Job ID = 9297531 sra ファイルのダウンロード中... Completed: 297102K bytes transferred in 8 seconds (290534K 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 18887584 spots for /home/okishinya/chipatlas/results/dm3/SRX2745586/SRR5457523.sra Written 18887584 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: 00:07:51 18887584 reads; of these: 18887584 (100.00%) were unpaired; of these: 795198 (4.21%) aligned 0 times 13286597 (70.35%) aligned exactly 1 time 4805789 (25.44%) aligned >1 times 95.79% overall alignment rate Time searching: 00:07:51 Overall time: 00:07:51 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] 3548253 / 18092386 = 0.1961 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 @ Thu, 27 Jul 2017 15:39:37: # Command line: callpeak -t SRX2745586.bam -f BAM -g dm -n SRX2745586.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2745586.05 # format = BAM # ChIP-seq file = ['SRX2745586.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 @ Thu, 27 Jul 2017 15:39:37: #1 read tag files... INFO @ Thu, 27 Jul 2017 15:39:37: # Command line: callpeak -t SRX2745586.bam -f BAM -g dm -n SRX2745586.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2745586.10 # format = BAM # ChIP-seq file = ['SRX2745586.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 @ Thu, 27 Jul 2017 15:39:37: #1 read treatment tags... INFO @ Thu, 27 Jul 2017 15:39:37: #1 read tag files... INFO @ Thu, 27 Jul 2017 15:39:37: #1 read treatment tags... INFO @ Thu, 27 Jul 2017 15:39:37: # Command line: callpeak -t SRX2745586.bam -f BAM -g dm -n SRX2745586.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2745586.20 # format = BAM # ChIP-seq file = ['SRX2745586.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 @ Thu, 27 Jul 2017 15:39:37: #1 read tag files... INFO @ Thu, 27 Jul 2017 15:39:37: #1 read treatment tags... INFO @ Thu, 27 Jul 2017 15:39:44: 1000000 INFO @ Thu, 27 Jul 2017 15:39:44: 1000000 INFO @ Thu, 27 Jul 2017 15:39:45: 1000000 INFO @ Thu, 27 Jul 2017 15:39:51: 2000000 INFO @ Thu, 27 Jul 2017 15:39:51: 2000000 INFO @ Thu, 27 Jul 2017 15:39:52: 2000000 INFO @ Thu, 27 Jul 2017 15:39:59: 3000000 INFO @ Thu, 27 Jul 2017 15:39:59: 3000000 INFO @ Thu, 27 Jul 2017 15:40:00: 3000000 INFO @ Thu, 27 Jul 2017 15:40:06: 4000000 INFO @ Thu, 27 Jul 2017 15:40:06: 4000000 INFO @ Thu, 27 Jul 2017 15:40:07: 4000000 INFO @ Thu, 27 Jul 2017 15:40:13: 5000000 INFO @ Thu, 27 Jul 2017 15:40:13: 5000000 INFO @ Thu, 27 Jul 2017 15:40:15: 5000000 INFO @ Thu, 27 Jul 2017 15:40:20: 6000000 INFO @ Thu, 27 Jul 2017 15:40:20: 6000000 INFO @ Thu, 27 Jul 2017 15:40:23: 6000000 INFO @ Thu, 27 Jul 2017 15:40:27: 7000000 INFO @ Thu, 27 Jul 2017 15:40:27: 7000000 INFO @ Thu, 27 Jul 2017 15:40:30: 7000000 INFO @ Thu, 27 Jul 2017 15:40:35: 8000000 INFO @ Thu, 27 Jul 2017 15:40:35: 8000000 INFO @ Thu, 27 Jul 2017 15:40:38: 8000000 INFO @ Thu, 27 Jul 2017 15:40:42: 9000000 INFO @ Thu, 27 Jul 2017 15:40:42: 9000000 INFO @ Thu, 27 Jul 2017 15:40:45: 9000000 INFO @ Thu, 27 Jul 2017 15:40:49: 10000000 INFO @ Thu, 27 Jul 2017 15:40:49: 10000000 INFO @ Thu, 27 Jul 2017 15:40:53: 10000000 INFO @ Thu, 27 Jul 2017 15:40:56: 11000000 INFO @ Thu, 27 Jul 2017 15:40:56: 11000000 INFO @ Thu, 27 Jul 2017 15:41:01: 11000000 INFO @ Thu, 27 Jul 2017 15:41:03: 12000000 INFO @ Thu, 27 Jul 2017 15:41:03: 12000000 INFO @ Thu, 27 Jul 2017 15:41:08: 12000000 INFO @ Thu, 27 Jul 2017 15:41:10: 13000000 INFO @ Thu, 27 Jul 2017 15:41:11: 13000000 INFO @ Thu, 27 Jul 2017 15:41:16: 13000000 INFO @ Thu, 27 Jul 2017 15:41:18: 14000000 INFO @ Thu, 27 Jul 2017 15:41:18: 14000000 INFO @ Thu, 27 Jul 2017 15:41:22: #1 tag size is determined as 50 bps INFO @ Thu, 27 Jul 2017 15:41:22: #1 tag size = 50 INFO @ Thu, 27 Jul 2017 15:41:22: #1 total tags in treatment: 14544133 INFO @ Thu, 27 Jul 2017 15:41:22: #1 user defined the maximum tags... INFO @ Thu, 27 Jul 2017 15:41:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 27 Jul 2017 15:41:22: #1 tag size is determined as 50 bps INFO @ Thu, 27 Jul 2017 15:41:22: #1 tag size = 50 INFO @ Thu, 27 Jul 2017 15:41:22: #1 total tags in treatment: 14544133 INFO @ Thu, 27 Jul 2017 15:41:22: #1 user defined the maximum tags... INFO @ Thu, 27 Jul 2017 15:41:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 27 Jul 2017 15:41:22: #1 tags after filtering in treatment: 14544133 INFO @ Thu, 27 Jul 2017 15:41:22: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 27 Jul 2017 15:41:22: #1 finished! INFO @ Thu, 27 Jul 2017 15:41:22: #2 Build Peak Model... INFO @ Thu, 27 Jul 2017 15:41:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 27 Jul 2017 15:41:22: #1 tags after filtering in treatment: 14544133 INFO @ Thu, 27 Jul 2017 15:41:22: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 27 Jul 2017 15:41:22: #1 finished! INFO @ Thu, 27 Jul 2017 15:41:22: #2 Build Peak Model... INFO @ Thu, 27 Jul 2017 15:41:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 27 Jul 2017 15:41:23: #2 number of paired peaks: 105 WARNING @ Thu, 27 Jul 2017 15:41:23: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Thu, 27 Jul 2017 15:41:23: start model_add_line... INFO @ Thu, 27 Jul 2017 15:41:23: 14000000 INFO @ Thu, 27 Jul 2017 15:41:23: #2 number of paired peaks: 105 WARNING @ Thu, 27 Jul 2017 15:41:23: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Thu, 27 Jul 2017 15:41:23: start model_add_line... INFO @ Thu, 27 Jul 2017 15:41:23: start X-correlation... INFO @ Thu, 27 Jul 2017 15:41:23: end of X-cor INFO @ Thu, 27 Jul 2017 15:41:23: #2 finished! INFO @ Thu, 27 Jul 2017 15:41:23: #2 predicted fragment length is 82 bps INFO @ Thu, 27 Jul 2017 15:41:23: #2 alternative fragment length(s) may be 82 bps INFO @ Thu, 27 Jul 2017 15:41:23: #2.2 Generate R script for model : SRX2745586.05_model.r WARNING @ Thu, 27 Jul 2017 15:41:23: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 27 Jul 2017 15:41:23: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Thu, 27 Jul 2017 15:41:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 27 Jul 2017 15:41:23: #3 Call peaks... INFO @ Thu, 27 Jul 2017 15:41:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 27 Jul 2017 15:41:23: start X-correlation... INFO @ Thu, 27 Jul 2017 15:41:23: end of X-cor INFO @ Thu, 27 Jul 2017 15:41:23: #2 finished! INFO @ Thu, 27 Jul 2017 15:41:23: #2 predicted fragment length is 82 bps INFO @ Thu, 27 Jul 2017 15:41:23: #2 alternative fragment length(s) may be 82 bps INFO @ Thu, 27 Jul 2017 15:41:23: #2.2 Generate R script for model : SRX2745586.10_model.r WARNING @ Thu, 27 Jul 2017 15:41:23: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 27 Jul 2017 15:41:23: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Thu, 27 Jul 2017 15:41:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 27 Jul 2017 15:41:23: #3 Call peaks... INFO @ Thu, 27 Jul 2017 15:41:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 27 Jul 2017 15:41:27: #1 tag size is determined as 50 bps INFO @ Thu, 27 Jul 2017 15:41:27: #1 tag size = 50 INFO @ Thu, 27 Jul 2017 15:41:27: #1 total tags in treatment: 14544133 INFO @ Thu, 27 Jul 2017 15:41:27: #1 user defined the maximum tags... INFO @ Thu, 27 Jul 2017 15:41:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 27 Jul 2017 15:41:27: #1 tags after filtering in treatment: 14544133 INFO @ Thu, 27 Jul 2017 15:41:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 27 Jul 2017 15:41:27: #1 finished! INFO @ Thu, 27 Jul 2017 15:41:27: #2 Build Peak Model... INFO @ Thu, 27 Jul 2017 15:41:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 27 Jul 2017 15:41:28: #2 number of paired peaks: 105 WARNING @ Thu, 27 Jul 2017 15:41:28: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Thu, 27 Jul 2017 15:41:28: start model_add_line... INFO @ Thu, 27 Jul 2017 15:41:28: start X-correlation... INFO @ Thu, 27 Jul 2017 15:41:28: end of X-cor INFO @ Thu, 27 Jul 2017 15:41:28: #2 finished! INFO @ Thu, 27 Jul 2017 15:41:28: #2 predicted fragment length is 82 bps INFO @ Thu, 27 Jul 2017 15:41:28: #2 alternative fragment length(s) may be 82 bps INFO @ Thu, 27 Jul 2017 15:41:28: #2.2 Generate R script for model : SRX2745586.20_model.r WARNING @ Thu, 27 Jul 2017 15:41:28: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 27 Jul 2017 15:41:28: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Thu, 27 Jul 2017 15:41:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 27 Jul 2017 15:41:28: #3 Call peaks... INFO @ Thu, 27 Jul 2017 15:41:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 27 Jul 2017 15:41:53: #3 Call peaks for each chromosome... INFO @ Thu, 27 Jul 2017 15:41:54: #3 Call peaks for each chromosome... INFO @ Thu, 27 Jul 2017 15:42:00: #3 Call peaks for each chromosome... INFO @ Thu, 27 Jul 2017 15:42:09: #4 Write output xls file... SRX2745586.05_peaks.xls INFO @ Thu, 27 Jul 2017 15:42:09: #4 Write peak in narrowPeak format file... SRX2745586.05_peaks.narrowPeak INFO @ Thu, 27 Jul 2017 15:42:09: #4 Write summits bed file... SRX2745586.05_summits.bed INFO @ Thu, 27 Jul 2017 15:42:09: Done! pass1 - making usageList (13 chroms): 13 millis pass2 - checking and writing primary data (3346 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Thu, 27 Jul 2017 15:42:12: #4 Write output xls file... SRX2745586.10_peaks.xls INFO @ Thu, 27 Jul 2017 15:42:12: #4 Write peak in narrowPeak format file... SRX2745586.10_peaks.narrowPeak INFO @ Thu, 27 Jul 2017 15:42:12: #4 Write summits bed file... SRX2745586.10_summits.bed INFO @ Thu, 27 Jul 2017 15:42:12: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1912 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 27 Jul 2017 15:42:18: #4 Write output xls file... SRX2745586.20_peaks.xls INFO @ Thu, 27 Jul 2017 15:42:18: #4 Write peak in narrowPeak format file... SRX2745586.20_peaks.narrowPeak INFO @ Thu, 27 Jul 2017 15:42:18: #4 Write summits bed file... SRX2745586.20_summits.bed INFO @ Thu, 27 Jul 2017 15:42:18: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (950 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。