Generate R script for model : SRX4053303.05_model.r WARNING @ Sun, 03 Jun 2018 13:47:16: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:47:16: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Sun, 03 Jun 2018 13:47:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:47:16: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:47:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:47:51: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:47:53: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:47:56: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:48:12: #4 Write output xls file... SRX4053303.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:48:12: #4 Write peak in narrowPeak format file... SRX4053303.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:48:12: #4 Write summits bed file... SRX4053303.05_summits.bed INFO @ Sun, 03 Jun 2018 13:48:12: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2097 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:48:13: #4 Write output xls file... SRX4053303.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:48:13: #4 Write peak in narrowPeak format file... SRX4053303.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:48:13: #4 Write summits bed file... SRX4053303.10_summits.bed INFO @ Sun, 03 Jun 2018 13:48:13: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1511 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:48:16: #4 Write output xls file... SRX4053303.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:48:16: #4 Write peak in narrowPeak format file... SRX4053303.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:48:16: #4 Write summits bed file... SRX4053303.20_summits.bed INFO @ Sun, 03 Jun 2018 13:48:16: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (858 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。