Job ID = 11240798 sra ファイルのダウンロード中... Completed: 568741K bytes transferred in 10 seconds (438605K 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 18063386 spots for /home/okishinya/chipatlas/results/dm3/SRX4798845/SRR7965224.sra Written 18063386 spots for /home/okishinya/chipatlas/results/dm3/SRX4798845/SRR7965224.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: 00:05:00 18063386 reads; of these: 18063386 (100.00%) were unpaired; of these: 1857422 (10.28%) aligned 0 times 14389528 (79.66%) aligned exactly 1 time 1816436 (10.06%) aligned >1 times 89.72% overall alignment rate Time searching: 00:05:00 Overall time: 00:05:00 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 8 files... [bam_rmdupse_core] 1792701 / 16205964 = 0.1106 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, 07 Oct 2018 20:50:55: # Command line: callpeak -t SRX4798845.bam -f BAM -g dm -n SRX4798845.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4798845.05 # format = BAM # ChIP-seq file = ['SRX4798845.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, 07 Oct 2018 20:50:55: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:50:55: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:50:55: # Command line: callpeak -t SRX4798845.bam -f BAM -g dm -n SRX4798845.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4798845.10 # format = BAM # ChIP-seq file = ['SRX4798845.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, 07 Oct 2018 20:50:55: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:50:55: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:50:55: # Command line: callpeak -t SRX4798845.bam -f BAM -g dm -n SRX4798845.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4798845.20 # format = BAM # ChIP-seq file = ['SRX4798845.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, 07 Oct 2018 20:50:55: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:50:55: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:51:03: 1000000 INFO @ Sun, 07 Oct 2018 20:51:03: 1000000 INFO @ Sun, 07 Oct 2018 20:51:03: 1000000 INFO @ Sun, 07 Oct 2018 20:51:10: 2000000 INFO @ Sun, 07 Oct 2018 20:51:10: 2000000 INFO @ Sun, 07 Oct 2018 20:51:10: 2000000 INFO @ Sun, 07 Oct 2018 20:51:17: 3000000 INFO @ Sun, 07 Oct 2018 20:51:17: 3000000 INFO @ Sun, 07 Oct 2018 20:51:17: 3000000 INFO @ Sun, 07 Oct 2018 20:51:25: 4000000 INFO @ Sun, 07 Oct 2018 20:51:25: 4000000 INFO @ Sun, 07 Oct 2018 20:51:25: 4000000 INFO @ Sun, 07 Oct 2018 20:51:32: 5000000 INFO @ Sun, 07 Oct 2018 20:51:32: 5000000 INFO @ Sun, 07 Oct 2018 20:51:32: 5000000 INFO @ Sun, 07 Oct 2018 20:51:39: 6000000 INFO @ Sun, 07 Oct 2018 20:51:39: 6000000 INFO @ Sun, 07 Oct 2018 20:51:39: 6000000 INFO @ Sun, 07 Oct 2018 20:51:47: 7000000 INFO @ Sun, 07 Oct 2018 20:51:47: 7000000 INFO @ Sun, 07 Oct 2018 20:51:47: 7000000 INFO @ Sun, 07 Oct 2018 20:51:54: 8000000 INFO @ Sun, 07 Oct 2018 20:51:54: 8000000 INFO @ Sun, 07 Oct 2018 20:51:54: 8000000 INFO @ Sun, 07 Oct 2018 20:52:02: 9000000 INFO @ Sun, 07 Oct 2018 20:52:02: 9000000 INFO @ Sun, 07 Oct 2018 20:52:02: 9000000 INFO @ Sun, 07 Oct 2018 20:52:09: 10000000 INFO @ Sun, 07 Oct 2018 20:52:09: 10000000 INFO @ Sun, 07 Oct 2018 20:52:09: 10000000 INFO @ Sun, 07 Oct 2018 20:52:16: 11000000 INFO @ Sun, 07 Oct 2018 20:52:17: 11000000 INFO @ Sun, 07 Oct 2018 20:52:17: 11000000 INFO @ Sun, 07 Oct 2018 20:52:24: 12000000 INFO @ Sun, 07 Oct 2018 20:52:24: 12000000 INFO @ Sun, 07 Oct 2018 20:52:24: 12000000 INFO @ Sun, 07 Oct 2018 20:52:31: 13000000 INFO @ Sun, 07 Oct 2018 20:52:31: 13000000 INFO @ Sun, 07 Oct 2018 20:52:31: 13000000 INFO @ Sun, 07 Oct 2018 20:52:39: 14000000 INFO @ Sun, 07 Oct 2018 20:52:39: 14000000 INFO @ Sun, 07 Oct 2018 20:52:39: 14000000 INFO @ Sun, 07 Oct 2018 20:52:42: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:52:42: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:52:42: #1 total tags in treatment: 14413263 INFO @ Sun, 07 Oct 2018 20:52:42: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:52:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:52:43: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:52:43: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:52:43: #1 total tags in treatment: 14413263 INFO @ Sun, 07 Oct 2018 20:52:43: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:52:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:52:43: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:52:43: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:52:43: #1 total tags in treatment: 14413263 INFO @ Sun, 07 Oct 2018 20:52:43: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:52:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:52:43: #1 tags after filtering in treatment: 14413263 INFO @ Sun, 07 Oct 2018 20:52:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:52:43: #1 finished! INFO @ Sun, 07 Oct 2018 20:52:43: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:52:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:52:43: #1 tags after filtering in treatment: 14413263 INFO @ Sun, 07 Oct 2018 20:52:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:52:43: #1 finished! INFO @ Sun, 07 Oct 2018 20:52:43: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:52:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:52:43: #1 tags after filtering in treatment: 14413263 INFO @ Sun, 07 Oct 2018 20:52:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:52:43: #1 finished! INFO @ Sun, 07 Oct 2018 20:52:43: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:52:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:52:44: #2 number of paired peaks: 116 WARNING @ Sun, 07 Oct 2018 20:52:44: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Sun, 07 Oct 2018 20:52:44: start model_add_line... INFO @ Sun, 07 Oct 2018 20:52:44: #2 number of paired peaks: 116 WARNING @ Sun, 07 Oct 2018 20:52:44: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Sun, 07 Oct 2018 20:52:44: start model_add_line... INFO @ Sun, 07 Oct 2018 20:52:44: #2 number of paired peaks: 116 WARNING @ Sun, 07 Oct 2018 20:52:44: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Sun, 07 Oct 2018 20:52:44: start model_add_line... INFO @ Sun, 07 Oct 2018 20:52:44: start X-correlation... INFO @ Sun, 07 Oct 2018 20:52:44: end of X-cor INFO @ Sun, 07 Oct 2018 20:52:44: #2 finished! INFO @ Sun, 07 Oct 2018 20:52:44: #2 predicted fragment length is 92 bps INFO @ Sun, 07 Oct 2018 20:52:44: #2 alternative fragment length(s) may be 92,580 bps INFO @ Sun, 07 Oct 2018 20:52:44: #2.2 Generate R script for model : SRX4798845.20_model.r WARNING @ Sun, 07 Oct 2018 20:52:44: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:52:44: #2 You may need to consider one of the other alternative d(s): 92,580 WARNING @ Sun, 07 Oct 2018 20:52:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 20:52:44: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:52:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:52:44: start X-correlation... INFO @ Sun, 07 Oct 2018 20:52:44: end of X-cor INFO @ Sun, 07 Oct 2018 20:52:44: #2 finished! INFO @ Sun, 07 Oct 2018 20:52:44: #2 predicted fragment length is 92 bps INFO @ Sun, 07 Oct 2018 20:52:44: #2 alternative fragment length(s) may be 92,580 bps INFO @ Sun, 07 Oct 2018 20:52:44: #2.2 Generate R script for model : SRX4798845.10_model.r WARNING @ Sun, 07 Oct 2018 20:52:44: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:52:44: #2 You may need to consider one of the other alternative d(s): 92,580 WARNING @ Sun, 07 Oct 2018 20:52:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 20:52:44: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:52:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:52:44: start X-correlation... INFO @ Sun, 07 Oct 2018 20:52:44: end of X-cor INFO @ Sun, 07 Oct 2018 20:52:44: #2 finished! INFO @ Sun, 07 Oct 2018 20:52:44: #2 predicted fragment length is 92 bps INFO @ Sun, 07 Oct 2018 20:52:44: #2 alternative fragment length(s) may be 92,580 bps INFO @ Sun, 07 Oct 2018 20:52:44: #2.2 Generate R script for model : SRX4798845.05_model.r WARNING @ Sun, 07 Oct 2018 20:52:44: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:52:44: #2 You may need to consider one of the other alternative d(s): 92,580 WARNING @ Sun, 07 Oct 2018 20:52:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 20:52:44: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:52:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:53:15: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:53:16: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:53:17: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:53:33: #4 Write output xls file... SRX4798845.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:53:33: #4 Write peak in narrowPeak format file... SRX4798845.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:53:33: #4 Write summits bed file... SRX4798845.20_summits.bed INFO @ Sun, 07 Oct 2018 20:53:33: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (302 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:53:35: #4 Write output xls file... SRX4798845.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:53:36: #4 Write peak in narrowPeak format file... SRX4798845.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:53:36: #4 Write summits bed file... SRX4798845.10_summits.bed INFO @ Sun, 07 Oct 2018 20:53:36: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (2096 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:53:36: #4 Write output xls file... SRX4798845.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:53:36: #4 Write peak in narrowPeak format file... SRX4798845.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:53:36: #4 Write summits bed file... SRX4798845.05_summits.bed INFO @ Sun, 07 Oct 2018 20:53:36: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (6267 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。